Table 3.

FlyTF score based on computational predictions (DBD) and novel GO annotation (based on experimental data)

FlyTF score	Minimal criteria (GO term and/or evidence)	Number
1	Sequence-specific DNA binding (IDA or ISS) AND any evidence for regulation of transcription (IDA, IMP, or IGI)	133	This is analogous to previous annotations “Yes” and “maybe”.
2	DNA binding (IDA or ISS) AND any evidence for regulation of transcription (IDA, IMP, or IGI)	26
3	IDA for regulation of transcription AND assignment of a preferred DBD: homeodomain, Pax, POU, HLH, Forkhead, T-Box, Ets, bZIP, GATA, Cut, Prox1, Stat, GCM, C4 zinc finger, p53, HTH, SRF	13
4	IDA for regulation of transcription AND assignment of any other putative DBD	10
5	IDA for any kind of DNA binding, no experimental evidence for transcriptional regulation	110
6	Any kind of DBD assignment (including predictions from InterPro), no evidence for transcriptional regulation.	460
7	Little evidence for TF activity (but unlikely to be a site-specific TF)	191
8	No evidence for any TF activity (likely to be something else)	219

Candidate proteins in all categories can have an additional ‘chromatin’ call if the FlyTF curator felt the factor was more likely involved in general chromatin-related processes rather than gene-specific transcriptional regulation.