Mercurial > repos > eschen42 > mqppep_preproc
changeset 23:7560a4e80a1e draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
| author | eschen42 |
|---|---|
| date | Thu, 30 Jun 2022 16:15:57 +0000 |
| parents | 43f1fd0ff86b |
| children | 657663e89728 |
| files | MaxQuantProcessingScript.R PhosphoPeptide_Upstream_Kinase_Mapping.pl macros.xml mqppep_mrgfltr.py mqppep_preproc.xml test-data/pSTY_motifs.tabular workflow/ppenrich_suite_wf.ga |
| diffstat | 7 files changed, 628 insertions(+), 329 deletions(-) [+] |
line wrap: on
line diff
--- a/MaxQuantProcessingScript.R Wed Apr 13 19:48:01 2022 +0000 +++ b/MaxQuantProcessingScript.R Thu Jun 30 16:15:57 2022 +0000 @@ -86,37 +86,37 @@ for (chara in phosphoprobsequence) { # build peptide sequence if (!( - chara == " " | - chara == "(" | - chara == ")" | - chara == "." | - chara == "-" | - chara == "0" | - chara == "1" | - chara == "2" | - chara == "3" | - chara == "4" | - chara == "5" | - chara == "6" | - chara == "7" | - chara == "8" | + chara == " " || + chara == "(" || + chara == ")" || + chara == "." || + chara == "-" || + chara == "0" || + chara == "1" || + chara == "2" || + chara == "3" || + chara == "4" || + chara == "5" || + chara == "6" || + chara == "7" || + chara == "8" || chara == "9") ) { phosphopeptide <- paste(phosphopeptide, chara, sep = "") counter <- counter + 1 } # generate score_diff - if (chara == "-" | - chara == "." | - chara == "0" | - chara == "1" | - chara == "2" | - chara == "3" | - chara == "4" | - chara == "5" | - chara == "6" | - chara == "7" | - chara == "8" | + if (chara == "-" || + chara == "." || + chara == "0" || + chara == "1" || + chara == "2" || + chara == "3" || + chara == "4" || + chara == "5" || + chara == "6" || + chara == "7" || + chara == "8" || chara == "9" ) { score_diff <- paste(score_diff, chara, sep = "") @@ -388,7 +388,7 @@ read.table( file = input_file_name, sep = "\t", - header = T, + header = TRUE, quote = "" )
--- a/PhosphoPeptide_Upstream_Kinase_Mapping.pl Wed Apr 13 19:48:01 2022 +0000 +++ b/PhosphoPeptide_Upstream_Kinase_Mapping.pl Thu Jun 30 16:15:57 2022 +0000 @@ -62,18 +62,18 @@ my (@kinases_observed, $kinases); my (@kinases_observed_lbl, @phosphosites_observed_lbl); my ($p_sequence_kinase, $p_sequence, $kinase); -my (@motif_sequence, %motif_type, %motif_count); +my (@motif_sequence, @motif_description, @motif_type_key_ary, %motif_type, %motif_count); my (@kinases_PhosphoSite, $kinases_PhosphoSite); my ($p_sequence_kinase_PhosphoSite, $p_sequence_PhosphoSite, $kinase_PhosphoSite); my (%regulatory_sites_PhosphoSite_hash); my (%domain, %ON_FUNCTION, %ON_PROCESS, %ON_PROT_INTERACT, %ON_OTHER_INTERACT, %notes, %organism); my (%unique_motifs); -my ($kinase_substrate_NetworKIN_matches, $kinase_motif_matches, $kinase_substrate_PhosphoSite_matches); +my ($kinase_substrate_NetworKIN_matches, $kinase_substrate_PhosphoSite_matches); my %psp_regsite_protein_2; my (%domain_2, %ON_FUNCTION_2, %ON_PROCESS_2, %ON_PROT_INTERACT_2, %N_PROT_INTERACT, %ON_OTHER_INTERACT_2, %notes_2, %organism_2); my @timeData; my $PhosphoSitePlusCitation; -my %site_description; +my (%site_description, %site_id); my %kinase_substrate_NetworKIN_matches; my %kinase_motif_matches; @@ -997,12 +997,21 @@ ############################################################################################################################### # file format (tab separated): -# x[0] = primary key (character), e.g., '17' or '23a' +# x[0] = quasi-primary key (character), e.g., '17' or '23a' # x[1] = pattern (egrep pattern), e.g., '(M|I|L|V|F|Y).R..(pS|pT)' # x[2] = description, e.g., 'PKA_Phosida' or '14-3-3 domain binding motif (HPRD)' or 'Akt kinase substrate motif (HPRD & Phosida)' - -my $SITE_MOTIF = 2; -$site_description{$SITE_MOTIF} = "motif"; +# "counter" "pcre" "symbol" "description" "pubmed_id" "classification" "source" +# "1" "R.R..(pS|pT)(F|L)" "PKB_group" "Akt kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8985174" "kinase substrate" "HPRD" +# x[3] = old description, i.e., description in Amanchy (HPRD) and Phosida tables +# x[4] = pubmed id +# x[5] = classification +# x[6] = source (Phosida or HPRD) +my $SITE_HPRD = 2; +$site_description{$SITE_HPRD} = "HPRD"; +$site_id{$site_description{$SITE_HPRD}} = $SITE_HPRD; +my $SITE_PHOSIDA = 4; +$site_description{$SITE_PHOSIDA} = "Phosida"; +$site_id{$site_description{$SITE_PHOSIDA}} = $SITE_PHOSIDA; open (IN2, "$motifs_in") or die "I couldn't find $motifs_in\n"; print "Reading the Motifs file: $motifs_in\n"; @@ -1010,17 +1019,30 @@ while (<IN2>) { chomp; my (@x) = split(/\t/); + my $tmp_motif_description; + if ($#x == 6) { # weirdly, a @list of length seven has $#list == 6 + # remove double-quotes which are helpful or necessary for Excel + $x[6] =~ s/\"//g; + $tmp_motif_description = $x[6]; + } else { + $tmp_motif_description = "motif"; + } for my $i (0 .. 2) { + # remove any embedded CR or LF (none should exist) $x[$i] =~ s/\r//g; $x[$i] =~ s/\n//g; + # remove double-quotes which are helpful or necessary for Excel $x[$i] =~ s/\"//g; } - if (exists ($motif_type{$x[1]})) { - $motif_type{$x[1]} = $motif_type{$x[1]}." & ".$x[2]; + if (exists ($motif_type{$x[2]})) { + #ACE-2022.06.20 $motif_type{$x[1]} = $motif_type{$x[1]}." & ".$x[2]; + $motif_type{$x[2]} = $motif_type{$x[2]}."|".$x[2]; } else { - $motif_type{$x[1]} = $x[2]; + $motif_type{$x[2]} = $x[2]; $motif_count{$x[1]} = 0; push (@motif_sequence, $x[1]); + push (@motif_description, $tmp_motif_description); + push (@motif_type_key_ary, $x[2]) } } close (IN2); @@ -1111,7 +1133,6 @@ # # Columns: # (0) GENE -# (1) PROTEIN --> #ACE %psp_regsite_protein # (2) PROT_TYPE # (3) ACC_ID # (4) GENE_ID @@ -1503,8 +1524,9 @@ } } for my $i (0 .. $#motif_sequence) { + print "matching $motif_sequence[$i]" if ($verbose); if ($peptide =~ /$motif_sequence[$i]/) { - $kinase_motif_matches{$peptide}{$motif_sequence[$i]} = "X"; + $kinase_motif_matches{$peptide}{$motif_type{$motif_type_key_ary[$i]}} = "X"; } } for my $i (0 .. $#kinases_PhosphoSite) { @@ -1578,7 +1600,7 @@ $pSTY_sequence = $formatted_sequences[$k]; for my $i (0 .. $#motif_sequence) { if ($pSTY_sequence =~ /$motif_sequence[$i]/) { - $kinase_motif_matches{$peptide}{$motif_sequence[$i]} = "X"; + $kinase_motif_matches{$peptide}{$motif_type{$motif_type_key_ary[$i]}} = "X"; } } for my $i (0 .. $#kinases_PhosphoSite) { @@ -1741,6 +1763,8 @@ # Print to the output file # ############################################################################################################################### + + open (OUT, ">$file_out") || die "could not open the fileout: $file_out"; open (MELT, ">$file_melt") || die "could not open the fileout: $file_melt"; @@ -1760,11 +1784,12 @@ print OUT "$temp\t"; push(@kinases_observed_lbl, $temp); } -for my $i (0 .. $#motif_sequence) { - print OUT "$motif_type{$motif_sequence[$i]} ($motif_sequence[$i])\t"; +my @motif_type_keys = keys %motif_type; +for my $i (1 .. $#motif_type_keys) { + print OUT "$motif_type{$motif_type_keys[$i]}\t"; } for my $i (0 .. $#kinases_PhosphoSite) { - my $temp = $kinases_PhosphoSite[$i]."_PhosphoSite"; + my $temp = $kinases_PhosphoSite[$i]; # ."_PhosphoSite"; if ($i < $#kinases_PhosphoSite) { print OUT "$temp\t"; } if ($i == $#kinases_PhosphoSite) { print OUT "$temp\n"; } push(@phosphosites_observed_lbl, $temp); @@ -1861,8 +1886,9 @@ } } add_site_type($SITE_KINASE_SUBSTRATE, $site_description{$SITE_KINASE_SUBSTRATE}); -add_site_type($SITE_MOTIF, $site_description{$SITE_MOTIF}); -add_site_type($SITE_PHOSPHOSITE, $site_description{$SITE_PHOSPHOSITE}); +add_site_type($SITE_HPRD , $site_description{$SITE_HPRD }); +add_site_type($SITE_PHOSIDA , $site_description{$SITE_PHOSIDA }); +add_site_type($SITE_PHOSPHOSITE , $site_description{$SITE_PHOSPHOSITE }); # end store-to-SQLite "site_type" table # ... @@ -2070,7 +2096,7 @@ for my $i (0 .. $#kinases_observed) { if (exists($kinase_substrate_NetworKIN_matches{$peptide}{$kinases_observed[$i]})) { print OUT "X\t"; - my $NetworKIN_label = $kinases_observed[$i]."_NetworKIN"; + my $NetworKIN_label = $kinases_observed[$i]; #."_NetworKIN"; print MELT "$peptide\t$gene_names\t$site_description{$SITE_KINASE_SUBSTRATE}\t$NetworKIN_label\n"; # begin store-to-SQLite "ppep_gene_site" table # --- @@ -2088,26 +2114,36 @@ } my %wrote_motif; my $motif_parts_0; - for my $i (0 .. $#motif_sequence) { - if (exists($kinase_motif_matches{$peptide}{$motif_sequence[$i]})) { + my @motif_split; + my $one_motif; + + for my $i (0 .. $#motif_type_keys) { + if (exists($kinase_motif_matches{$peptide}{$motif_type_keys[$i]})) { print OUT "X\t"; - $motif_parts_0 = $motif_type{$motif_sequence[$i]}." ".$motif_sequence[$i]; - my $key = "$peptide\t$gene_names\t$motif_parts_0"; - if (!exists($wrote_motif{$key})) { - $wrote_motif{$key} = $key; - print MELT "$peptide\t$gene_names\t$site_description{$SITE_MOTIF}\t$motif_parts_0\n"; - # print "Line 657: i is $i\t$kinase_motif_matches{$peptide}{$motif_sequence[$i]}\n"; #debug - # begin store-to-SQLite "ppep_gene_site" table - # --- - $ppep_gene_site_stmth->bind_param(1, $ppep_id); # ppep_gene_site.ppep_id - $ppep_gene_site_stmth->bind_param(2, $gene_names); # ppep_gene_site.gene_names - $ppep_gene_site_stmth->bind_param(3, $motif_parts_0); # ppep_gene_site.kinase_map - $ppep_gene_site_stmth->bind_param(4, $SITE_MOTIF); # ppep_gene_site.site_type_id - if (not $ppep_gene_site_stmth->execute()) { - print "Error writing tuple ($peptide,$gene_names,$motif_parts_0): $ppep_gene_site_stmth->errstr\n"; + #ACE-2022.06.20 $motif_parts_0 = $motif_type{$motif_sequence[$i]}." ".$motif_sequence[$i]; + $motif_parts_0 = $motif_type{$motif_type_keys[$i]}; + @motif_split = split("[|]", $motif_parts_0); + #ACE-2022.06.20 my $key = "$peptide\t$gene_names\t$motif_parts_0"; + for my $j (0 .. $#motif_split) { + $one_motif = $motif_split[$j]; + #ACE-2022.06.20 my $key = "$peptide\t$gene_names\t$motif_parts_0"; + my $key = "$peptide\t$gene_names\t$one_motif"; + if (!exists($wrote_motif{$key})) { + $wrote_motif{$key} = $key; + print MELT "$peptide\t$gene_names\t$motif_description[$i]\t$one_motif\n"; + # print "Line 657: i is $i\t$kinase_motif_matches{$peptide}{$motif_sequence[$i]}\n"; #debug + # begin store-to-SQLite "ppep_gene_site" table + # --- + $ppep_gene_site_stmth->bind_param(1, $ppep_id); # ppep_gene_site.ppep_id + $ppep_gene_site_stmth->bind_param(2, $gene_names); # ppep_gene_site.gene_names + $ppep_gene_site_stmth->bind_param(3, $one_motif); # ppep_gene_site.kinase_map + $ppep_gene_site_stmth->bind_param(4, $site_id{$motif_description[$i]}); # ppep_gene_site.site_type_id + if (not $ppep_gene_site_stmth->execute()) { + print "Error writing tuple ($peptide,$gene_names,$one_motif): $ppep_gene_site_stmth->errstr\n"; + } + # ... + # end store-to-SQLite "ppep_gene_site" table } - # ... - # end store-to-SQLite "ppep_gene_site" table } } else { print OUT "\t";}
--- a/macros.xml Wed Apr 13 19:48:01 2022 +0000 +++ b/macros.xml Thu Jun 30 16:15:57 2022 +0000 @@ -1,17 +1,30 @@ <macros> - <token name="@TOOL_VERSION@">0.1.12</token> + <token name="@TOOL_VERSION@">0.1.13</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="0.4.0" >r-sass</requirement> - <requirement type="package" version="1.14.2" >r-data.table</requirement> <requirement type="package" version="1.56.0" >bioconductor-preprocesscore</requirement> - <requirement type="package" version="5.26.2" >perl</requirement> + <requirement type="package" version="1.22.2" >numpy</requirement> <requirement type="package" version="0.3.3" >openblas</requirement> - <requirement type="package" version="1.22.2" >numpy</requirement> + <requirement type="package" version="1.4.1" >pandas</requirement> + <requirement type="package" version="1.64" >perl-dbd-sqlite</requirement> + <requirement type="package" version="5.26.2" >perl</requirement> + <requirement type="package" version="1.4.0" >pyahocorasick</requirement> + <requirement type="package" version="3.9.10" >python</requirement> + <requirement type="package" version="1.14.2" >r-data.table</requirement> + <requirement type="package" version="1.1.2" >r-dbi</requirement> <requirement type="package" version="3.3.5" >r-ggplot2</requirement> + <requirement type="package" version="3.1.3" >r-gplots</requirement> + <requirement type="package" version="0.9.4" >r-latex2exp</requirement> + <requirement type="package" version="1.7.1" >r-optparse</requirement> + <requirement type="package" version="1.4.4" >r-reshape2</requirement> + <requirement type="package" version="2.11" >r-rmarkdown</requirement> + <requirement type="package" version="2.2.8" >r-rsqlite</requirement> + <requirement type="package" version="0.4.0" >r-sass</requirement> + <requirement type="package" version="0.4_11" >r-sqldf</requirement> + <requirement type="package" version="1.4.0" >r-stringr</requirement> + <requirement type="package" version="0.37" >r-tinytex</requirement> <requirement type="package" version="0.3.7" >r-vioplot</requirement> - <requirement type="package" version="0.37" >r-tinytex</requirement> <!-- It would be nice to use conda-forge/texlive-core rather than r-tinytex because the former installs texlive when the package is built, but issue 23 blocked PDF-creation. @@ -19,14 +32,58 @@ with boxes) unless I specified the build as well as the version when building a conda environment, e.g.: texlive-core=20210325=h97429d4_0 --> - <requirement type="package" version="3.9.10" >python</requirement> - <requirement type="package" version="0.9.4" >r-latex2exp</requirement> - <requirement type="package" version="1.4.0" >r-stringr</requirement> - <requirement type="package" version="1.64" >perl-dbd-sqlite</requirement> - <requirement type="package" version="1.4.0" >pyahocorasick</requirement> - <requirement type="package" version="2.11" >r-rmarkdown</requirement> - <requirement type="package" version="1.4.1" >pandas</requirement> - <requirement type="package" version="1.7.1" >r-optparse</requirement> </requirements> + <!-- I specified the versions above because it takes a VERY long time to search for package versions when they are not omitted; also, version numbers should lead to reproducible behavior. Contrast execution times of this (about 18 seconds): + echo n | time conda create -n mqppep_ver -c conda-forge -c bioconda \ + bioconductor-preprocesscore=1.56.0 \ + numpy=1.22.2 \ + openblas=0.3.3 \ + pandas=1.4.1 \ + perl-dbd-sqlite=1.64 \ + perl-dbd-sqlite=1.64 \ + perl=5.26.2 \ + pyahocorasick=1.4.0 \ + python=3.9.10 \ + r-data.table=1.14.2 \ + r-dbi=1.1.2 \ + r-ggplot2=3.3.5 \ + r-gplots=3.1.3 \ + r-latex2exp=0.9.4 \ + r-optparse=1.7.1 \ + r-reshape2=1.4.4 \ + r-rmarkdown=2.11 \ + r-rsqlite=2.2.8 \ + r-sass=0.4.0 \ + r-sqldf=0.4_11 \ + r-stringr=1.4.0 \ + r-tinytex=0.37 \ + r-vioplot=0.3.7 + with this (42 or more seconds): + echo n | time conda create -n mqppep_nover -c conda-forge -c bioconda \ + bioconductor-preprocesscore= \ + numpy \ + openblas=0.3.3 \ + pandas \ + perl \ + perl-dbd-sqlite \ + perl-dbd-sqlite \ + pyahocorasick \ + python \ + r-data.table \ + r-dbi \ + r-ggplot2 \ + r-gplots \ + r-latex2exp \ + r-optparse \ + r-reshape2 \ + r-rmarkdown \ + r-rsqlite \ + r-sass \ + r-sqldf \ + r-stringr \ + r-tinytex \ + r-vioplot + + --> </xml> </macros>
