Table 2.

REST API arguments and parameters supported by BRCA-Pathway

arg1	arg2	arg3	Parameters	Description
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