CyTRANSFINDER: a Cytoscape 3.3 plugin for three-component (TF, gene, miRNA) signal transduction pathway construction

Table 1 STPP Specification Language

#	Regulation type	Description	Notation
1	TF ↦ gene	A transcription factor controlling the rate of transcription of a gene	tf,gene
2	TF ↦ TF	A transcription factor controlling the rate of transcription of a another transcription factor	tf,tf
3	TF ↦ miRNA	A transcription factor hosting a miRNA	tf,mirna
4	gene ↦ miRNA	A gene hosting a miRNA	gene,mirna
5	miRNA ↦ gene	A miRNA post-transcriptionally targeting a gene	mirna,gene
6	miRNA ↦ TF	A miRNA post-transcriptionally targeting a TF	mirna,tf

The list of interactions that can be used in CyTRANSFINDER to build a STPP. For each interaction the related notation is reported. The user is free to combine the interactions in order to describe the desired pattern. The first element of the list must be a gene or miRNA and must be preceded by the term “source”, while the last element must a gene and has to be be preceded by the term “target”

ISSN: 1471-2105