--- a/mqppep_mrgfltr.py Wed Apr 13 19:48:01 2022 +0000 +++ b/mqppep_mrgfltr.py Thu Jun 30 16:15:57 2022 +0000 @@ -608,6 +608,33 @@ file=sys.stderr, ) # timer + # ######################################################################## + # # trim upstream_data to include only the upstream map columns + # old_cols = upstream_data.columns.tolist() + # i = 0 + # first_intensity = -1 + # last_intensity = -1 + # intensity_re = re.compile("Intensity.*") + # for col_name in old_cols: + # m = intensity_re.match(col_name) + # if m: + # last_intensity = i + # if first_intensity == -1: + # first_intensity = i + # i += 1 + # # print('last intensity = %d' % last_intensity) + # col_PKCalpha = last_intensity + 2 + # + # data_in_cols = [old_cols[0]] + old_cols[ + # first_intensity: last_intensity + 1 + # ] + # + # if upstream_data.empty: + # print("upstream_data is empty") + # exit(0) + # + # data_in = upstream_data.copy(deep=True)[data_in_cols] + ######################################################################## # trim upstream_data to include only the upstream map columns old_cols = upstream_data.columns.tolist() i = 0 @@ -625,6 +652,9 @@ col_PKCalpha = last_intensity + 2 data_in_cols = [old_cols[0]] + old_cols[ + first_intensity - 1: last_intensity + ] + data_col_names = [old_cols[0]] + old_cols[ first_intensity: last_intensity + 1 ] @@ -633,6 +663,10 @@ exit(0) data_in = upstream_data.copy(deep=True)[data_in_cols] + data_in.columns = data_col_names + print("data_in") + print(data_in) + ######################################################################## # Convert floating-point integers to int64 integers # ref: https://stackoverflow.com/a/68497603/15509512 @@ -1181,8 +1215,12 @@ file=sys.stderr, ) # timer + print("old_cols[:col_PKCalpha]") + print(old_cols[:col_PKCalpha]) cols = [old_cols[0]] + old_cols[col_PKCalpha - 1:] upstream_data = upstream_data[cols] + print("upstream_data.columns") + print(upstream_data.columns) end_time = time.process_time() # timer print(
--- a/mqppep_preproc.xml Wed Apr 13 19:48:01 2022 +0000 +++ b/mqppep_preproc.xml Thu Jun 30 16:15:57 2022 +0000 @@ -2,20 +2,28 @@ id="mqppep_preproc" name="MaxQuant Phosphopeptide Preprocessing" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" - python_template_version="3.5" profile="21.05" > <description> - Transform the output of MaxQuant for phosphoproteome-enriched samples to prepare it for statistical anlaysis. + Prep phosphoproteomic MaxQuant output for statistical anlaysis. </description> <macros> <import>macros.xml</import> </macros> + <edam_topics> + <edam_topic>topic_0121</edam_topic><!-- Proteomics --> + <edam_topic>topic_3520</edam_topic><!-- Proteomics experiment--> + </edam_topics> + <edam_operations> + <edam_operation>operation_0338</edam_operation><!-- Sequence database search --> + <edam_operation>operation_0361</edam_operation><!-- Sequence annotation --> + <edam_operation>operation_3434</edam_operation><!-- Conversion --> + <edam_operation>operation_3436</edam_operation><!-- Aggregation --> + </edam_operations> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ - ( - echo '--- localization-filter step:' - ) && ( + echo '--- localization-filter step:' + && ( Rscript '$__tool_directory__/MaxQuantProcessingScript.R' -i '$phosphoSites' #if $pst_py_selector == "y" @@ -27,7 +35,7 @@ --startCol '$startcol_script' --intervalCol $intervalCol --localProbCutoff $localProbCutoff - --collapse_func $collapseFunc + --collapse_func $collapse_func -o '$phosphoPepIntensities' --locProbCutoffGraph $locProbCutoffGraph --enrichGraph $enrichGraph @@ -35,9 +43,9 @@ --enrichGraph_svg $enrichGraph_svg --filtered_data $filteredData_tabular --quant_data $quantData_tabular - ) && ( - echo '... end localization-filter.' - ) && ( + ) && + echo '... end localization-filter.' + && ( echo '--- kinase-mapping step:' ) && ( perl '$__tool_directory__/PhosphoPeptide_Upstream_Kinase_Mapping.pl' @@ -57,11 +65,11 @@ -O '$melted_phophopeptide_map' -D '$mqppep_output_sqlite' -s '$species' - ) && ( + ) && echo '... end kinase-mapping.' - ) && ( + && echo '--- merge-and-filter step:' - ) && ( + && ( python '$__tool_directory__/mqppep_mrgfltr.py' --phosphopeptides='$mapped_phophopeptides' --ppep_mapping_db='$mqppep_output_sqlite' @@ -69,9 +77,8 @@ --mrgfltr_tab='$preproc_tab' --mrgfltr_csv='$preproc_csv' --mrgfltr_sqlite='$preproc_sqlite' - ) && ( - echo '... end merge-and-filter.' ) + && echo '... end merge-and-filter.' ]]></command> <configfiles> <configfile name="phosphocol_script">$phosphoCol @@ -82,11 +89,11 @@ <inputs> <param name="phosphoSites" type="data" format="tabular" label="Phospho (STY)Sites.txt" - help="[phosphoSites] Tabular 'Phospho (STY)Sites.txt' produced by MaxQuant" + help="Tabular 'Phospho (STY)Sites.txt' produced by MaxQuant" /> <param name="phosphoCol" type="text" label="pattern for column 'Number of Phospho (STY)'" - help="[phosphoCol] PERL-compatible regular expression matching header of column having number of 'Phospho (STY)'" + help="PERL-compatible regular expression matching header of column having number of 'Phospho (STY)'" value="^Number of Phospho [(]STY[)]$"> <sanitizer> <valid initial="string.printable"> @@ -96,7 +103,7 @@ </param> <param name="startCol" type="text" label="pattern for first column of intensity values" - help="[startCol] PERL-compatible regular expression matching column header having first sample intensity" + help="PERL-compatible regular expression matching column header having first sample intensity" value="^Intensity[^_]"> <sanitizer> <valid initial="string.printable"> @@ -106,46 +113,46 @@ </param> <param name="intervalCol" type="integer" value="1" min="1" label="Interval between the intensity column of samples" - help="[intervalCol] E.g., 1 if subsequent column is next sample; 2 if next sample is two columns away, etc."/> + help="E.g., 1 if subsequent column is next sample; 2 if next sample is two columns away, etc."/> <param name="pst_py_selector" type="select" label="Phosphopeptide enrichment type" - help="[enrichment] Were samples enriched for pS and pT, or were they enriched for pY instead?" + help="Were samples enriched for pS and pT, or were they enriched for pY instead?" > <option value="st" selected="true">pST</option> <option value="y">pY</option> </param> - <param name="collapseFunc" type="select" + <param name="collapse_func" type="select" label="Intensity merge function" - help="[collapseFunc] When a peptide is multiply phosphorylated, how should intensities be merged? [default: sum]" + help="When a peptide is multiply phosphorylated, how should intensities be merged? [default: sum]" > <option value="sum" selected="true">sum</option> <option value="mean">average</option> </param> <param name="localProbCutoff" type="float" value="0.75" min="0" max="1.0" label="Localization Probability Cutoff" - help="[localProbCutoff] See help below for an explanation." + help="See help below for an explanation." /> <param name="merge_function" type="select" label="intensity merge-function" - help="[merge_function] Specifies how intensities for identical phosphosites should be merged"> + help="Specifies how intensities for identical phosphosites should be merged"> <option value="sum" selected="true">sum</option> <option value="average">average</option> </param> <param name="protein_fasta" type="data" format="fasta" label="UniProtKB/SwissProt FASTA database" - help="[protein_fasta] Sequence database; supply the same FASTA file as you supplied to by MaxQuant" + help="Sequence database; supply the same FASTA file as you supplied to by MaxQuant" /> <param name="networkin" type="data" format="tabular" label="NetworKIN file" - help="[networkin] NetworKIN file; see help section below"/> + help="NetworKIN file; see help section below"/> <param name="p_sty_motifs" type="data" format="tabular" label="pSTY_Motifs file" - help="[p_sty_motifs] pS/pT/pY phosphorylation site motifs; see help section below"/> + help="pS/pT/pY phosphorylation site motifs; see help section below"/> <param name="psp_kinase_substrate" type="data" format="tabular" label="PSP_Kinase_Substrate_Dataset" - help="[psp_kinase_substrate] 'Kinase-substrate dataset'; see help section below"/> + help="'Kinase-substrate dataset'; see help section below"/> <param name="psp_regulatory_sites" type="data" format="tabular" label="PSP_Regulatory_sites" - help="[psp_regulatory_sites] 'Regulatory sites'; see help section below"/> + help="'Regulatory sites'; see help section below"/> <param name="species" type="text" value = "human" label="filter to limit PhosphoSitePlus records to indicated species" - help="[species] (field may be empty) [default: human]" + help="(field may be empty) [default: human]. If you supply this parameter, use the species indentifier seen as a suffix in UniProtKB" /> </inputs> <outputs> @@ -180,7 +187,7 @@ <param name="phosphoCol" value="^Number of Phospho [(][STY][STY]*[)]$"/> <param name="startCol" value="^Intensity[^_]"/> <param name="intervalCol" value="1"/> - <param name="collapseFunc" value="sum"/> + <param name="collapse_func" value="sum"/> <param name="localProbCutoff" value="0.75"/> <param name="species" value="human"/> @@ -200,36 +207,35 @@ <has_text text="cell cycle regulation" /> <has_text text="PPP2CA(INDUCES)" /> <has_text text="SNCA(DISRUPTS)" /> - <has_text text="Casein Kinase II substrate" /> - <has_text text="PKC kinase substrate" /> - <has_text text="PKCiota" /> - <has_text text="Csnk2a1" /> <has_text text="CDK7" /> <has_text text="CK1alpha" /> - <has_text text="CK2a2" /> <has_text text="CK2alpha" /> <has_text text="DNAPK" /> <has_text text="HIPK2" /> <has_text text="IKKalpha" /> <has_text text="PKCalpha" /> <has_text text="PKCbeta" /> + <has_text text="PKC" /> + <has_text text="CK2a2" /> + <has_text text="CK2alpha" /> + <has_text text="Csnk2a1" /> </assert_contents> </output> <output name="melted_phophopeptide_map"> <assert_contents> - <has_text text="CDK7_NetworKIN" /> - <has_text text="CK1alpha_NetworKIN" /> - <has_text text="CK2a2_NetworKIN" /> - <has_text text="CK2alpha_NetworKIN" /> - <has_text text="DNAPK_NetworKIN" /> - <has_text text="HIPK2_NetworKIN" /> - <has_text text="IKKalpha_NetworKIN" /> - <has_text text="PKCalpha_NetworKIN" /> - <has_text text="PKCbeta_NetworKIN" /> - <has_text text="PKC kinase substrate motif" /> - <has_text text="Casein Kinase II substrate motif" /> - <has_text text="Csnk2a1_PhosphoSite" /> + <has_text text="CDK7" /> + <has_text text="CK1alpha" /> + <has_text text="CK2alpha" /> + <has_text text="DNAPK" /> + <has_text text="HIPK2" /> + <has_text text="IKKalpha" /> + <has_text text="PKCalpha" /> + <has_text text="PKCbeta" /> + <has_text text="PKC" /> + <has_text text="CK2a2" /> + <has_text text="CK2alpha" /> + <has_text text="Csnk2a1" /> </assert_contents> </output> </test> @@ -246,7 +252,7 @@ <param name="phosphoCol" value="^Number of Phospho [(][STY][STY]*[)]$"/> <param name="startCol" value="^Intensity[^_]"/> <param name="intervalCol" value="1"/> - <param name="collapseFunc" value="sum"/> + <param name="collapse_func" value="sum"/> <param name="localProbCutoff" value="0.75"/> <param name="species" value="human"/> @@ -274,9 +280,9 @@ <output name="melted_phophopeptide_map"> <assert_contents> - <has_text text="Casein Kinase II substrate motif (HPRD)" /> - <has_text text="EPHA4_PhosphoSite" /> - <has_text text="EphA4_NetworKIN" /> + <has_text text="EphA6" /> + <has_text text="EPHA4" /> + <has_text text="EphA4" /> </assert_contents> </output> </test> @@ -355,8 +361,11 @@ **Authors** +``Nicholas A. Graham`` + (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) initiated the original script. + ``Larry C. Cheng`` - (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) wrote the original script. + (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) updated the original script. ``Arthur C. Eschenlauer`` (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy. @@ -482,10 +491,10 @@ **Authors** ``Nicholas A. Graham`` - (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) may have initiated the original script. + (`ORCiD 0000-0002-6811-1941 <https://orcid.org/0000-0002-6811-1941>`_) initiated the original script. ``Larry C. Cheng`` - (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) may have updated the original script. + (`ORCiD 0000-0002-6922-6433 <https://orcid.org/0000-0002-6922-6433>`_) updated the original script. ``Arthur C. Eschenlauer`` (`ORCiD 0000-0002-2882-0508 <https://orcid.org/0000-0002-2882-0508>`_) adapted the script to run in Galaxy.
