Table 1.

Top-ranked TrFs that have significantly lower co-expression with cell cycle arrest genes in HMM compared to NHMM from the GSE6477 analysis. The TrFs in Tables 1–3 are selected by the permutation p-value threshold of 0.06 and linear regression p-value threshold of 1E−5. For the column of “Known roles in cancer”, see Supplementary Tables for literature references.

Symbol	Gene	Pattern Score	Chromosome	Regression p-value	Permutation p-value	Known roles in cancer
HOXA9	NM_152739	−311.0993844	Chr7	7.76E-29	0.018	myeloma
FOXD1	NM_004472	−284.6487066	Chr5	8.72E-21	0.016	associated with placental growth factor (PLGF)
CEBPB	NM_005194	−258.7742785	Chr20	3.68E-12	0.015	myeloma
BPTF	NM_004459	−237.042492	Chr17	6.31E-21	0.03
PAX3	NM_181460	−257.9273348	Chr2	5.4E-09	0.039	PAX3-FKHR fusion; chromosomal rearrangements
IRF1	NM_002198	−231.9772177	Chr5	7.76E-11	0.012	myeloma
TAL1	NM_003189	−228.7284582	Chr1	3.4E-10	0.051	TAL1/SCL; leukemia
MZF1	NM_003422	−226.4785758	Chr19	2.44E-15	0.052	Myeloid malignancies
MYC	NM_002467	−206.9462599	Chr8	3.71E-08	0.06	myeloma; hyperdiploid
NFE2L1	NM_003204	−185.2599543	Chr17	0.000000467	0.018
ATF2	NM_001880	−160.7918875	Chr2	0.000000271	0.028	associated with AP-1 complex
STAT3	NM_003150	−159.6504808	Chr17	0.00000699	0.057	myeloma
ATF6	NM_007348	−140.8047495	Chr1	0.00000868	0.018	myeloma
REL	NM_002908	−94.94920668	Chr2	4.78E-09	0.047	myeloma