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author proteore
date Fri, 09 Nov 2018 05:11:46 -0500
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16 This tool map a list of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package. 16 This tool map a list of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package.
17 17
18 Select your identifier type : UniprotAC or Entrez gene ID 18 You can map Entrez gene IDs / Uniprot accession number from three species : human, mouse and rat.
19 19
20 Select an input file containing ids in a column, set header and column number or copy/paste your ids. 20 If your input have another type of IDs, please use the ID_Converter tool.
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22 You can import 1 to 3 column(s) of expression values if you are importing ids from a file. 22 **Input:**
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24 Select a species of interest.
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26 Select one or several pathways of interest from the dropdown menu or copy/paste KEGG pathway id(s) or import it from a file. 25 - KEGG Pathways IDs to be used for mapping can be set by:
26 - chosing from the KEGG pathways name list
27 - giving a list (copy/paste)
28 - importing a list from a dataset (column) - output of KEGG pathways identification and coverage can be used (1st column)
29 - Genes/proteins ids to map can be either a list of Entrez genes IDs / Uniprot accession number or a file (tabular, tsv, txt) containing at least one column of Entrez genes IDs / Uniprot accession number.
30 - fold change values (up to three columns) from a dataset (same dataset as for Genes/proteins ids to map)
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28 Select the graph format : KEGG (jpg) or graphviz (pdf) 32 You can see below an example of an input file with identifiers (uniprot_AC) and fold_change values.
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30 Uniprot accession number converted to Entrez geneID or Entrez geneID are mapped to each selected pathways. 34 .. csv-table:: Simulated data
35 :header: "Uniprot_AC","Protein.name","Number_of_peptides","fc_values 1","fc_values 2","fc_values 3"
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32 Output : One file (png or pdf) for each selected pathway. 37 "P15924","Desmoplakin","69","0.172302292051025","-0.757435966487116","0.0411240398990759"
38 "P02538","Keratin, type II cytoskeletal 6A","53","-0.988842456122076","0.654626325100182","-0.219153396366064"
39 "P02768","Serum albumin","44","-0.983493243315454","0.113752002761474","-0.645886132600729"
40 "P08779","Keratin, type I cytoskeletal 16","29","0.552302597284443","-0.329045605110646","2.10616106806788"
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42 |
43
44 **Output:**
45
46 - a **collection dataset** named 'KEGG pathways map from <dataset>', one file (png or pdf) for each given pathway.
47 - a **summary text file** (.tsv) of the mapping(s) with the following columns
48 - **KEGG pathway ID**: KEGG pathway(s) used to map given genes/proteins ids
49 - **pathway name**: name(s) of KEGG pathway(s) used for mapping
50 - **nb of Uniprot_AC used** (only when Uniprot accession number is given): number of Uniprot accession number which will be converted to Entrez genes IDs
51 - **nb of Entrez gene ID used**: number of Entrez gene IDs used for mapping
52 - **nb of Entrez gene ID mapped**: number of Entrez gene IDs mapped on a given pathway
53 - **nb of Entrez gene ID in the pathway**: number total of Entrez gene IDs in a given pathway
54 - **ratio of Entrez gene ID mapped**: number of Entrez gene IDs mapped / number total of Entrez gene IDs
55 - **Entrez gene ID mapped**: list of mapped Entrez gene IDs
56 - **uniprot_AC mapped** (only when Uniprot accession number is given): list of Uniprot accession number corresponding to the mapped Entrez gene IDs
57
58 -----
59
60 .. class:: infomark
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62 **Database:**
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64 KEGG Pathways names list are from http://rest.kegg.jp/list/pathway/
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66 User manual / Documentation: http://www.bioconductor.org/packages/release/bioc/html/pathview.html