--- a/test-data/pSTY_motifs.tabular Wed Apr 13 19:48:01 2022 +0000 +++ b/test-data/pSTY_motifs.tabular Thu Jun 30 16:15:57 2022 +0000 @@ -1,196 +1,355 @@ -1 ((E|D|A)(D|E)(E|D)(E|D)pS(E|D|A)(D|E|A)(E|D)(E|D))|(pS.(E|pS|pT))|(pS..(E|pS|pT))|((pS|pT)..(E|D))|(pS(D|E).(D|E).(D|E))|((D|E)pS(D|E).(D|E))|(pS(D|E)(D|E)(D|E))|((pS|pT)..(D|E))|((pS|pT)..(E|D|pS|pY))|((S|E|P|G)(D|S|N|E|P)(E|D|G|Q|W)(Y|E|D|S|W|T)(W|E|D)pS(D|E)(D|E|W|N)(E|D)(E|D|N|Q)) Casein Kinase II substrate motif (HPRD) -2 ((L|F|I)...R(Q|S|T)L(pS|pT)(M|L|I|V))|(..B.R..pS..)|(pS...(pS|pT)) MAPKAPK2 kinase substrate motif (HPRD) -3 ((M|V|L|I|F)(R|K|H)...(pS|pT)...(M|V|L|I|F))|((M|V|L|I)..(R|K|H).(pS|pT)...(M|V|L|I))|((M|V|L|I|F)(R|K|H)..(pS|pT)...(M|V|L|I|F)) AMP-activated protein kinase substrate motif (HPRD) -4 ((P|L|I|M).(L|I|D|E)pSQ)|(LpSQE)|(pSQ) ATM kinase substrate motif (HPRD) -5 ((R|K).R..(pS|pT)(M|L|V|I))|(VFLGFpTYVAP) p70 Ribosomal S6 kinase substrate motif (HPRD) -6 ((R|K).R..pS)|(RRR.pS) MAPKAPK1 kinase substrate motif (HPRD) -7 ((R|K)pSP(R|P)(R|K|H))|((pS|pT)P.(R|K))|(HHH(R|K)pSPR(R|K)R) Cdc2 kinase substrate motif (HPRD) -8 ((R|N)(F|L|M)(R|K)(R|K)pS(R|I|V|M)(R|I|M|V)(M|I|F|V)(I|F|M))|(FR.(pS|pT))|(RF(R|K)(R|K)pS(R|I)(R|I)MI) NIMA kinase substrate motif (HPRD) -9 ((pS|pT)P.(K|R))|((K|R)(pS|pT)P)|((pS|pT)P(K|R)) Growth associated histone HI kinase substrate motif (HPRD) -10 (..(pS|pT)E)|(.(pS|pT)...(A|P|S|T)) G protein-coupled receptor kinase 1 substrate motif (HPRD) -11 (.R..(pS|pT).R.)|((pS|pT).(R|K))|((R|K)..(pS|pT))|((R|K)..(pS|pT).(R|K))|((K|R).(pS|pT))|((R|K).(pS|pT).(R|K)) PKC kinase substrate motif (HPRD) -12 (.pSQ)|(P(pS|pT).) DNA dependent Protein kinase substrate motif (HPRD) -13 (AKRRRLSpSLRA)|(VRKRpTLRRL) PAK1 kinase substrate motif (HPRD) -14 (ARKGpSLRQ)|(R(R|F)RR(R|K)GpSF(R|K)(R|K)) PKC alpha kinase substrate motif (HPRD) -15 (HpSTSDD)|(YRpSVDE) Branched chain alpha-ketoacid dehydrogenase kinase substrate motif (HPRD) -16 (KCSpTWP)|(R..pS)|(R.R..pS.P)|(YpTV)|(RS.(pS|pT).P)|(R.(Y|F).pS.P)|(RPVSSAApSVY) 14-3-3 domain binding motif (HPRD) -17 (KK.RRpT(L|V).)|(KKR.RpT(L|V).)|((R|K).RR.(pS|pT)(L|V).) DMPK1 kinase substrate motif (HPRD) -18 (KKKKKK(pS|pT)...)|((R|K|Q|N)(M|C|W)(R|T|S|N)(E|D|S|N)(R|K|E|D|N)pS(S|D|E)(S|GC|D)(SM|R|N)(N|H|S|R|C)) TGF beta receptor kinase substrate motif (HPRD) -19 (KRKQIpSVR)|((F|M|K)(R|K)(M|R|Q|F)(M|F|L|I)pS(F|I|M|L)(F|R|K)(L|I)(F|L|I))|((K|R)..pS(V|I)) Phosphorylase kinase substrate motif (HPRD) -20 (KRQGpSVRR)|(R(K|E|R).pS) PKC epsilon kinase substrate motif (HPRD) -21 (P.(pS|pT)P)|(pSP) ERK1, ERK2 Kinase substrate motif (HPRD) -22 (P.(pS|pT)PP)|(..P.(pS|pT)PPP.) ERK1,2 kinase substrate motif (HPRD) -23 (PL(pS|pT)PIP(K|R|H))|(PL(pS|pT)P.(K|R|H)) CDK4 kinase substrate motif (HPRD) -24 (PLpTLP)|(PLLpTP)|(PLpTP)|(PpTLP)|(PLpTLP)|(PpTLP)|(LpTP) RAF1 kinase substrate motif (HPRD) -25 (R..(pS|pT))|((K|F)(R|K)(Q|M)(Q|M|K|L|F)pS(F|I|M|L|V)(D|E|I)(L|M|K|I)(F|K))|((M|V|L|I|F).(R|K)..(pS|pT)..)|(R..pS) Calmodulin-dependent protein kinase II substrate motif (HPRD) -26 (R..pSPV)|(K(pS|pT)P.K)|(KpSP...K)|(KpSP..K)|(KpSP....K)|(KpTPAKEE)|(P.pSP)|(.(pS|pT)P)|(..pSP) GSK-3, ERK1, ERK2, CDK5 substrate motif (HPRD) -27 (R.R..(pS|pT)(F|L))|(R.R..(pS|pT))|(GRART(S|T)pSFAE)|((R|Q|K)(R|K|N|Q|P|H)(R|K)(R|S|T)(N|K|Q|H|D|P)pS(F|W|I|M|N|S)(S|T|H)(R|S|K)(S|T|P|Q))|((R|K).(R|K)(S|T).pS) Akt kinase substrate motif (HPRD) -28 (RR..pS)|(KR.RpS)|(KRR.pT) ZIP kinase substrate motif (HPRD) -29 (RR.pS(M|I|L|V|F|Y))|(R.pS)|(KR..pS)|(R..pS)|((R|K).(pS|pT))|(K..(pS|pT))|((R|K)(R|K).(pS|pT))|(K...(pS|pT))|((pS|pT).(R|K))|(RRRRpSIIFI)|(RR.pS)|(R(R|K).(pS|pT)(I|L|V|F|Y)(D|C|.).D)|(RR.pS)|(RRR(R|N)pSII(F|D))|((R|C|P|K)(R|A|P)(R|K)(R|K|S)(N|L|S|M|P)Ps(I|L|V|C)(S|P|H|Q)(S|W|Q)(S|L|G)) PKA kinase substrate motif (HPRD) -30 (RRFGpSBRRF)|(RRFGpS(M|L|V|I|F)RR(M|L|V|I|F)) MEKK kinase substrate motif (HPRD) -31 (VPGKARKKpSSCQLL)|(PLARTLpSVAGLP)|((M|I|L|V|F|Y).R..(pS|pT)) Calmodulin-dependent protein kinase IV substrate motif (HPRD) -32 (pSD.E)|(pS..(E|D)) Casein kinase II substrate motif (HPRD) -33 (pSP..(pS|pT))|((D|E)..(pS|pT))|((pS|pT)..(S|T))|((pS|pT)...(S|T)(M|L|V|I|F)) Casein Kinase I substrate motif (HPRD) -34 (pTP.K)|((K|H|G)H(H|P)(K|G|H)pSP(R|K)(H|R|K)(R|H|K))|((pS|pT)PG(pS|pT)PGTP) CDK5 kinase substrate motif (HPRD) -35 (R|K).R..pS...(R|K) AMP-activated protein kinase 2 substrate motif (HPRD) -36 (R|K|N)R.(pS|pT)(M|L|V|I) Aurora-A kinase substrate motif (HPRD) -37 (D|E)(pS|pT)... b-Adrenergic Receptor kinase substrate motif (HPRD) -38 (M|V|L|I|F).R..(pS|pT)...(M|V|L|I|F) Calmodulin-dependent protein kinase I substrate motif (HPRD) -39 (M|I|L|V|F|Y).R..(pS|pT)(M|I|L|V|F|Y) Calmodulin-dependent protein kinase II alpha substrate motif (HPRD) -40 E(F|E)D(T|A|G)GpSI(I|F|Y|G)(I|G|F)(F|G)(F|P|L) Casein Kinase I delta substrate motif (HPRD) -41 Y(Y|E)(D|Y)(A|D)(A|G)pSI(I|Y|F|G)(I|G|F)(F|G)(F|P|L) Casein Kinase I gamma substrate motif (HPRD) -42 P.(pS|pT)PKK.KK Cdc2 like protein kinase substrate motif (HPRD) -43 (pS|pT)P.(R|K) CDK1,2, 4, 6 kinase substrate motif (HPRD) -44 pSP.(R|K). CDK kinase substrate motif (HPRD) -45 (M|I|L|V).(R|K)..(pS|pT) Chk1 kinase substrate motif (HPRD) -46 R..(pS|pT)..R CLK1 kinase substrate motif (HPRD) -47 (R|K).(R|K).(R|K).pS..R CLK1,2 kinase substrate motif (HPRD) -48 R(R|H)(R|H)(R|E)RE(R|H)pSR(R|D)L CLK2 kinase substrate motif (HPRD) -49 R..(pS|pT)(L|V)R DMPK1,2 kinase substrate motif (HPRD) -50 R(R|K)R(E|R)R(E|A)(H|R)pSRR(R|D)(L|E) DOA/CDC-like kinase 2 substrate motif (HPRD) -51 (I|L|V|F|M)RR..(pS|pT)(I|L|M|V|F) Doublecortin kinase-1 kinase substrate motif (HPRD) -52 E.pS.R..R elF2 alpha kinase substrate motif (HPRD) -53 (T|P|S)(G|P|E|Y)(P|L|I)(L|M|P)pSP(G|P|F)(P|F|G|Y)(F|Y|I) ERK1 kinase substrate motif (HPRD) -54 pTEpY ERK1 Kinase substrate motif (HPRD) -55 KpSPP ERK1, ERK2, SAPK, CDK5 and GSK3 kinase substrate motif (HPRD) -56 (D|Y|W|E)(C)(P|S|C|E)(P|C|S|L|T|V)(L|M|T)pS(P|A)(T|S|G|R|C|F)(W|P|S)(W|F) ERK2 kinase substrate motif (HPRD) -57 pS...pS GSK3 kinase substrate motif (HPRD) -58 P.pTP GSK3, Erk1, Erk2 and CDK5 kinase motif (HPRD) -59 (M|L|V|I|F)(R|K|H)..pS...(M|L|V|I|F) HMGCoA Reductase kinase substrate motif (HPRD) -60 GP(Q|M)pSPI JNK1 Kinase substrate motif (HPRD) -61 LRpT LKB1 Kinase substrate motif (HPRD) -62 pT(G|P|E)pY MAPK 11,13,14 Kinase substrate motif (HPRD) -63 KKR..pS.(R|K)(R|K) MLCK kinase substrate motif (HPRD) -64 FpTY mTOR kinase substrate motif (HPRD) -65 IRRLpSTRRR Nek 2 kinase substrate motif (HPRD) -66 (R|K)(R|.).(pS|pT) PAK2 kinase substrate motif (HPRD) -67 F..F(pS|pT)(F|Y) PDK1 kinase substrate motif (HPRD) -68 (R|K)(R|K)(R|K).(pS|pT). Pim1 kinase substrate sequence (HPRD) -69 (R|K)(R|K|A|Q|P)(R|K)(R|Q|H|N|Y)(P|H|K)pS(G|S|T)(P|S|G|Q|H|S|T)(S|P|Q|G|D)(T|S|P|G) Pim2 kinase substrate sequence (HPRD) -70 R(R|K).(pS|pT)B PKA, PKG kinase substrate motif (HPRD) -71 (L|R|F)(R|K)R(K|Q)GpS(F|M)KK.A PKC beta kinase substrate motif (HPRD) -72 R.RKGpSF PKC delta kinase substrate motif (HPRD) -73 AR..R(R|K)RpSFRR PKC eta kinase substrate motif (HPRD) -74 F..F(pS|pT)(F|Y) PKC family kinase substrate motif (HPRD) -75 RRRK(G|K)SF(R|K)(R|K)KA PKC gamma kinase substrate motif (HPRD) -76 (L|V)(V|L|A)R(Q|K|E)MpS PKC mu kinase substrate motif (HPRD) -77 (R|F|W|M)(W|A|K|S)(R|S|K|H)(R|H|S|Q)(R|K|N|P|G|Q)pS(I|F|R|V|K|S|L|M)(K|M|R|S|T)(R|S|K|W)(R|K|G) PKC theta kinase substrate motif (HPRD) -78 F.R..pS(F|M)(F|M) PKC zeta kinase substrate motif (HPRD) -79 (L|V|I)(R|K|Q)(R|K)(R|K|T|Q|M)(N|K|R|L|M|H)pS(F|W|I|M|L|V)(S|N)(R|S|P|Y|W)(S|R|N|L) PKD kinase substrate motif (HPRD) -80 R(R|K).(pS|pT)B PKG kinase substrate motif (HPRD) -81 R..(pS|pT).R..R PKR kinase substrate motif (HPRD) -82 (D|E).(pS|pT)(I|L|V|M).(D|E) Plk1 kinase substrate motif (HPRD) -83 .pS..D.. Pyruvate dehydrogenase kinase substrate motif (HPRD) -84 pTEY Dual specificity protein phosphatase 1 substrate motif (HPRD) -85 pT.pY Dual specificity protein phosphatase 6 substrate motif (HPRD) -86 RRA(pS|pT)VA PP2A, PP2C substrate motif (HPRD) -87 .R..pSVA PP2B substrate motif (HPRD) -88 .pT.pY. PP2C delta substrate motif (HPRD) -89 pS(D|E)(D|E)E BARD1 BRCT domain binding motif (HPRD) -90 DpSG..pS Beta-TrCP1 domain binding motif (HPRD) -91 pS(F|Y|H)(V|F|Y)(F|Y) BRCA1 BRCT domain binding motif (HPRD) -92 (I|L)(I|L|P)pTP(R|K) CDC4 WD40 domain binding motif (HPRD) -93 HFDpTYLI Chk2 FHA domain binding motif (HPRD) -94 (R|D|H)(L|Y)(L|M)(K|A)pT(Q|L|M|E|V)(K|L|I|R) FHA domain binding motif (HPRD) -95 S(pS|pT). MDC1 BRCT domain binding motif (HPRD) -96 S(pS|pT). Plk1 PBD domain binding motif (HPRD) -97 pSYII RAD9 BRCT domain binding motif (HPRD) -98 (pS|pT)P WW domain binding motif (HPRD) -99 ((pS|pT)P.(K|R))|((pS|pT)P(K|R)) CDK1_Phosida -100 (P.(pS|pT)P)|(V.(pS|pT)P)|(PE(pS|pT)P) ERK/MAPK_Phosida -101 (R(R|S|T).(pS|pT).(S|T))|(R.R..(pS|pT)) PKB/AKT_Phosida -102 (R.(pS|pT))|(R(R|K).(pS|pT))|(KR..(pS|pT)) PKA_Phosida -103 (R..(pS|pT))|(R..(pS|pT)V) CAMK2_Phosida -104 (S..(pS|pT))|((S|T)...pS) CK1_Phosida -105 (pS|pT)..E CK2_Phosida -106 pS...S GSK3_Phosida -107 (pS|pT)P.(K|R) CDK2_Phosida -108 R..(pS|pT).R PKC_Phosida -109 (L|V|I).(R|K)..(pS|pT) PKD_Phosida -110 (I|E|V)pY(E|G)(E|D|P|N)(I|V|L) LCK_Phosida -111 (I|V|L)pY..(P|F) ABL_Phosida -112 (E|D)..pY..(D|E|A|G|S|T) SRC_Phosida -113 pY..(I|L|V|M) ALK_Phosida -114 (D|P|S|A|E|N).pY(V|L|D|E|I|N|P) EGFR_Phosida -115 (R|K).(pS|pT)(I|L|V) AURORA_Phosida -116 (R|K|N)R.(pS|pT)(M|L|V|I) AURORA-A_Phosida -117 (D|E).(pS|pT)(V|I|L|M).(D|E) PLK_Phosida -118 (E|D).(pS|pT)(F|L|I|Y|W|V|M) PLK1_Phosida -119 L..(pS|pT) NEK6_Phosida -120 L.R..(pS|pT) CHK1/2_Phosida -121 (M|I|L|V).(R|K)..(pS|pT) CHK1_Phosida -122 F..F(pS|pT)(F|Y) PDK1_Phosida -123 (F|L|M)(R|K)(R|K)(pS|pT) NIMA_Phosida -124 ((D|E)(D|E)...pYVA)|((E|D|Y)pY) TC-PTP phosphatase substrate motif (HPRD) -125 ((D|E).(L|I|V).pY..(L|I|V))|((D|E).(L|I|V)..pY..(L|I|V))|((D|E)(D|E)(D|E|L).pY..(F|M|L|V|I)(D|E))|((D|E).pY)|((E|P)(F|I|L)pYA.(F|I|L|V)) SHP1 phosphatase substrate motif (HPRD) -126 ((D|E).......(D|E)..pY..L.......Y..(L|I))|((I|V|L|S).pY..(L|I)) Src family kinase substrate motif (HPRD) -127 ((D|E)pYpY(R|K))|(EFpY(G|A)TY(G|A))|(E(Y|F|D)pYM)|((E|P)(M|L|I|V|F)pY(G|A).(M|L|I|V|F|Y)A)|(RD.Y.TDYpYR)|(E(F|D|Y)pY) PTP1B phosphatase substrate motif (HPRD) -128 ((H|F).V.(T|S|A)pY)|((I|V|L).pY(F|M).P)|(pY(I|V).(I|V))|((I|L|V|M).pY(T|V|A).(I|V|L|F))|((I|V).pY(L|M|T)Y(A|P|T)SG)|(W(M|T|V)pY(Y|R)(I|L).) SHP2 N-terminal SH2 domain binding motif (HPRD) -129 ((V|I|L).pYA.(L|V))|(..pYYM(K|R)) SHP1 C-terminal SH2 domain binding motif (HPRD) -130 (.E.IpYGVLF)|(E.(I|V|L|F)pY(G|A)V(L|V|F|I)(F|L|V|I)) Lck kinase substrate motif (HPRD) -131 (DEEIpY(E|G)EL.)|((D|E).......(D|E)..pY..L.......Y..(L|I)) Lyn kinase substrate motif (HPRD) -132 (EE(D|E)IpYFFFF)|(...IpY(M|I|F)FFF) CSK kinase substrate motif (HPRD) -133 (EEEEpYFELV)|((E|D|R|A)(D|E)(D|E)(E|D|I)pY(F|V|I|E)(E|F|D)(L|I|F|V)V)|(.(D|E)pY.)|(pYIPP)|(.(D|E)pY(I|L|V)) EGFR kinase substrate motif (HPRD) -134 (EEEEpYVFI.)|((L|N)(R|I)TpY)|((D|E)(D|E)(D|E)(D|E)pY(V|E|I)F(I|V|F)) PDGFR kinase substrate motif (HPRD) -135 (EEEIpYEEIE)|((E|A|D)(E|A)(E|A)(I|E|V)pY(D|E)(D|E)(I|V|E)(E|I|V)) Fes kinase substrate motif (HPRD) -136 (EEEpYFFLF)|(A(E|A)EEpY(F|V)F(L|F|M|I|V)F) FGFR kinase substrate motif (HPRD) -137 (L(Y|H)pY(M|F).