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author proteore
date Thu, 22 Nov 2018 04:37:54 -0500
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1 Wrapper for Pathview tool
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2 =============================
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4 **Authors**
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6 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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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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10 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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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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14 =============================
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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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18 You can map Entrez gene IDs / Uniprot accession number from three species : human, mouse and rat.
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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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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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32 You can see below an example of an input file with identifiers (uniprot_AC) and fold_change values.
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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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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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42 |
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44 **Output:**
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46 - a **collection dataset** named 'KEGG pathways map from <dataset>', one file (png or pdf) for each given pathway.
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47 - a **summary text file** (.tsv) of the mapping(s) with the following columns
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48 - **KEGG pathway ID**: KEGG pathway(s) used to map given genes/proteins ids
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49 - **pathway name**: name(s) of KEGG pathway(s) used for mapping
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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
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51 - **nb of Entrez gene ID used**: number of Entrez gene IDs used for mapping
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52 - **nb of Entrez gene ID mapped**: number of Entrez gene IDs mapped on a given pathway
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53 - **nb of Entrez gene ID in the pathway**: number total of Entrez gene IDs in a given pathway
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54 - **ratio of Entrez gene ID mapped**: number of Entrez gene IDs mapped / number total of Entrez gene IDs
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55 - **Entrez gene ID mapped**: list of mapped Entrez gene IDs
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56 - **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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58 -----
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60 .. class:: infomark
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61
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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