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1 Wrapper for Pathview tool
2 =============================
3
4 **Authors**
5
6 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
7
8 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
9
10 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
11
12 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
13
14 =============================
15
16 This tool map a list of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package.
17
18 You can map Entrez gene IDs / Uniprot accession number from three species : human, mouse and rat.
19
20 If your input have another type of IDs, please use the ID_Converter tool.
21
22 **Input:**
23
24
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)
31
32 You can see below an example of an input file with identifiers (uniprot_AC) and fold_change values.
33
34 .. csv-table:: Simulated data
35 :header: "Uniprot_AC","Protein.name","Number_of_peptides","fc_values 1","fc_values 2","fc_values 3"
36
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"
41
42 |
43
44
45
46 .. class:: warningmark
47
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:
49
50 .. csv-table:: Simulated data
51 :header: "Ensembl_Gene","UniProt.AC","UniProt.ID"
52
53 "ENSG00000136881","Q14032","BAAT_HUMAN"
54 "ENSG00000170099","P08185;G3V350;G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
55 "ENSG00000244731","P0C0L4","CO4A_HUMAN"
56
57 |
58
59 will become:
60
61 .. csv-table:: Simulated data
62 :header: "Ensembl_Gene","UniProt.AC","UniProt.ID"
63
64 "ENSG00000136881","Q14032","BAAT_HUMAN"
65 "ENSG00000170099","P08185","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
66 "ENSG00000170099","G3V350","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
67 "ENSG00000170099","G3V4V7","CBG_HUMAN;G3V350_HUMAN;G3V4V7_HUMAN"
68 "ENSG00000244731","P0C0L4","CO4A_HUMAN"
69
70 |
71
72 **Output:**
73
74 - a **collection dataset** named 'KEGG maps visualization from <dataset>', one file (png or pdf) for each given pathway.
75 - a **summary text file** (.tsv) of the mapping(s) with the following columns
76 - **KEGG pathway ID**: KEGG pathway(s) used to map given genes/proteins ids
77 - **pathway name**: name(s) of KEGG pathway(s) used for mapping
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
79 - **nb of Entrez gene ID used**: number of Entrez gene IDs used for mapping
80 - **nb of Entrez gene ID mapped**: number of Entrez gene IDs mapped on a given pathway
81 - **nb of Entrez gene ID in the pathway**: number total of Entrez gene IDs in a given pathway
82 - **ratio of Entrez gene ID mapped**: number of Entrez gene IDs mapped / number total of Entrez gene IDs
83 - **Entrez gene ID mapped**: list of mapped Entrez gene IDs
84 - **uniprot_AC mapped** (only when Uniprot accession number is given): list of Uniprot accession number corresponding to the mapped Entrez gene IDs
85
86 -----
87
88 .. class:: infomark
89
90 **Database:**
91
92 KEGG Pathways names list are from http://rest.kegg.jp/list/pathway/
93
94 User manual / Documentation: http://www.bioconductor.org/packages/release/bioc/html/pathview.html