(F|M))|(L.pYA.L) SHP1 N-terminal SH2 domain binding motif (HPRD) -138 (pY(M|L|E)EP)|(pYESP) Vav SH2 domain binding motif (HPRD) -139 (pY(Y|I|V)N(F|L|I|V))|(pY(Q|Y|V)N(Y|Q|F))|(pY.N) Grb2 SH2 domain binding motif (HPRD) -140 (pY..P)|(pYDHP) Crk SH2 domain binding motif (HPRD) -141 (pY..Q)|(pY(M|L|V|I|F)(P|R|K|H)Q) STAT3 SH2 domain binding motif (HPRD) -142 (pY..YY)|(pY(D|E).(I|L|V|M))|((D|E)..pY)|(pY....(F|Y)) ALK kinase substrate motif (HPRD) -143 (pYIDL)|(pYASI)|(EFpYA.(V|I)G(R|K|H)S) SHP2 phosphatase substrate motif (HPRD) -144 (pYM.M)|(EDAIpY)|(.VIpYAAPF)|(EAIpYAAPF)|(EEIpYEEpY)|(E.IpY..P.)|(EEIpYYYVH)|(ERIpYARTK)|(AEV(I|V|L|F)pYAA(P|F)F) Abl kinase substrate motif (HPRD) -145 (pYM.M)|(EE(E|N|D)pY(M|F)(M|F)(M|F|I|E)(M|F))|(.EEEpYMMMM)|(KKSRGDpYMTMQIG)|(KKKLPATGDpYMNMSPVGD) Insulin receptor kinase substrate motif (HPRD) -146 (pYM.M)|(YIpYGSFK)|(EEEIpY(G|E)EFD)|(D(D|E)(E|D|G)(I|V|L)pY(G|E)E(F|I)F)|((D|E).......(D|E)..pY..L.......Y..(L|I))|((D|E)(D|E)(E|D|G)(I|V|L)pY(G|E|D)E(F|I|L|V)(D|E))|(pY(A|G|S|T|D|E)) Src kinase substrate motif (HPRD) -147 (pYM.M)|(pY..M)|(pYMPMS) PI3 Kinase p85 SH2 domain binding motif (HPRD) -148 ME(E|N)(I|V)pY(G|E)IFF Fgr kinase substrate motif (HPRD) -149 KKKSPGEpYVNIEFG IGF1 receptor kinase substrate motif (HPRD) -150 pY..(L|I|V) JAK2 kinase substrate motif (HPRD) -151 pTPpY JNK kinase substrate motif (HPRD) -152 (E|D|pT|pY).pYEE Syk kinase substrate motif (HPRD) -153 DpYpYR PTP1B, TC-PTP phosphatase substrate motif (HPRD) -154 (D|E)FpY(G|A)(F|Y)(A|G) PTPRH phosphatase substrate motif (HPRD) -155 F(M|L|V|I)pY PTPRJ phosphatase substrate motif (HPRD) -156 pY(E|M|V)(N|V|I) 3BP2 SH2 domain binding motif (HPRD) -157 pYENP Abl SH2 domain binding motif (HPRD) -158 pY(T|A|S)(K|R|Q|N)(M|I|V|R) Csk SH2 domain binding motif (HPRD) -159 pYE.(V|I) Fes SH2 domain binding motif (HPRD) -160 pYEE(I|V) Fgr SH2 domain binding motif (HPRD) -161 pYEDP Fyn SH2 domain binding motif (HPRD) -162 pY(M|I|L|V).(M|I|L|V) GRB2, 3BP2, Csk, Fes, Syk C-terminal SH2 domain binding motif (HPRD) -163 (F|Y)pY(E|T|Y|S)N(I|L|V|P|T|Y|S) GRB7, GRB10 SH2 domain binding motif (HPRD) -164 pYF.(F|P|L|Y) HCP SH2 domain binding motif (HPRD) -165 pY(A|E|V)(Y|F|E|S|N|V)(P|F|I|H) Itk SH2 domain binding motif (HPRD) -166 pYDYV Lck and Src SH2 domain binding motif (HPRD) -167 pYDEP Nck SH2 domain binding motif (HPRD) -168 pY(L|I|V)E(L|I|V) PLCgamma C and N-terminal SH2 domain binding motif (HPRD) -169 pY..P RasGAP C-terminal SH2 domain binding motif (HPRD) -170 pYILV.(M|L|I|V|P) RasGAP N-terminal SH2 domain binding motif (HPRD) -171 TIpY..(V|I) SAP and EAT2 SH2 domain binding motif (HPRD) -172 pY(L|V)N(V|P) Sem5 SH2 domain binding motif (HPRD) -173 pY(T|V|I).L Shb SH2 domain binding motif (HPRD) -174 pY(I|E|Y|L).(I|L|M) SHC SH2 domain binding motif (HPRD) -175 (I|V|L|S).pY..(L|I) SHIP2 SH2 domain binding motif (HPRD) -176 (I|V).pY..(L|V) SHP1 SH2 domain binding motif (HPRD) -177 (V|I|L).pY(M|L|F).P SHP1, SHP2 SH2 domain binding motif (HPRD) -178 (T|V|I|Y).pY(A|S|T|V).(I|V|L) SHP2 CSH2 domain binding motif (HPRD) -179 (I|L|V)(I|L|V)(I|L|V|F|T|Y)pY(T|I|L|V)(I|L)(I|L|V|P) SHP2 C-terminal SH2 domain binding motif (HPRD) -180 pYIPP SHP2, PLCgamma SH2 domain binding motif (HPRD) -181 pYM.M Src and Abl SH2 domain binding motif (HPRD) -182 pY(R|K|H|Q|E|D)(R|K|H|Q|E|D)(I|P) Src, Fyn, Lck, Fgr, Abl, Crk, Nck SH2 domain binding motif (HPRD) -183 PP.pY Src, Fyn,Csk, Nck and SHC SH2 domain binding motif (HPRD) -184 pYEEI Src,Lck and Fyn SH2 domains binding motif (HPRD) -185 pY(D|E)(P|R)(R|P|Q) STAT1 SH2 domain binding motif (HPRD) -186 pY(Q|T|E)(E|Q)(L|I) Syk C-terminal SH2 domain binding motif (HPRD) -187 pYTT(I|L|M) Syk N-terminal SH2 domain binding motif (HPRD) -188 (D|E).......(D|E)..pY..L.......Y..(L|I) Syk, ZAP-70, Shc, Lyn SH2 domain binding motif (HPRD) -189 pYEN(F|I|V) Tensin SH2 domain binding motif (HPRD) -190 D(N|D).pY Cbl PTB domain binding motif (HPRD) -191 N.LpY Dok1 PTB domain binding motif (HPRD) -192 N..pY FRIP PTB domain binding motif (HPRD) -193 NP.pY Shc PTB domain binding motif (HPRD) -194 DD.pY Shb PTB domain binding motif (HPRD) -195 NP.pYF.R ShcA PTB domain binding motif (HPRD) -196 HN(M|L|V|I)(M|L|V|I|N)NP(S|T)pY ShcC PTB domain binding motif (HPRD) +"counter" "pcre" "symbol" "description" "pubmed_id" "classification" "source" +"1" "R.R..(pS|pT)(F|L)" "PKB_group" "Akt kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8985174" "kinase substrate" "HPRD" +"2" "R.R..(pS|pT)" "PKB_group" "Akt kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=10945990" "kinase substrate" "HPRD" +"3" "GRART(S|T)pSFAE" "PKB_group" "Akt kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8524413" "kinase substrate" "HPRD" +"4" "(R|Q|K)(R|K|N|Q|P|H)(R|K)(R|S|T)(N|K|Q|H|D|P)pS(F|W|I|M|N|S)(S|T|H)(R|S|K)(S|T|P|Q)" "PKB_group" "Akt kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=15782149" "kinase substrate" "HPRD" +"5" "(R|K).(R|K)(S|T).pS" "PKB_group" "Akt kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=16273072" "kinase substrate" "HPRD" +"6" "(M|V|L|I|F)(R|K|H)...(pS|pT)...(M|V|L|I|F)" "AMPK_group" "AMP-activated protein kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7902296,7698321" "kinase substrate" "HPRD" +"7" "(M|V|L|I)..(R|K|H).(pS|pT)...(M|V|L|I)" "AMPK_group" "AMP-activated protein kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7902296" "kinase substrate" "HPRD" +"8" "(M|V|L|I|F)(R|K|H)..(pS|pT)...(M|V|L|I|F)" "AMPK_group" "AMP-activated protein kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7698321" "kinase substrate" "HPRD" +"9" "(R|K).R..pS...(R|K)" "AMPK_group" "AMP-activated protein kinase 2 substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7698321" "kinase substrate" "HPRD" +"10" "(P|L|I|M).(L|I|D|E)pSQ" "ATM" "ATM kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=10608806" "kinase substrate" "HPRD" +"11" "LpSQE" "ATM" "ATM kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=10801797,11544175" "kinase substrate" "HPRD" +"12" "pSQ" "ATM" "ATM kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=16273072" "kinase substrate" "HPRD" +"13" "(R|K|N)R.(pS|pT)(M|L|V|I)" "Aurora A" "Aurora-A kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=16083426" "kinase substrate" "HPRD" +"14" "(D|E)(pS|pT)..." "GRK-2" "b-Adrenergic Receptor kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1645191" "kinase substrate" "HPRD" +"15" "HpSTSDD" "BCKDK" "Branched chain alpha-ketoacid dehydrogenase kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=3947057" "kinase substrate" "HPRD" +"16" "YRpSVDE" "BCKDK" "Branched chain alpha-ketoacid dehydrogenase kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=3947057" "kinase substrate" "HPRD" +"17" "(M|V|L|I|F).R..(pS|pT)...(M|V|L|I|F)" "CaM-KI_group" "Calmodulin-dependent protein kinase I substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9452427,7698321,8022798" "kinase substrate" "HPRD" +"18" "(M|I|L|V|F|Y).R..(pS|pT)(M|I|L|V|F|Y)" "CaM-KII_alpha" "Calmodulin-dependent protein kinase II alpha substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9452427" "kinase substrate" "HPRD" +"19" "R..(pS|pT)" "CaM-KII_group" "Calmodulin-dependent protein kinase II substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=1956339" "kinase substrate" "HPRD" +"20" "(K|F)(R|K)(Q|M)(Q|M|K|L|F)pS(F|I|M|L|V)(D|E|I)(L|M|K|I)(F|K)" "CaM-KII_group" "Calmodulin-dependent protein kinase II substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=8887677" "kinase substrate" "HPRD" +"21" "(M|V|L|I|F).(R|K)..(pS|pT).." "CaM-KII_group" "Calmodulin-dependent protein kinase II substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=8280084" "kinase substrate" "HPRD" +"22" "R..pS" "CaM-KII_group" "Calmodulin-dependent protein kinase II substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=16273072" "kinase substrate" "HPRD" +"23" "VPGKARKKpSSCQLL" "CaM-KIV" "Calmodulin-dependent protein kinase IV substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=1901412" "kinase substrate" "HPRD" +"24" "PLARTLpSVAGLP" "CaM-KIV" "Calmodulin-dependent protein kinase IV substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=1309765" "kinase substrate" "HPRD" +"25" "(M|I|L|V|F|Y).R..(pS|pT)" "CaM-KIV" "Calmodulin-dependent protein kinase IV substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9452427" "kinase substrate" "HPRD" +"26" "E(F|E)D(T|A|G)GpSI(I|F|Y|G)(I|G|F)(F|G)(F|P|L)" "CK1_delta|CK1_group" "Casein Kinase I delta substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=8887677" "kinase substrate" "HPRD" +"27" "Y(Y|E)(D|Y)(A|D)(A|G)pSI(I|Y|F|G)(I|G|F)(F|G)(F|P|L)" "CK1_group|CK1_gamma Q9HCP0" "Casein Kinase I gamma substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=8887677" "kinase substrate" "HPRD" +"28" "pSP..(pS|pT)" "CK1_group" "Casein Kinase I substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=1956339" "kinase substrate" "HPRD" +"29" "(D|E)..(pS|pT)" "CK1_group" "Casein Kinase I substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=12925738" "kinase substrate" "HPRD" +"30" "(pS|pT)..(S|T)" "CK1_group" "Casein Kinase I substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=12925738" "kinase substrate" "HPRD" +"31" "(pS|pT)...(S|T)(M|L|V|I|F)" "CK1_group" "Casein Kinase I substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=12925738" "kinase substrate" "HPRD" +"32" "(E|D|A)(D|E)(E|D)(E|D)pS(E|D|A)(D|E|A)(E|D)(E|D)" "CK2_group" "Casein Kinase II substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=8887677" "kinase substrate" "HPRD" +"33" "pS.(E|pS|pT)" "CK2_group" "Casein Kinase II substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=1650349,3474230" "kinase substrate" "HPRD" +"34" "pS..(E|pS|pT)" "CK2_group" "Casein Kinase II substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=1650349,12925738" "kinase substrate" "HPRD" +"35" "(pS|pT)..(E|D)" "CK2_group" "Casein Kinase II substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9272871" "kinase substrate" "HPRD" +"36" "pSD.E" "CK2_group" "Casein kinase II substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=16273072" "kinase substrate" "HPRD" +"37" "pS..(E|D)" "CK2_group" "Casein kinase II substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=16273072" "kinase substrate" "HPRD" +"38" "pS(D|E).(D|E).(D|E)" "CK2_group" "Casein Kinase II substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=16273072" "kinase substrate" "HPRD" +"39" "(D|E)pS(D|E).(D|E)" "CK2_group" "Casein Kinase II substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=16273072" "kinase substrate" "HPRD" +"40" "pS(D|E)(D|E)(D|E)" "CK2_group" "Casein Kinase II substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=16273072" "kinase substrate" "HPRD" +"41" "(pS|pT)..(D|E)" "CK2_group" "Casein Kinase II substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=2044770,2117608" "kinase substrate" "HPRD" +"42" "(pS|pT)..