Table 2.

Experimental procedures accepted to confirm transcriptional regulatory property of candidate proteins, and evidence codes in support of GO terms dealing with regulatory function

FlyTF term	Explanation	GO evidence code for GO:0030528 or children thereof
Reporter assay in vivo	Any experiment that used the putative target sequence of the TF joined to a reporter gene, and showed specific activation (or repression) of the reporter through this sequence by the TF in vivo (embryo, larva, adult eye, etc.)	IDA
Reporter assay in cell culture	As above, but showing activity in a cell culture assay	IDA
Expression analysis	Analysis of the expression of a (or more) putative target gene(s) of the TF in mutant backgrounds (loss- or gain-of-function)	IMP
Genetic interaction analysis	Factor deemed a TF as a result of a modifier screen (not a strong evidence)	IGI
In vitro transcription assay	Transcription assay in a cell-free medium	IDA
Mutant phenotype analysis	Analysis of the phenotype after loss- or gain-of-function of the TF gene	Not assigned
Microarray	Gene expression changes as determined by microarray	Not assigned
Fusion protein with DNA binding domain followed by reporter assay	Regulatory domain of the putative TF fused to a DNA-binding domain (e.g. LexA), followed by reporter assay in vitro	IDA