Table 2 REST API arguments and parameters supported by BRCA-Pathway

landscape

-

-

type=[JSON | LIST]

fields=[KEGGPathway_update

| KEGGPathways

| Pathway_Pathway_Membership

KEGG pathways, TCGA-

| TCGAGenes

BRCA data status

| TCGA_BRCA_Patients

| TCGA_BRCA_update

| TFTG_relation | driver_genes]

search

-

-

keyword

type=[ JSON | LIST ]

Get search result by

fields=[ keyword

keyword.

| gene_labels

Gene or pathway names

| rate

with input_type.

| pathID | pathname ]

genes

(pathIDs,

-

type=[ JSON | LIST ]

sep=“+”)

count

fields=[ pathID

Retrieve pathways

| gene_symbol

information.

| pathname

related_pathways operation

| geneID

supported.

| count** ]

**given only arg3 related_pathways

pathways

(pathIDs,

-

type=[ JSON | LIST ]

sep=“+”)

related_pathways

fields=[ pathID | pathname

Retrieve pathways

| category_level2_id

information.

| description

related_pathways operation

| related_pathID**]

supported.

**given only arg3 related_pathways

TCGA-BRCA

patient_list

-

type=[ JSON | LIST ]

patient_count

-

** arg2 patient_list

(pathIDs,

(given pathIDs,)

fields=[patient_barcode]

Retrieve pathways and

sep=“+”)

fold_change

TCGA-BRCA omics data.

mutation

** arg2 patient_count

Gene expression with

CNV

fields=[count]

fold_change value,

mutation with the number

** arg3 fold_change

of patients having

fields=[geneID |gene_symbol

mutation, and CNV with

| exp_select

GISTIC2 result range from

| exp_tumor

-2 to 2.

| exp_normal

Each omics result will be

| fc_select_tumor | fc_select_normal ]

given by gene level

aggregating patients

group omics data

** arg3 mutation

patient_list,

fields=[ geneID | gene_symbol

patient_count operation

|count ]

supported.

** arg3 CNV

fields=[geneID | gene_symbol

| cnv_pos

| cnv_zero

| cnv_neg ]

** And patient_options

described_above