(E|D|pS|pY)" "CK2_group" "Casein Kinase II substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7735314" "kinase substrate" "HPRD" +"43" "(S|E|P|G)(D|S|N|E|P)(E|D|G|Q|W)(Y|E|D|S|W|T)(W|E|D)pS(D|E)(D|E|W|N)(E|D)(E|D|N|Q)" "CK2_group" "Casein Kinase II substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=15782149" "kinase substrate" "HPRD" +"44" "(R|K)pSP(R|P)(R|K|H)" "CDK1" "Cdc2 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=12586835" "kinase substrate" "HPRD" +"45" "(pS|pT)P.(R|K)" "CDK1" "Cdc2 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7874496,9003781" "kinase substrate" "HPRD" +"46" "HHH(R|K)pSPR(R|K)R" "CDK1" "Cdc2 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7874496" "kinase substrate" "HPRD" +"47" "P.(pS|pT)PKK.KK" "CDK1" "Cdc2 like protein kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8407912" "kinase substrate" "HPRD" +"48" "(pS|pT)P.(R|K)" "CDK1|CDK2|CDK4|CDK6" "CDK1,2, 4, 6 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=12501191,10607671" "kinase substrate" "HPRD" +"49" "pSP.(R|K)." "CDK_group" "CDK kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=16273072" "kinase substrate" "HPRD" +"50" "PL(pS|pT)PIP(K|R|H)" "CDK4" "CDK4 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=9003781" "kinase substrate" "HPRD" +"51" "PL(pS|pT)P.(K|R|H)" "CDK4" "CDK4 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=9003781" "kinase substrate" "HPRD" +"52" "pTP.K" "CDK5" "CDK5 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=11684694" "kinase substrate" "HPRD" +"53" "(K|H|G)H(H|P)(K|G|H)pSP(R|K)(H|R|K)(R|H|K)" "CDK5" "CDK5 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8887677" "kinase substrate" "HPRD" +"54" "(pS|pT)PG(pS|pT)PGTP" "CDK5" "CDK5 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=9003781" "kinase substrate" "HPRD" +"55" "(M|I|L|V).(R|K)..(pS|pT)" "CHK1" "Chk1 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=10648819" "kinase substrate" "HPRD" +"56" "R..(pS|pT)..R" "CLK1" "CLK1 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=10954422" "kinase substrate" "HPRD" +"57" "(R|K).(R|K).(R|K).pS..R" "CLK1" "CLK1|CLK2 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=10480872" "kinase substrate" "HPRD" +"58" "R(R|H)(R|H)(R|E)RE(R|H)pSR(R|D)L" "CLK1" "CLK2 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=11827553" "kinase substrate" "HPRD" +"59" "KK.RRpT(L|V)." "DMPK_group" "DMPK1 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=12897125" "kinase substrate" "HPRD" +"60" "KKR.RpT(L|V)." "DMPK_group" "DMPK1 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=12897125" "kinase substrate" "HPRD" +"61" "(R|K).RR.(pS|pT)(L|V)." "DMPK_group" "DMPK1 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=12897125" "kinase substrate" "HPRD" +"62" "R..(pS|pT)(L|V)R" "DMPK_group" "DMPK1|DMPK2 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=10913253" "kinase substrate" "HPRD" +"63" ".pSQ" "DNA-PK" "DNA dependent Protein kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1751287" "kinase substrate" "HPRD" +"64" "P(pS|pT)." "DNA-PK" "DNA dependent Protein kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8086496" "kinase substrate" "HPRD" +"65" "R(R|K)R(E|R)R(E|A)(H|R)pSRR(R|D)(L|E)" "CLK1" "DOA/CDC-like kinase 2 substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=11827553" "kinase substrate" "HPRD" +"66" "(I|L|V|F|M)RR..(pS|pT)(I|L|M|V|F)" "DCAMKL1" "Doublecortin kinase-1 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=12590608" "kinase substrate" "HPRD" +"67" "E.pS.R..R" "HRI|EIF2AK2|EIF2AK3" "elF2 alpha kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8982275,1671834" "kinase substrate" "HPRD" +"68" "(T|P|S)(G|P|E|Y)(P|L|I)(L|M|P)pSP(G|P|F)(P|F|G|Y)(F|Y|I)" "MAP2K1|MAP2K2|MAP2K_group" "ERK1 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8887677" "kinase substrate" "HPRD" +"69" "pTEpY" "MAP2K1|MAP2K2|MAP2K_group" "ERK1 Kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=12646559" "kinase substrate" "HPRD" +"70" "P.(pS|pT)PP" "MAP2K1|MAP2K2|MAP2K_group" "ERK1,2 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1939237" "kinase substrate" "HPRD" +"71" "..P.(pS|pT)PPP." "MAP2K1|MAP2K2|MAP2K_group" "ERK1,2 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1939237" "kinase substrate" "HPRD" +"72" "P.(pS|pT)P" "MAP2K1|MAP2K2|MAP2K_group" "ERK1, ERK2 Kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=9792705" "kinase substrate" "HPRD" +"73" "pSP" "MAP2K1|MAP2K2|MAP2K_group" "ERK1, ERK2 Kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=16273072" "kinase substrate" "HPRD" +"74" "KpSPP" "MAP2K1|MAP2K2|MAP2K_group|CDK5|GSK-3 (HPRD)" "ERK1, ERK2, SAPK, CDK5 and GSK3 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=12586839" "kinase substrate" "HPRD" +"75" "(D|Y|W|E)(C)(P|S|C|E)(P|C|S|L|T|V)(L|M|T)pS(P|A)(T|S|G|R|C|F)(W|P|S)(W|F)" "MAP2K1|MAP2K_group" "ERK2 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=15782149" "kinase substrate" "HPRD" +"76" "..(pS|pT)E" "GRK-1" "G protein-coupled receptor kinase 1 substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=1645191" "kinase substrate" "HPRD" +"77" ".(pS|pT)...(A|P|S|T)" "GRK-1" "G protein-coupled receptor kinase 1 substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=1645191" "kinase substrate" "HPRD" +"78" "(pS|pT)P.(K|R)" "CDK2|MOD_CDK_SPxK_1" "Growth associated histone HI kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1956339" "kinase substrate|ELM" "HPRD" +"79" "(K|R)(pS|pT)P" "GSK-3 (HPRD)|MAP2K1|MAP2K2|MAP2K_group|CDK5|MOD_ProDKin_1" "Growth associated histone HI kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1956339" "kinase substrate|ELM" "HPRD" +"80" "(pS|pT)P(K|R)" "CDK2|MOD_CDK_SPK_2" "Growth associated histone HI kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1956339" "kinase substrate|ELM" "HPRD" +"81" "pS...pS" "GSK-3 (HPRD)" "GSK3 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1956339,16141410" "kinase substrate" "HPRD" +"82" "P.pTP" "GSK-3 (HPRD)|MAP2K1|MAP2K2|MAP2K_group|CDK5" "GSK3, Erk1, Erk2 and CDK5 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=16377132" "kinase substrate" "HPRD" +"83" "R..pSPV" "GSK-3 (HPRD)|MAP2K1|MAP2K2|MAP2K_group|CDK5" "GSK-3, ERK1, ERK2, CDK5 substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=15358237" "kinase substrate" "HPRD" +"84" "K(pS|pT)P.K" "GSK-3 (HPRD)|MAP2K1|MAP2K2|MAP2K_group|CDK5" "GSK-3, ERK1, ERK2, CDK5 substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9592082" "kinase substrate" "HPRD" +"85" "KpSP...K" "GSK-3 (HPRD)|MAP2K1|MAP2K2|MAP2K_group|CDK5" "GSK-3, ERK1, ERK2, CDK5 substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9592082" "kinase substrate" "HPRD" +"86" "KpSP..K" "GSK-3 (HPRD)|MAP2K1|MAP2K2|MAP2K_group|CDK5" "GSK-3, ERK1, ERK2, CDK5 substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9592082" "kinase substrate" "HPRD" +"87" "KpSP....K" "GSK-3 (HPRD)|MAP2K1|MAP2K2|MAP2K_group|CDK5" "GSK-3, ERK1, ERK2, CDK5 substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9592082" "kinase substrate" "HPRD" +"88" "KpTPAKEE" "GSK-3 (HPRD)|MAP2K1|MAP2K2|MAP2K_group|CDK5" "GSK-3, ERK1, ERK2, CDK5 substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9819213" "kinase substrate" "HPRD" +"89" "P.pSP" "GSK-3 (HPRD)|MAP2K1|MAP2K2|MAP2K_group|CDK5" "GSK-3, ERK1, ERK2, CDK5 substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=16020478" "kinase substrate" "HPRD" +"90" ".(pS|pT)P" "GSK-3 (HPRD)|MAP2K1|MAP2K2|MAP2K_group|CDK5" "GSK-3, ERK1, ERK2, CDK5 substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=16020478" "kinase substrate" "HPRD" +"91" "..pSP" "GSK-3 (HPRD)|MAP2K1|MAP2K2|MAP2K_group|CDK5" "GSK-3, ERK1, ERK2, CDK5 substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=16020478" "kinase substrate" "HPRD" +"93" "GP(Q|M)pSPI" "JNK_group" "JNK1 Kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=15629715" "kinase substrate" "HPRD" +"94" "LRpT" "LKB1" "LKB1 Kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=14985505" "kinase substrate" "HPRD" +"95" "(R|K).R..pS" "RSK-1|RSK-2|RSK_group" "MAPKAPK1 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7498520" "kinase substrate" "HPRD" +"96" "RRR.pS" "RSK_group" "MAPKAPK1 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7498520" "kinase substrate" "HPRD" +"97" "(L|F|I)...R(Q|S|T)L(pS|pT)(M|L|I|V)" "MAPKAPK2" "MAPKAPK2 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=15807522" "kinase substrate" "HPRD" +"98" "..[^P].R..pS.." "MAPKAPK2" "MAPKAPK2 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8280084" "kinase substrate" "HPRD" +"99" "pS...(pS|pT)" "MAPKAPK2" "MAPKAPK2 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=15629715,8280084" "kinase substrate" "HPRD" +"100" "pT(G|P|E)pY" "MAPK11|MAPK13|MAPK14" "MAPK 11,13,14 Kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=9295308,7535770" "kinase substrate" "HPRD" +"101" "RRFGpS[^P]RRF" "MEKK (HPRD)" "MEKK kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7874496" "kinase substrate" "HPRD" +"102" "RRFGpS(M|L|V|I|F)RR(M|L|V|I|F)" "MEKK (HPRD)" "MEKK kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7874496" "kinase substrate" "HPRD" +"103" "KKR..pS.(R|K)(R|K)" "MLCK_group" "MLCK kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7961752" "kinase substrate" "HPRD" +"104" "FpTY" "mTOR" "mTOR kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=14560963" "kinase substrate" "HPRD" +"105" "IRRLpSTRRR" "NEK2" "Nek 2 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8982275,7759549" "kinase substrate" "HPRD" +"106" "(R|N)(F|L|M)(R|K)(R|K)pS(R|I|V|M)(R|I|M|V)(M|I|F|V)(I|F|M)" "NIMA (HPRD)" "NIMA kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8887677,1416988" "kinase substrate" "HPRD" +"107" "FR.(pS|pT)" "NIMA (HPRD)" "NIMA kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7759549,8120013" "kinase substrate" "HPRD" +"108" "RF(R|K)(R|K)pS(R|I)(R|I)MI" "NIMA (HPRD)" "NIMA kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8120013,8982275" "kinase substrate" "HPRD" +"109" "(R|K).R..(pS|pT)(M|L|V|I)" "p70S6K" "p70 Ribosomal S6 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7498520,1737763" "kinase substrate" "HPRD" +"110" "VFLGFpTYVAP" "p70S6K" "p70 Ribosomal S6 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7498520" "kinase substrate" "HPRD" +"111" "AKRRRLSpSLRA" "PAK1" "PAK1 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8051089" "kinase substrate" "HPRD" +"112" "VRKRpTLRRL" "PAK1" "PAK1 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8051089" "kinase substrate" "HPRD" +"113" "(R|K)(R|.).(pS|pT)" "PAK2" "PAK2 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=9405039" "kinase substrate" "HPRD" +"114" "F..F(pS|pT)(F|Y)" "PDK-1" "PDK1 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=11516946" "kinase substrate" "HPRD" +"115" "KRKQIpSVR" "PHK_group" "Phosphorylase kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8180216" "kinase substrate" "HPRD" +"116" "(F|M|K)(R|K)(M|R|Q|F)(M|F|L|I)pS(F|I|M|L)(F|R|K)(L|I)(F|L|I)" "PHK_group" "Phosphorylase kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8887677" "kinase substrate" "HPRD" +"117" "(K|R)..pS(V|I)" "PHK_group" "Phosphorylase kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1956339" "kinase substrate" "HPRD" +"118" "(R|K)(R|K)(R|K).