Table 1.

Query options in Transcriptomine

Query Parameter	Options	Strategy
Gene(s) of interest	any gene	return any gene that matches the query parameters
	single gene (AC)	specify a single gene of interest
	GO term (AC)	specify a gene ontology biological process, cellular component, or molecular function as a surrogate for gene(s) of interest
	disease term (AC)	specify a disease term as a surrogate for gene(s) of interest
	upload gene list	upload a custom gene list (≤5,000 genes)
Regulation	fold change	options: ≥twofold (default); enter custom value
	direction	options: up- or downregulated (default); upregulated; downregulated
	significance	options: any (default); P < 0.05; enter custom value
Regulating molecule	single molecule (AC)	specify a regulating NR ligand, NR or coregulator; if a ligand is entered, Time Treated becomes available [options: ≤1 h (default); >1 h-≤4 h; >4 h-≤24 h; >24 h]
RNA source	species	options: all (default), human; mouse; rat
	tissue/cell line (AC or select from list)	specify individual tissues (e.g., liver) or cell lines (e.g., MCF-7) or all tissues and cell lines within a given tissue type or organ (e.g., adipose tissue, all tissues and cell lines)

AC, autocomplete text field.