Question: Reactome Pathway Analysis from command line
0
gravatar for saamar.rajput
10 months ago by
Germany
saamar.rajput10 wrote:

I have a list of genes or may be a file containing a list of genes. I want to see the pathways from Reactome that are enriched with the gene list i have (not just a list of pathway but the visualization from the Reactome Pathway database), But I want to do this by a command line. Is it possible ?

I have tried

curl -X GET "https://reactome.org/ContentService/data/pathways/low/diagram/identifier/IFNB1/allForms?species=9606" -H  "accept: application/json"

But it gives a list of pathways which contain IFNB1 gene, Plus i can only give a single at a time.

[
  {
    "dbId": 2559580,
    "displayName": "Oxidative Stress Induced Senescence",
    "stId": "R-HSA-2559580",
    "isInDisease": false,
    "isInferred": false,
    "name": [
      "Oxidative Stress Induced Senescence"
    ],
    "releaseDate": "2013-09-18",
    "speciesName": "Homo sapiens",
    "hasDiagram": true,
    "schemaClass": "Pathway",
    "className": "Pathway"
  },
  {
    "dbId": 933541,
    "displayName": "TRAF6 mediated IRF7 activation",
    "stId": "R-HSA-933541",
    "isInDisease": false,
    "isInferred": false,
    "name": [
      "TRAF6 mediated IRF7 activation"
    ],
    "releaseDate": "2010-12-14",
    "speciesName": "Homo sapiens",
    "hasDiagram": false,
    "schemaClass": "Pathway",
    "className": "Pathway"
  },
  {
    "dbId": 983231,
    "displayName": "Factors involved in megakaryocyte development and platelet production",
    "stId": "R-HSA-983231",
    "isInDisease": false,
    "isInferred": false,
    "name": [
      "Factors involved in megakaryocyte development and platelet production"
    ]

I also tried

    curl -H "Content-Type: text/plain" --data-binary @genes.txt -X POST --url https://reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1

Which takes in a file with list of genes and gives a TOKEN number for my query and i use this TOKEN to produce pathway analysis list with a command

     https://reactome.org/PathwayBrowser/#/DTAB=AN&ANALYSIS={TOKEN}

All this is very good but i additionally want to open my list of genes in Reactome pathway database and show my genes in the network. Is it possible?

rna-seq gene • 309 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by saamar.rajput10

Does this help?

https://github.com/wdecoster/enrichr_cli

ADD REPLYlink written 10 months ago by WouterDeCoster35k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 528 users visited in the last hour