(pS|pT)." "Pim1 (HPRD)" "Pim1 kinase substrate sequence" "https://pubmed.ncbi.nlm.nih.gov/?term=1416988" "kinase substrate" "HPRD" +"119" "(R|K)(R|K|A|Q|P)(R|K)(R|Q|H|N|Y)(P|H|K)pS(G|S|T)(P|S|G|Q|H|S|T)(S|P|Q|G|D)(T|S|P|G)" "Pim2 (HPRD)" "Pim2 kinase substrate sequence" "https://pubmed.ncbi.nlm.nih.gov/?term=15782149" "kinase substrate" "HPRD" +"120" "RR.pS(M|I|L|V|F|Y)" "PKA_group" "PKA kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8463304,194899" "kinase substrate" "HPRD" +"121" "R.pS" "PKA_group" "PKA kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1956339" "kinase substrate" "HPRD" +"122" "KR..pS" "PKA_group" "PKA kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1956339" "kinase substrate" "HPRD" +"123" "R..pS" "PKA_group" "PKA kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1956339" "kinase substrate" "HPRD" +"124" "(R|K).(pS|pT)" "PKA_group" "PKA kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1956339" "kinase substrate" "HPRD" +"125" "K..(pS|pT)" "PKA_group" "PKA kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1956339" "kinase substrate" "HPRD" +"126" "(R|K)(R|K).(pS|pT)" "PKA_group" "PKA kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1956339" "kinase substrate" "HPRD" +"127" "K...(pS|pT)" "PKA_group" "PKA kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1956339" "kinase substrate" "HPRD" +"128" "(pS|pT).(R|K)" "PKA_group" "PKA kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1956339" "kinase substrate" "HPRD" +"129" "RRRRpSIIFI" "PKA_group" "PKA kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7874496" "kinase substrate" "HPRD" +"130" "RR.pS" "PKA_group" "PKA kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8982275,1848111" "kinase substrate" "HPRD" +"131" "R(R|K).(pS|pT)(I|L|V|F|Y)(D|C|.).D" "PKA_group" "PKA kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=14679191" "kinase substrate" "HPRD" +"132" "RR.pS" "PKA_group" "PKA kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8163498" "kinase substrate" "HPRD" +"133" "RRR(R|N)pSII(F|D)" "PKA_group" "PKA kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8887677" "kinase substrate" "HPRD" +"135" "R(R|K).(pS|pT)[^P]" "PKA_alpha|MOD_PKA_1" "PKA, PKG kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7654713" "kinase substrate|ELM" "HPRD" +"136" "ARKGpSLRQ" "PKC_alpha" "PKC alpha kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8887677" "kinase substrate" "HPRD" +"137" "R(R|F)RR(R|K)GpSF(R|K)(R|K)" "PKC_alpha" "PKC alpha kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8887677" "kinase substrate" "HPRD" +"138" "(L|R|F)(R|K)R(K|Q)GpS(F|M)KK.A" "PKC_beta" "PKC beta kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=12566450,10574945" "kinase substrate" "HPRD" +"139" "R.RKGpSF" "PKC_delta" "PKC delta kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8995387" "kinase substrate" "HPRD" +"140" "KRQGpSVRR" "PKC_epsilon" "PKC epsilon kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8995387" "kinase substrate" "HPRD" +"141" "R(K|E|R).pS" "PKC_epsilon" "PKC epsilon kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8995387" "kinase substrate" "HPRD" +"142" "AR..R(R|K)RpSFRR" "PKC_eta" "PKC eta kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8995387" "kinase substrate" "HPRD" +"143" "F..F(pS|pT)(F|Y)" "PKC_group" "PKC family kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8995387" "kinase substrate" "HPRD" +"145" ".R..(pS|pT).R." "PKC_group" "PKC kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=2473066" "kinase substrate" "HPRD" +"146" "(pS|pT).(R|K)" "PKC_group" "PKC kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1956339" "kinase substrate" "HPRD" +"147" "(R|K)..(pS|pT)" "PKC_group" "PKC kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1956339" "kinase substrate" "HPRD" +"148" "(R|K)..(pS|pT).(R|K)" "PKC_group" "PKC kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1956339" "kinase substrate" "HPRD" +"149" "(K|R).(pS|pT)" "PKC_group" "PKC kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1956339" "kinase substrate" "HPRD" +"150" "(R|K).(pS|pT).(R|K)" "PKC_group" "PKC kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1956339" "kinase substrate" "HPRD" +"151" "(L|V)(V|L|A)R(Q|K|E)MpS" "PKD1" "PKC mu kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8995387" "kinase substrate" "HPRD" +"152" "(R|F|W|M)(W|A|K|S)(R|S|K|H)(R|H|S|Q)(R|K|N|P|G|Q)pS(I|F|R|V|K|S|L|M)(K|M|R|S|T)(R|S|K|W)(R|K|G)" "PKC_theta" "PKC theta kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=15782149" "kinase substrate" "HPRD" +"153" "F.R..pS(F|M)(F|M)" "PKC_zeta" "PKC zeta kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8995387" "kinase substrate" "HPRD" +"154" "(L|V|I)(R|K|Q)(R|K)(R|K|T|Q|M)(N|K|R|L|M|H)pS(F|W|I|M|L|V)(S|N)(R|S|P|Y|W)(S|R|N|L)" "PKD" "PKD kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=15782149" "kinase substrate" "HPRD" +"155" "R(R|K).(pS|pT)[^P]" "PKA_group|MOD_PKA_1" "PKG kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7654713" "kinase substrate|ELM" "HPRD" +"156" "R..(pS|pT).R..R" "EIF2AK2" "PKR kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=1671834" "kinase substrate" "HPRD" +"157" "(D|E).(pS|pT)(I|L|V|M).(D|E)" "PLK1" "Plk1 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=12738781" "kinase substrate" "HPRD" +"158" ".pS..D.." "PDHK1" "Pyruvate dehydrogenase kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=3002277" "kinase substrate" "HPRD" +"159" "PLpTLP" "RAF1" "RAF1 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8376361" "kinase substrate" "HPRD" +"160" "PLLpTP" "RAF1" "RAF1 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8376361" "kinase substrate" "HPRD" +"161" "PLpTP" "RAF1" "RAF1 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8376361" "kinase substrate" "HPRD" +"162" "PpTLP" "RAF1" "RAF1 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8376361" "kinase substrate" "HPRD" +"163" "PLpTLP" "RAF1" "RAF1 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8376361" "kinase substrate" "HPRD" +"164" "PpTLP" "RAF1" "RAF1 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8376361" "kinase substrate" "HPRD" +"165" "LpTP" "RAF1" "RAF1 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8376361" "kinase substrate" "HPRD" +"166" "KKKKKK(pS|pT)..." "TGF-beta (HPRD)" "TGF beta receptor kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8524844" "kinase substrate" "HPRD" +"167" "(R|K|Q|N)(M|C|W)(R|T|S|N)(E|D|S|N)(R|K|E|D|N)pS(S|D|E)(S|GC|D)(SM|R|N)(N|H|S|R|C)" "TGF-beta (HPRD)" "TGF beta receptor kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=15782149" "kinase substrate" "HPRD" +"168" "RR..pS" "DAPK3" "ZIP kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=15001356" "kinase substrate" "HPRD" +"169" "KR.RpS" "DAPK3" "ZIP kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=15001356" "kinase substrate" "HPRD" +"170" "KRR.pT" "DAPK3" "ZIP kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=15001356" "kinase substrate" "HPRD" +"171" "pTEY" "DUSP1 P28562" "Dual specificity protein phosphatase 1 substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=16183637" "phosphatase substrate" "HPRD" +"172" "pT.pY" "DUSP6 Q16828" "Dual specificity protein phosphatase 6 substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=11432864" "phosphatase substrate" "HPRD" +"173" "RRA(pS|pT)VA" "PKA_group|MOD_PKA_1" "PP2A, PP2C substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7508382,1653021,3027075" "kinase substrate|ELM" "HPRD" +"174" ".R..pSVA" "Calcineurin (HPRD)" "PP2B substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7508382" "kinase substrate" "HPRD" +"175" ".pT.pY." "Wip1 O15297" "PP2C delta substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=15807522" "kinase substrate" "HPRD" +"1" "KCSpTWP" "14-3-3 (HPRD)" "14-3-3 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=12819209" "domain binding" "HPRD" +"2" "R..pS" "14-3-3 (HPRD)" "14-3-3 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9524113,9341175" "domain binding" "HPRD" +"3" "R.R..pS.P" "14-3-3 (HPRD)" "14-3-3 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9524113" "domain binding" "HPRD" +"4" "YpTV" "14-3-3 (HPRD)" "14-3-3 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=12196105" "domain binding" "HPRD" +"5" "RS.(pS|pT).P" "14-3-3 (HPRD)" "14-3-3 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=15139812" "domain binding" "HPRD" +"6" "R.(Y|F).pS.P" "LIG_14-3-3_CanoR_1" "14-3-3 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9428519" "domain binding|ELM" "HPRD" +"7" "RPVSSAApSVY" "14-3-3 (HPRD)" "14-3-3 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9524113" "domain binding" "HPRD" +"8" "pS(D|E)(D|E)E" "BARD1 Q99728" "BARD1 BRCT domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=14578343" "domain binding" "HPRD" +"9" "DpSG..pS" "BTRC WD40" "Beta-TrCP1 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=15070733,12820959" "domain binding" "HPRD" +"10" "pS(F|Y|H)(V|F|Y)(F|Y)" "LIG_BRCT_BRCA1_1" "BRCA1 BRCT domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=14578343" "domain binding|ELM" "HPRD" +"11" "(I|L)(I|L|P)pTP(R|K)" "hCDC4 Q969H0" "CDC4 WD40 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=11734846" "domain binding" "HPRD" +"12" "HFDpTYLI" "LIG_FHA_1" "Chk2 FHA domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=11106755,12049740" "domain binding|ELM" "HPRD" +"13" "(R|D|H)(L|Y)(L|M)(K|A)pT(Q|L|M|E|V)(K|L|I|R)" "FHA (HPRD)" "FHA domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=11106755" "domain binding" "HPRD" +"14" "S(pS|pT)." "MDC1 FHA" "MDC1 BRCT domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=14578343" "domain binding" "HPRD" +"15" "S(pS|pT)." "PLK1 PBD" "Plk1 PBD domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=15139812,12595692,14532005" "domain binding" "HPRD" +"16" "pSYII" "RAD9 BRCT (HPRD)" "RAD9 BRCT domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=14578343" "domain binding" "HPRD" +"17" "(pS|pT)P" "DOC_WW_Pin1_4" "WW domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=11607836,11248545,15139812,10037602" "domain binding|ELM" "HPRD" +"1" "pYM.M" "Abl" "Abl kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8227078" "kinase substrate" "HPRD" +"2" "EDAIpY" "Abl" "Abl kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8125961" "kinase substrate" "HPRD" +"3" ".VIpYAAPF" "Abl" "Abl kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8578591" "kinase substrate" "HPRD" +"4" "EAIpYAAPF" "Abl" "Abl kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=11860343,7845468" "kinase substrate" "HPRD" +"5" "EEIpYEEpY" "Abl" "Abl kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=11860343" "kinase substrate" "HPRD" +"6" "E.IpY..P." "Abl" "Abl kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=11860343" "kinase substrate" "HPRD" +"7" "EEIpYYYVH" "Abl" "Abl kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=11860343" "kinase substrate" "HPRD" +"8" "ERIpYARTK" "Abl" "Abl kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=11860343" "kinase substrate" "HPRD" +"9" "AEV(I|V|L|F)pYAA(P|F)F" "Abl" "Abl kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7845468" "kinase substrate" "HPRD" +"10" "pY...YY" "ALK|PLCG1 SH2" "ALK kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=15938644" "kinase substrate" "HPRD" +"11" "pY(D|E).