. 2010 May 21;38(Web Server issue):W109–W117. doi: 10.1093/nar/gkq424

Table 2.

Identification of signaling pathways upstream of transcription factor in THP-1 cells

Top-ranked pathway	Transcription factor
MAPK+PI3K	CEBPA (27), EGR1, (28), ETS2 (29), FLI1 (30), MLLT3, MYBL2 (31), NFE2L1, NFYA, NRAS^a, SP1 (32), ZNF238
JAK-STAT	FOXJ3, FOXP1, GFI1 (33), MXI1, RUNX1 (34), STAT1 (35), YY1
TLR	BMI1, CEBPG, GATA2 (36), IRF8 (37), SPI1 (38)
TGF-β	MYB (39)

SPEED was run programatically on lists of differentially expressed genes following 52 transcription factor knockdowns. For 24 transcription factors, the corresponding differentially expressed gene lists had an overrepresentation of at least one upstream signaling pathway. The top-ranking signaling pathway with a minimum FDR of 0.05 is listed for each of the 24 transcription factors. Literature references for transcription factors known to be associated with identified signaling pathways are noted.

^aAlthough NRAS is not a transcription factor, the significant overlap with MAPK+PI3K signature genes serves as validation of the SPEED algorithm because NRAS is upstream of both the MAPK and PI3K signaling pathways (25,26).