Table 1.
Transcription factor seed motifs currently available in CoMoDis
| In-house curated motifs | Xie et al. motifs (19) | Ettwiller et al. (CpG) motifs (20) | |||
|---|---|---|---|---|---|
| Name | Consensus | Identifier | Consensus | Identifier | Consensus |
| AML1 | TGYGGT | #1 (NRF-1) | RCGCANGCGY | #1 (CAAT) | CCAATC |
| AP1 | NNNSTCA | #2 (MYC) | CACGTG | #2 (SP1) | GGGCGG |
| CRE | TGACGTCA | #3 (ELK-1) | SCGGAAGY | #3 (CRE) | TGACGTCA |
| CRE | TGACG (half) | #4 (Novel) | ACTAYRNNNCCCR | #4 (ETS) | CGGAAG |
| CEBP | SYAAY | #5 (NK-Y) | GATTGGY | #5 (Ebox) | CACGTG |
| EBF | CCCNNGRG | #6 (SP1) | GGGCGGR | #6 | ACTACA |
| Ebox | CANNTG | #7 (AP-1) | TGANTCA | #7 (CRE-like) | GTGACG |
| Ebox-GATA | CANNTG-GATA | #8 (Novel) | TMTCGCGANR | #8 | CTTTGT |
| c-Myc | CAYGYG | #9 (ATF3) | TGAYRTCA | #9 (SP1-like) | CCCTCCCCC |
| MyoD | CANCWG | #10 (YY1) | GCCATNTTG | #10 | GCGCAGGCGC |
| ETS | GGAW | #11 (GABP) | MGGAAGTG | #11 | GCGCGC |
| GATA | GATA | #12 (E12) | CAGGTG | #12 | AACTTT |
| GLI1 | GACCACCCA | #13 (LEF1) | CTTTGT | #13 | CCTTTAA |
| HMG | WWCAAWG | #14 (ATF3) | TGACGTCA | #14 | TGCGCA |
| HNF1 | GTTAAT | #15 (AP-4) | CAGCTG | #15 | CTCGCGAGA |
| HNF3 | TRTTTRY | #16 (C-ETS-2) | RYTTCCTG | #16 | TTGGCT |
| HNF4 | CAAAGK | #17 (IRF1) | AACTTT | #17 (TATA) | TATAAA |
| Ikaros | HRGGAW | #18 (SREBP-1) | TCANNTGAY | #18 | AAGATGGCGG |
| Iroquois | ACANNTGT | #19 (Novel) | GKCGCN(7)TGAYG | #19 | TTTGTT |
| MEF2 | CTAWWWWTAR | #20 (E4F1) | GTGACGY | #20 | ATGCAAAT |
| MEIS1 | TGACAS | #21 (Novel) | GGAANCGGAANY | #21 | TAATTA |
| MYB | YAACNG | #22 (Novel) | TGCGCANK | #22 | TTTAAG |
| NBOX | CACNAG | #23 (CHX10) | TAATTA | #23 | CGCATGCG |
| NANOG | SATTANS | #24 (MAZ) | GGGAGGRR | #24 | ATAAAT |
| NFAT | GGAAA | #25 (ESRRA) | TGACCTY | #25 | TTTAAA |
| NFAT-AP1 | WGGAAA-TGASTCA | #26 (E4BP4) | TTAYRTAA | #26 | GCCATTTT |
| NFAT-AP1 | WGGAAA-STCA (half) | #27 (Novel) | TGGN(6)KCCAR | #27 | ATAAAA |
| NFKB | GGGRNNYYY | #28 (RSRFC4) | CTAWWWATA | #28 | TAAATA |
| NKX2.5 | CAMTTNR | #29 (Novel) | CTTTAAR | #29 (HTH) | CAGGTG |
| OCT3/4 | ATGMWWVW | #30 (Novel) | YGCGYRCGC | #30 | CTAGCAAC |
| OTX | TAATCY | #31 (Novel) | GGGYGTGNY | #31 (CRE) | TGACGC |
| p53 | RCNWGYNN*0-1*NNRCAWGY | #32 (NF-E2) | TGASTMAGC | #32 | CATTGT |
| PAX5 | RNKMANBSNWGNRKRMM | #33 (MEF-2) | YTATTTTNR | #33 | GCCATCTT |
| RE1 | NTYAGMRCCNNRGMSAG | #34 (Novel) | CYTAGCAAY | #34 | ATTTAT |
| SOX2 | CWTTGTD | #35 (MYOD) | GCANCTGNY | #35 | ATGAAT |
| SP1 (1) | GGGHGGG | #36 (FREAC-2) | RTAAACA | Ettwiller et al. (non-CpG) motifs (20) | |
| SP1 (2) | GGGSWGGG | #37 (Novel) | GTTRYCATRR | ||
| SP1 (3) | GGKGYGGG | #38 (ERR-alpha) | TGACCTTG | #1 | TAATTA |
| SRF | CCWWWWWWGG | (Novel) | TCCCRNNRTGC | #2 | CAGCTG |
| STAT5 | TTCYNRGAA | #40 (STAT5A) | TTCYNRGAA | #3 (TRE) | TGAGTCA |
| TEF | CATTCC | #41 (MEIS1) | TGACAGNY | #4 (ETS) | CAGGAAGT |
| #42 (Novel) | TGACATY | #5 | CCCTCCC | ||
| #43 (Novel) | GTTGNYNNRGNAAC | #6 | AATAAA | ||
| #44 (OCT-X) | YATGNWAAT | #7 (Homeo-like) | AATTAA | ||
| #45 (Novel) | CCANNAGRKGGC | #8 | AGAAAA | ||
| #46 (Novel) | WTTGKCTG | #9 | ATAAAA | ||
| #47 (NF-1) | TGCCAAR | #10 | TTTCCA | ||
| #48 (C-REL) | GCGNNANTTCC | #11 (TATA-box) | TATAAATAG | ||
| #49 (SOX-9) | CATTGTYY | #12 | AGGAAA | ||
| #50 (PU.1) | RGAGGAARY | #13 | TTTCCT | ||
| #14 | TTCAAA | ||||
| #15 | TGACCT | ||||
| #16 | ATTTGCAT | ||||
| #17 | TTGTTT | ||||
| #18 | TTTAAA | ||||
| #19 | TTTCAG | ||||