(I|L|V|M)" "ALK" "ALK kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=16273072" "kinase substrate" "HPRD" +"12" "(D|E)..pY" "ALK" "ALK kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=16273072" "kinase substrate" "HPRD" +"13" "pY....(F|Y)" "ALK" "ALK kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=16273072" "kinase substrate" "HPRD" +"14" "EE(D|E)IpYFFFF" "Csk" "CSK kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=9425036" "kinase substrate" "HPRD" +"15" "...IpY(M|I|F)FFF" "Csk" "CSK kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8982275" "kinase substrate" "HPRD" +"16" "EEEEpYFELV" "EGFR" "EGFR kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8578591" "kinase substrate" "HPRD" +"17" "(E|D|R|A)(D|E)(D|E)(E|D|I)pY(F|V|I|E)(E|F|D)(L|I|F|V)V" "EGFR" "EGFR kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7845468,8578591" "kinase substrate" "HPRD" +"18" ".(D|E)pY." "EGFR" "EGFR kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8578591" "kinase substrate" "HPRD" +"19" "pYIPP" "EGFR" "EGFR kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=12522132" "kinase substrate" "HPRD" +"20" ".(D|E)pY(I|L|V)" "EGFR" "EGFR kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8578591" "kinase substrate" "HPRD" +"21" "EEEIpYEEIE" "Fes" "Fes kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8578591" "kinase substrate" "HPRD" +"22" "(E|A|D)(E|A)(E|A)(I|E|V)pY(D|E)(D|E)(I|V|E)(E|I|V)" "Fes" "Fes kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7845468" "kinase substrate" "HPRD" +"23" "EEEpYFFLF" "FGFR (HPRD)" "FGFR kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8578591" "kinase substrate" "HPRD" +"24" "A(E|A)EEpY(F|V)F(L|F|M|I|V)F" "FGFR (HPRD)" "FGFR kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7845468,8578591" "kinase substrate" "HPRD" +"25" "ME(E|N)(I|V)pY(G|E)IFF" "Fgr" "Fgr kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8982275" "kinase substrate" "HPRD" +"26" "KSPGEpYVNIEFG" "IGF1R|INSR" "IGF1 receptor kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8530377" "kinase substrate" "HPRD" +"27" "pYM.M" "INSR" "Insulin receptor kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8227078,1312712" "kinase substrate" "HPRD" +"28" "EE(E|N|D)pY(M|F)(M|F)(M|F|I|E)(M|F)" "INSR" "Insulin receptor kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7845468,8578591" "kinase substrate" "HPRD" +"29" ".EEEpYMMMM" "INSR" "Insulin receptor kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8578591" "kinase substrate" "HPRD" +"30" "KKSRGDpYMTMQIG" "INSR" "Insulin receptor kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8530377,1312712" "kinase substrate" "HPRD" +"31" "KKKLPATGDpYMNMSPVGD" "INSR" "Insulin receptor kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8530377,1312712" "kinase substrate" "HPRD" +"32" "pY..(L|I|V)" "JAK2" "JAK2 kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=15143187" "kinase substrate" "HPRD" +"33" "pTPpY" "MAP2K7|MAP2K6" "JNK kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=11390361" "kinase substrate" "HPRD" +"34" ".E.IpYGVLF" "Lck" "Lck kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8578591" "kinase substrate" "HPRD" +"35" "E.(I|V|L|F)pY(G|A)V(L|V|F|I)(F|L|V|I)" "Lck" "Lck kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7845468" "kinase substrate" "HPRD" +"36" "DEEIpY(E|G)EL." "Lyn" "Lyn kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8982275" "kinase substrate" "HPRD" +"37" "(D|E).......(D|E)..pY..L.......Y..(L|I)" "Lyn" "Lyn kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7526393,10452987" "kinase substrate" "HPRD" +"38" "EEEEpYVFI." "PDGFR_group" "PDGFR kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8578591" "kinase substrate" "HPRD" +"39" "(L|N)(R|I)TpY" "PDGFR_group" "PDGFR kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8843147" "kinase substrate" "HPRD" +"40" "(D|E)(D|E)(D|E)(D|E)pY(V|E|I)F(I|V|F)" "PDGFR_group" "PDGFR kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7845468,8578591" "kinase substrate" "HPRD" +"41" "(D|E).......(D|E)..pY..L.......Y..(L|I)" "SRC_group" "Src family kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7526393,10452987" "kinase substrate" "HPRD" +"42" "(I|V|L|S).pY..(L|I)" "SRC_group" "Src family kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=9469421" "kinase substrate" "HPRD" +"43" "pYM.M" "SRC" "Src kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8227078" "kinase substrate" "HPRD" +"44" "YIpYGSFK" "SRC" "Src kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7558590" "kinase substrate" "HPRD" +"45" "EEEIpY(G|E)EFD" "SRC" "Src kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8578591" "kinase substrate" "HPRD" +"46" "D(D|E)(E|D|G)(I|V|L)pY(G|E)E(F|I)F" "SRC" "Src kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7845468" "kinase substrate" "HPRD" +"47" "(D|E).......(D|E)..pY..L.......Y..(L|I)" "SRC" "Src kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7612891,15173175" "kinase substrate" "HPRD" +"48" "(D|E)(D|E)(E|D|G)(I|V|L)pY(G|E|D)E(F|I|L|V)(D|E)" "SRC" "Src kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=7845468" "kinase substrate" "HPRD" +"49" "pY(A|G|S|T|D|E)" "SRC" "Src kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=16273072" "kinase substrate" "HPRD" +"50" "(E|D|pT|pY).pYEE" "SYK" "Syk kinase" "https://pubmed.ncbi.nlm.nih.gov/?term=8982275" "kinase substrate" "HPRD" +"51" "(D|E)pYpY(R|K)" "PTP1B (HPRD)" "PTP1B phosphatase substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=11694501,11163213" "phosphatase substrate" "HPRD" +"52" "EFpY(G|A)TY(G|A)" "PTP1B (HPRD)" "PTP1B phosphatase substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=14578355" "phosphatase substrate" "HPRD" +"53" "E(Y|F|D)pYM" "PTP1B (HPRD)" "PTP1B phosphatase substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=12237455" "phosphatase substrate" "HPRD" +"54" "(E|P)(M|L|I|V|F)pY(G|A).(M|L|I|V|F|Y)A" "PTP1B (HPRD)" "PTP1B phosphatase substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=14578355" "phosphatase substrate" "HPRD" +"55" "RD.Y.TDYpYR" "PTP1B (HPRD)" "PTP1B phosphatase substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=12237455" "phosphatase substrate" "HPRD" +"56" "E(F|D|Y)pY" "PTP1B (HPRD)" "PTP1B phosphatase substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9527843,9843364,12237455" "phosphatase substrate" "HPRD" +"57" "DpYpYR" "PTPN6 SH2|PTPN11 SH2" "PTP1B, TC-PTP phosphatase substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=11163213" "phosphatase substrate" "HPRD" +"58" "(D|E)FpY(G|A)(F|Y)(A|G)" "PTPRH SH2 (HPRD)" "PTPRH phosphatase substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=14578355" "phosphatase substrate" "HPRD" +"59" "F(M|L|V|I)pY" "PTPRJ SH2 (HPRD)" "PTPRJ phosphatase substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=14578355" "phosphatase substrate" "HPRD" +"60" "(D|E).(L|I|V).pY..(L|I|V)" "PTPN6 SH2" "SHP1 phosphatase substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=10660565" "phosphatase substrate" "HPRD" +"61" "(D|E).(L|I|V)..pY..(L|I|V)" "PTPN6 SH2" "SHP1 phosphatase substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=10660565" "phosphatase substrate" "HPRD" +"62" "(D|E)(D|E)(D|E|L).pY..(F|M|L|V|I)(D|E)" "PTPN6 SH2" "SHP1 phosphatase substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=14699166" "phosphatase substrate" "HPRD" +"63" "(D|E).pY" "PTPN6 SH2" "SHP1 phosphatase substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=11994017" "phosphatase substrate" "HPRD" +"64" "(E|P)(F|I|L)pYA.(F|I|L|V)" "PTPN6 SH2" "SHP1 phosphatase substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=14578355" "phosphatase substrate" "HPRD" +"65" "pYIDL" "PTPN11 SH2" "SHP2 phosphatase substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7504175,9756938" "phosphatase substrate" "HPRD" +"66" "pYASI" "PTPN11 SH2" "SHP2 phosphatase substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=16020478,9756938" "phosphatase substrate" "HPRD" +"67" "EFpYA.(V|I)G(R|K|H)S" "PTPN11 SH2" "SHP2 phosphatase substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=14578355" "phosphatase substrate" "HPRD" +"68" "(D|E)(D|E)...pYVA" "TC-PTP SH2 (HPRD)" "TC-PTP phosphatase substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7678807" "phosphatase substrate" "HPRD" +"69" "(E|D|Y)pY" "TC-PTP SH2 (HPRD)" "TC-PTP phosphatase substrate motif" "https://pubmed.ncbi.nlm.nih.gov/?term=11352902,12237455" "phosphatase substrate" "HPRD" +"1" "pY(E|M|V)(N|V|I)" "SH3BP2 SH2" "3BP2 SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7511210" "domain binding" "HPRD" +"2" "pYENP" "ABL1 SH2" "Abl SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7511210,7680959" "domain binding" "HPRD" +"3" "pY..P" "CRK SH2" "Crk SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=11994738,11607838,7511210" "domain binding" "HPRD" +"4" "pYDHP" "CRK SH2" "Crk SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=11994738,7680959" "domain binding" "HPRD" +"5" "pY(T|A|S)(K|R|Q|N)(M|I|V|R)" "Csk SH2" "Csk SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=11994738" "domain binding" "HPRD" +"6" "pY(Y|I|V)N(F|L|I|V)" "GRB2 SH2" "Grb2 SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7511210" "domain binding" "HPRD" +"7" "pYE.(V|I)" "FES SH2" "Fes SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=11994738,7511210" "domain binding" "HPRD" +"8" "pYEE(I|V)" "FGR SH2" "Fgr SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7680959" "domain binding" "HPRD" +"9" "pYEDP" "Fyn SH2" "Fyn SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=8622893" "domain binding" "HPRD" +"10" "pY(M|I|L|V).(M|I|L|V)" "FES SH2|SH3BP2 SH2|Csk SH2|GRB2 SH2|SYK SH2" "GRB2, 3BP2, Csk, Fes, Syk C-terminal SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7511210,7680959" "domain binding" "HPRD" +"11" "pY(Q|Y|V)N(Y|Q|F)" "GRB2 SH2" "Grb2 SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7511210" "domain binding" "HPRD" +"12" "pY.N" "GRB2 SH2" "Grb2 SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7511210,11994738" "domain binding" "HPRD" +"13" "(F|Y)pY(E|T|Y|S)N(I|L|V|P|T|Y|S)" "GRB7 SH2|GRB10 SH2" "GRB7, GRB10 SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=14679191" "domain binding" "HPRD" +"14" "pYF.(F|P|L|Y)" "PTPN6 SH2" "HCP SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7511210" "domain binding" "HPRD" +"15" "pY(A|E|V)(Y|F|E|S|N|V)(P|F|I|H)" "ITK SH2" "Itk SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=10636929" "domain binding" "HPRD" +"16" "pYDYV" "Lck SH2|Src SH2" "Lck and Src SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=16245368" "domain binding" "HPRD" +"17" "pYDEP" "NCK SH2" "Nck SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7511210,7680959" "domain binding" "HPRD" +"18" "pYM.M" "PIK3R1 SH2" "PI3 Kinase p85 SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7511210,11994738" "domain binding" "HPRD" +"19" "pY..M" "PIK3R1 SH2" "PI3 Kinase p85 SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=1380456" "domain binding" "HPRD" +"20" "pYMPMS" "PIK3R1 SH2" "PI3 Kinase p85 SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=16020478" "domain binding" "HPRD" +"21" "pY(L|I|V)E(L|I|V)" "PLCG1 SH2|PTPN11 SH2" "PLCgamma C and N-terminal SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7511210,7680959" "domain binding" "HPRD" +"22" "pY..P" "RASA_group SH2" "RasGAP C-terminal SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9233798" "domain binding" "HPRD" +"23" "pYILV.