Mercurial > repos > proteore > proteore_maps_visualization

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author proteore
date Mon, 10 May 2021 12:45:44 +0000
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1 Wrapper for Pathview tool
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2 =============================
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3
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4 **Authors**
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5
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6 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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7
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8 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
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9
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10 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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11
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12 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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13
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14 =============================
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15
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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.
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17
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18 You can map Entrez gene IDs / Uniprot accession number from three species : human, mouse and rat.
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19
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20 If your input have another type of IDs, please use the ID_Converter tool.
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21
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22 **Input:**
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23
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24
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25 - KEGG Pathways IDs to be used for mapping can be set by:
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26 - chosing from the KEGG pathways name list
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27 - giving a list (copy/paste)
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28 - importing a list from a dataset (column) - output of KEGG pathways identification and coverage can be used (1st column)
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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.
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30 - fold change values (up to three columns) from a dataset (same dataset as for Genes/proteins ids to map)
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31
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32 You can see below an example of an input file with identifiers (uniprot_AC) and fold_change values.
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33
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34 .. csv-table:: Simulated data
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35 :header: "Uniprot_AC","Protein.name","Number_of_peptides","fc_values 1","fc_values 2","fc_values 3"
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36
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37 "P15924","Desmoplakin","69","0.172302292051025","-0.757435966487116","0.0411240398990759"
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38 "P02538","Keratin, type II cytoskeletal 6A","53","-0.988842456122076","0.654626325100182","-0.219153396366064"
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39 "P02768","Serum albumin","44","-0.983493243315454","0.113752002761474","-0.645886132600729"
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40 "P08779","Keratin, type I cytoskeletal 16","29","0.552302597284443","-0.329045605110646","2.10616106806788"
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41
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42 |
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45
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46 .. class:: warningmark
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47
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48 If there's more than one id per line in the defined column, it will be split to have only one id per line. For example this table:
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49
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50 .. csv-table:: Simulated data
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51 :header: "Ensembl_Gene","UniProt.AC","UniProt.ID"
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52
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53 "ENSG00000136881","Q14032","BAAT_HUMAN"
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54 "ENSG00000170099","P08185;G3V350;G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
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55 "ENSG00000244731","P0C0L4","CO4A_HUMAN"
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56
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57 |
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58
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59 will become:
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60
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61 .. csv-table:: Simulated data
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62 :header: "Ensembl_Gene","UniProt.AC","UniProt.ID"
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63
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64 "ENSG00000136881","Q14032","BAAT_HUMAN"
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65 "ENSG00000170099","P08185","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
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66 "ENSG00000170099","G3V350","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
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67 "ENSG00000170099","G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
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68 "ENSG00000244731","P0C0L4","CO4A_HUMAN"
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69
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70 |
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71
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72 **Output:**
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73
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74 - a **collection dataset** named 'KEGG maps visualization from <dataset>', one file (png or pdf) for each given pathway.
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75 - a **summary text file** (.tsv) of the mapping(s) with the following columns
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76 - **KEGG pathway ID**: KEGG pathway(s) used to map given genes/proteins ids
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77 - **pathway name**: name(s) of KEGG pathway(s) used for mapping
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78 - **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
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79 - **nb of Entrez gene ID used**: number of Entrez gene IDs used for mapping
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80 - **nb of Entrez gene ID mapped**: number of Entrez gene IDs mapped on a given pathway
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81 - **nb of Entrez gene ID in the pathway**: number total of Entrez gene IDs in a given pathway
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82 - **ratio of Entrez gene ID mapped**: number of Entrez gene IDs mapped / number total of Entrez gene IDs
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83 - **Entrez gene ID mapped**: list of mapped Entrez gene IDs
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84 - **uniprot_AC mapped** (only when Uniprot accession number is given): list of Uniprot accession number corresponding to the mapped Entrez gene IDs
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85
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86 -----
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87
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88 .. class:: infomark
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89
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90 **Database:**
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91
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92 KEGG Pathways names list are from http://rest.kegg.jp/list/pathway/
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93
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94 User manual / Documentation: http://www.bioconductor.org/packages/release/bioc/html/pathview.html