providing cBioPortal parameters

##Introduction On this page we aim to describe the necessary parameters for cBioPortal to:

1. See the homepage with provided parameters filled in
2. Query a study using the provided parameters, resulting in the oncoprint page
3. Query a study using the provided parameters, resulting in the mutations page

###POST method :warning: In order to support a large number of sample identifiers and genes, the POST method should be used.

The parameters are described below. At the bottom of the page we provide some jsfiddle examples how this could be done.

###URL The URL to be used is http://<your_server>/index.do, e.g. http://www.cbioportal.org/index.do

To display specific tabs in the results page, you can add the tab id to the URL. Examples:

• http:/<your_server>/index.do: show the query results in the default oncoprint tab
• http://<your_server>/index.do#mutation_details: show the query results in the mutations tab
• http://<your_server>/index.do#enrichementTabDiv: show the query results in the enrichment analysis view
• http://<your_server>/index.do#plots: plots view (e.g. mRNA x CNA plots)
• http://<your_server>/index.do#coexp: coexpression analysis view

###Parameters The following parameters should be provided:

cancer_study_id

• Description: Used to identify the study in cBioPortal
• Values: <study_id>
• Example: acc_tcga

genetic_profile_ids_PROFILE_MUTATION_EXTENDED

• Description: Used to identify the mutations profile in cBioPortal
• Values: <study_id>_mutations
• Example: acc_tcga_mutations

case_set_id

• Description: Used to determine which case list to use or whether to use a custom set of case identifiers
• Values:
  • When interested in all samples in the study, use <study_id>_all
  • When interested in a custom set of samples or patients, set to -1
• Example: acc_tcga_all

case_ids

• Description: Used to describe the case identifiers
• Values:
  • When interested in all samples, this parameter is not necessary, or the value should be left empty
  • When interested in a custom set of samples, separate them by a white space, e.g. SAMPLE1 SAMPLE2
  • When interested in a custom set of patients, separate them by a white space, e.g. PATIENT1 PATIENT2
    • This does not seem to work. Created an issue asking whether query by patient is possible (https://github.com/cBioPortal/cbioportal/issues/1073)
• Example: SAMPLE1 SAMPLE2

patient_case_select

• Description: Describes whether the provided identifiers are sample or patient identifiers
• Values:
  • When interested in all samples or in a set of samples, set to sample
  • When interested in a set of patients, set to patient
    • This does not seem to work. Created an issue asking whether query by patient is possible (https://github.com/cBioPortal/cbioportal/issues/1073)
• Example: sample

gene_list

• Description: List of genes to use in the query
• Values: List with genes separated by a white space
• Example: ZFPM1 MUC5B

tab_index

• Description: Set to tab_visualize, which is the main results tab with the oncoprint
• Values: tab_visualize
  • ⚠️ If not used, result page will just be the homepage.
• Example: tab_visualize

Action

• Description: Decides whether to submit the form, which will lead to the oncoprint or the mutation details view.
• Values:
  • Set to Submit to show oncoprint as result page
  • ⚠️ If not used, result page will just be the homepage.
• Example: Submit

###Examples: Homepage with the acc_tcga study, the mutations profile, 2 genes and a custom case set with one sample: http://jsfiddle.net/nfTWL/59/

Oncoprint for the acc_tcga study, the mutations profile, 2 genes and a custom case set with one sample. http://jsfiddle.net/nfTWL/60/

Mutations view for the acc_tcga study, the mutations profile, 2 genes and a custom case set with one sample. http://jsfiddle.net/nfTWL/64/

Oncoprint for the acc_tcga study, the mutations profile, 2 genes and all samples. http://jsfiddle.net/nfTWL/62/