(M|L|I|V|P)" "RASA_group SH2" "RasGAP N-terminal SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9233798" "domain binding" "HPRD" +"24" "TIpY..(V|I)" "SH2D1A SH2|SH2D1B SH2" "SAP and EAT2 SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=10549287" "domain binding" "HPRD" +"25" "pY(L|V)N(V|P)" "GRB2 SH2|STAT3 SH2" "Sem5 SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7680959" "domain binding" "HPRD" +"26" "pY(T|V|I).L" "SHB SH2" "Shb SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7537362" "domain binding" "HPRD" +"27" "pY(I|E|Y|L).(I|L|M)" "SHC_group SH2|SHC1 SH2|SHC2 SH2" "SHC SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7511210" "domain binding" "HPRD" +"28" "(I|V|L|S).pY..(L|I)" "PTPN11 SH2|PTPN6 SH2" "SHIP2 SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=10789675" "domain binding" "HPRD" +"29" "(V|I|L).pYA.(L|V)" "PTPN6 SH2" "SHP1 C-terminal SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=11052678" "domain binding" "HPRD" +"30" "..pYYM(K|R)" "PTPN6 SH2" "SHP1 C-terminal SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=11052678" "domain binding" "HPRD" +"31" "L(Y|H)pY(M|F).(F|M)" "PTPN6 SH2" "SHP1 N-terminal SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=11052678" "domain binding" "HPRD" +"32" "L.pYA.L" "PTPN6 SH2" "SHP1 N-terminal SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=11052678" "domain binding" "HPRD" +"33" "(I|V).pY..(L|V)" "PTPN6 SH2" "SHP1 SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9148918" "domain binding" "HPRD" +"34" "(V|I|L).pY(M|L|F).P" "PTPN6 SH2|PTPN11 SH2" "SHP1, SHP2 SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=16274240" "domain binding" "HPRD" +"35" "(T|V|I|Y).pY(A|S|T|V).(I|V|L)" "PTPN11 SH2" "SHP2 CSH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=16274240" "domain binding" "HPRD" +"36" "(I|L|V)(I|L|V)(I|L|V|F|T|Y)pY(T|I|L|V)(I|L)(I|L|V|P)" "PTPN11 SH2" "SHP2 C-terminal SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=14679191" "domain binding" "HPRD" +"37" "(H|F).V.(T|S|A)pY" "PTPN11 SH2" "SHP2 N-terminal SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=16142918" "domain binding" "HPRD" +"38" "(I|V|L).pY(F|M).P" "PTPN11 SH2" "SHP2 N-terminal SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=16274240" "domain binding" "HPRD" +"39" "pY(I|V).(I|V)" "PTPN11 SH2" "SHP2 N-terminal SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7680959" "domain binding" "HPRD" +"40" "(I|L|V|M).pY(T|V|A).(I|V|L|F)" "PTPN11 SH2" "SHP2 N-terminal SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=16274240" "domain binding" "HPRD" +"41" "(I|V).pY(L|M|T)Y(A|P|T)SG" "PTPN11 SH2" "SHP2 N-terminal SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=16274240" "domain binding" "HPRD" +"42" "W(M|T|V)pY(Y|R)(I|L)." "PTPN11 SH2" "SHP2 N-terminal SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=11052678" "domain binding" "HPRD" +"43" "pYIPP" "PLCG1 SH2|PTPN11 SH2" "SHP2, PLCgamma SH2 domain binding motifs" "https://pubmed.ncbi.nlm.nih.gov/?term=9516477" "domain binding" "HPRD" +"44" "pYM.M" "PIK3R1 SH2|Src SH2" "Src and Abl SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=8227078" "domain binding" "HPRD" +"45" "pY(R|K|H|Q|E|D)(R|K|H|Q|E|D)(I|P)" "Src SH2|Fyn SH2|Lck SH2|FGR SH2|ABL1 SH2|CRK SH2|NCK SH2" "Src, Fyn, Lck, Fgr, Abl, Crk, Nck SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7680959" "domain binding" "HPRD" +"46" "PP.pY" "Src SH2|Fyn SH2|Lck SH2|Csk SH2|NCK SH2|SHC1 SH2" "Src, Fyn,Csk, Nck and SHC SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=11724572" "domain binding" "HPRD" +"47" "pYEEI" "Src SH2|Fyn SH2|Lck SH2" "Src,Lck and Fyn SH2 domains binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=8578591,7680959" "domain binding" "HPRD" +"48" "pY(D|E)(P|R)(R|P|Q)" "STAT1 SH2" "STAT1 SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=12591923" "domain binding" "HPRD" +"49" "pY..Q" "STAT3 SH2" "STAT3 SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=14966128" "domain binding" "HPRD" +"50" "pY(M|L|V|I|F)(P|R|K|H)Q" "STAT3 SH2" "STAT3 SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=12591923" "domain binding" "HPRD" +"51" "pY(Q|T|E)(E|Q)(L|I)" "SYK SH2" "Syk C-terminal SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7511210" "domain binding" "HPRD" +"52" "pYTT(I|L|M)" "SYK SH2" "Syk N-terminal SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=8578591" "domain binding" "HPRD" +"53" "(D|E).......(D|E)..pY..L.......Y..(L|I)" "SYK SH2|SHC_group SH2|Lyn SH2|ZAP70" "Syk, ZAP-70, Shc, Lyn SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=10452987" "domain binding" "HPRD" +"54" "pYEN(F|I|V)" "FES SH2|SH3BP2 SH2" "Tensin SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=8578591" "domain binding" "HPRD" +"55" "pY(M|L|E)EP" "VAV1 SH2|VAV2 SH2|VAV_group SH2" "Vav SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7511210" "domain binding" "HPRD" +"56" "pYESP" "VAV1 SH2|VAV2 SH2|VAV_group SH2" "Vav SH2 domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9151714" "domain binding" "HPRD" +"57" "D(N|D).pY" "CBL PTB" "Cbl PTB domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9407100,10078535" "domain binding" "HPRD" +"58" "N.LpY" "DOK_group PTB" "Dok1 PTB domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=14607833,12665569" "domain binding" "HPRD" +"59" "N..pY" "FRS2 PTB" "FRIP PTB domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9697832" "domain binding" "HPRD" +"60" "NP.pY" "SHC1 PTB" "Shc PTB domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=7542744,7541030" "domain binding" "HPRD" +"61" "DD.pY" "SHB SH2" "Shb PTB domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=9484780" "domain binding" "HPRD" +"62" "NP.pYF.R" "ShcA PTB" "ShcA PTB domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=8662772" "domain binding" "HPRD" +"63" "HN(M|L|V|I)(M|L|V|I|N)NP(S|T)pY" "ShcC PTB" "ShcC PTB domain binding motif" "https://pubmed.ncbi.nlm.nih.gov/?term=8662772" "domain binding" "HPRD" +"1" "R.(pS|pT)" "PKA_group" "PKA" "https://pubmed.ncbi.nlm.nih.gov/1956339" "kinase substrate" "Phosida" +"2" "R(R|K).(pS|pT)" "PKA_group" "PKA" "https://pubmed.ncbi.nlm.nih.gov/1956339" "kinase substrate" "Phosida" +"3" "KR..(pS|pT)" "PKA_group" "PKA" "https://pubmed.ncbi.nlm.nih.gov/1956339" "kinase substrate" "Phosida" +"4" "S..(pS|pT)" "CK1_group" "CK1" "https://pubmed.ncbi.nlm.nih.gov/1956339" "kinase substrate" "Phosida" +"5" "(S|T)...pS" "CK1_group" "CK1" "https://pubmed.ncbi.nlm.nih.gov/1956339" "kinase substrate" "Phosida" +"6" "(pS|pT)..E" "CK2_group" "CK2" "https://pubmed.ncbi.nlm.nih.gov/1956339" "kinase substrate" "Phosida" +"7" "pS...S" "GSK3" "GSK3" "https://pubmed.ncbi.nlm.nih.gov/2156841" "kinase substrate" "Phosida" +"8" "(pS|pT)P.(K|R)" "CDK2" "CDK2" "https://pubmed.ncbi.nlm.nih.gov/1956339" "kinase substrate" "Phosida" +"9" "R..(pS|pT)" "CaM-KII_group" "CAMK2" "https://pubmed.ncbi.nlm.nih.gov/1956339" "kinase substrate" "Phosida" +"10" "R..(pS|pT)V" "CaM-KII_group" "CAMK2" "https://pubmed.ncbi.nlm.nih.gov/1956339" "kinase substrate" "Phosida" +"11" "P.(pS|pT)P" "MAP2K_group" "ERK/MAPK" "https://pubmed.ncbi.nlm.nih.gov/8325833" "kinase substrate" "Phosida" +"12" "V.(pS|pT)P" "MAP2K_group" "ERK/MAPK" "https://pubmed.ncbi.nlm.nih.gov/8325833" "kinase substrate" "Phosida" +"13" "PE(pS|pT)P" "MAP2K_group" "ERK/MAPK" "https://pubmed.ncbi.nlm.nih.gov/8325833" "kinase substrate" "Phosida" +"14" "R(R|S|T).(pS|pT).(S|T)" "PKB_group" "PKB/AKT" "https://pubmed.ncbi.nlm.nih.gov/15789031" "kinase substrate" "Phosida" +"15" "R.R..(pS|pT)" "PKB_group" "PKB/AKT" "https://pubmed.ncbi.nlm.nih.gov/15789031" "kinase substrate" "Phosida" +"16" "R..(pS|pT).R" "PKC_group" "PKC" "https://pubmed.ncbi.nlm.nih.gov/15782149" "kinase substrate" "Phosida" +"17" "(L|V|I).(R|K)..(pS|pT)" "PKD" "PKD" "https://pubmed.ncbi.nlm.nih.gov/15782149" "kinase substrate" "Phosida" +"18" "(I|E|V)pY(E|G)(E|D|P|N)(I|V|L)" "Lck" "LCK" "https://pubmed.ncbi.nlm.nih.gov/7845468" "kinase substrate" "Phosida" +"19" "(I|V|L)pY..(P|F)" "ABL1" "ABL" "https://pubmed.ncbi.nlm.nih.gov/7845468" "kinase substrate" "Phosida" +"20" "(E|D)..pY..(D|E|A|G|S|T)" "SRC_group" "SRC" "https://pubmed.ncbi.nlm.nih.gov/16273072" "kinase substrate" "Phosida" +"21" "pY..(I|L|V|M)" "ALK" "ALK" "https://pubmed.ncbi.nlm.nih.gov/16273072" "kinase substrate" "Phosida" +"22" "(D|P|S|A|E|N).pY(V|L|D|E|I|N|P)" "EGFR" "EGFR" "https://pubmed.ncbi.nlm.nih.gov/16381900" "kinase substrate" "Phosida" +"23" "(pS|pT)P.(K|R)" "CDK1" "CDK1" "https://pubmed.ncbi.nlm.nih.gov/12501191" "kinase substrate" "Phosida" +"24" "(pS|pT)P(K|R)" "CDK1" "CDK1" "https://pubmed.ncbi.nlm.nih.gov/12501191" "kinase substrate" "Phosida" +"25" "(R|K).(pS|pT)(I|L|V)" "Aurora A" "AURORA" "https://pubmed.ncbi.nlm.nih.gov/12408861" "kinase substrate" "Phosida" +"26" "(R|K|N)R.(pS|pT)(M|L|V|I)" "Aurora A" "AURORA-A" "https://pubmed.ncbi.nlm.nih.gov/16083426" "kinase substrate" "Phosida" +"27" "(D|E).(pS|pT)(V|I|L|M).(D|E)" "PLK" "PLK" "https://pubmed.ncbi.nlm.nih.gov/12738781" "kinase substrate" "Phosida" +"28" "(E|D).(pS|pT)(F|L|I|Y|W|V|M)" "PLK" "PLK1" "https://pubmed.ncbi.nlm.nih.gov/12738781" "kinase substrate" "Phosida" +"29" "L..(pS|pT)" "NEK6" "NEK6" "https://pubmed.ncbi.nlm.nih.gov/12023960" "kinase substrate" "Phosida" +"30" "L.R..(pS|pT)" "CHK1" "CHK1/2" "https://pubmed.ncbi.nlm.nih.gov/17464182" "kinase substrate" "Phosida" +"31" "(M|I|L|V).(R|K)..(pS|pT)" "CHK1" "CHK1" "https://pubmed.ncbi.nlm.nih.gov/10648819" "kinase substrate" "Phosida" +"32" "F..F(pS|pT)(F|Y)" "PDK1" "PDK1" "https://pubmed.ncbi.nlm.nih.gov/11516946" "kinase substrate" "Phosida" +"33" "(F|L|M)(R|K)(R|K)(pS|pT)" "NIMA" "NIMA" "https://pubmed.ncbi.nlm.nih.gov/8887677" "kinase substrate" "Phosida"
--- a/workflow/ppenrich_suite_wf.ga Wed Apr 13 19:48:01 2022 +0000 +++ b/workflow/ppenrich_suite_wf.ga Thu Jun 30 16:15:57 2022 +0000 @@ -390,7 +390,7 @@ }, "11": { "annotation": "Transform the output of MaxQuant for phosphoproteome-enriched samples to prepare it for statistical anlaysis.", - "content_id": "testtoolshed.g2.bx.psu.edu/repos/eschen42/mqppep_preproc/mqppep_preproc/0.1.9+galaxy0", + "content_id": "mqppep_preproc", "errors": null, "id": 11, "input_connections": { @@ -792,7 +792,7 @@ }, "13": { "annotation": "Perform ANOVA. For imputing missing values, create random values.", - "content_id": "testtoolshed.g2.bx.psu.edu/repos/eschen42/mqppep_anova/mqppep_anova/0.1.9+galaxy0", + "content_id": "mqppep_anova", "errors": null, "id": 13, "input_connections": {