TCF7.H13RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	TCF7.H13RSNP.0.PSM.A
Gene (human)	TCF7 (GeneCards)
Gene synonyms (human)	TCF1
Gene (mouse)	Tcf7
Gene synonyms (mouse)	Tcf-1, Tcf1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	15
Consensus	dvMMACAWSAMARvn
GC content	44.17%
Information content (bits; total / per base)	11.016 / 0.734
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	552
Previous names	TCF7.H12RSNP.0.PSM.A

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	pseudo-log-auROC, median	pseudo-log-auROC, best	Centrality, median	Centrality, best
Human	10 (59)	0.764	0.87	0.636	0.816	0.801	0.894	2.574	4.102	31.602	296.229
Mouse	5 (32)	0.731	0.813	0.624	0.725	0.773	0.852	2.645	3.332	79.464	164.013

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.821	0.785	0.699	0.683	0.604	0.613
Overall, 2 experiments	best	0.843	0.81	0.709	0.698	0.606	0.62
Methyl HT-SELEX, 1 experiments	median	0.843	0.81	0.709	0.698	0.606	0.62
Methyl HT-SELEX, 1 experiments	best	0.843	0.81	0.709	0.698	0.606	0.62
Non-Methyl HT-SELEX, 1 experiments	median	0.8	0.759	0.689	0.669	0.603	0.606
Non-Methyl HT-SELEX, 1 experiments	best	0.8	0.759	0.689	0.669	0.603	0.606

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.532	0.059	0.482	0.343

TF superclass	Other all-alpha-helical DNA-binding domains {4} (TFClass)
TF class	High-mobility group (HMG) domain factors {4.1} (TFClass)
TF family	TCF7-related {4.1.3} (TFClass)
TF subfamily	{4.1.3.0} (TFClass)
TFClass ID	TFClass: 4.1.3.0.1
HGNC	HGNC:11639
MGI	MGI:98507
EntrezGene (human)	GeneID:6932 (SSTAR profile)
EntrezGene (mouse)	GeneID:21414 (SSTAR profile)
UniProt ID (human)	TCF7_HUMAN
UniProt ID (mouse)	TCF7_MOUSE
UniProt AC (human)	P36402 (TFClass)
UniProt AC (mouse)	Q00417 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	10 human, 5 mouse
HT-SELEX	1
Methyl-HT-SELEX	1
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	TCF7.H13RSNP.0.PSM.A.pcm
PWM	TCF7.H13RSNP.0.PSM.A.pwm
PFM	TCF7.H13RSNP.0.PSM.A.pfm
Threshold to P-value map	TCF7.H13RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	TCF7.H13RSNP.0.PSM.A_jaspar_format.txt
MEME format	TCF7.H13RSNP.0.PSM.A_meme_format.meme
Transfac format	TCF7.H13RSNP.0.PSM.A_transfac_format.txt
Homer format	TCF7.H13RSNP.0.PSM.A_homer_format_0.001.txt TCF7.H13RSNP.0.PSM.A_homer_format_0.0005.txt TCF7.H13RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	263.0	75.0	110.0	104.0
02	255.0	141.0	130.0	26.0
03	102.0	355.0	46.0	49.0
04	94.0	385.0	55.0	18.0
05	504.0	15.0	14.0	19.0
06	24.0	418.0	107.0	3.0
07	441.0	20.0	4.0	87.0
08	95.0	21.0	56.0	380.0
09	42.0	384.0	107.0	19.0
10	498.0	10.0	3.0	41.0
11	416.0	69.0	64.0	3.0
12	475.0	10.0	39.0	28.0
13	98.0	71.0	367.0	16.0
14	193.0	110.0	188.0	61.0
15	173.0	150.0	133.0	96.0

PFM

	A	C	G	T
01	0.476	0.136	0.199	0.188
02	0.462	0.255	0.236	0.047
03	0.185	0.643	0.083	0.089
04	0.17	0.697	0.1	0.033
05	0.913	0.027	0.025	0.034
06	0.043	0.757	0.194	0.005
07	0.799	0.036	0.007	0.158
08	0.172	0.038	0.101	0.688
09	0.076	0.696	0.194	0.034
10	0.902	0.018	0.005	0.074
11	0.754	0.125	0.116	0.005
12	0.861	0.018	0.071	0.051
13	0.178	0.129	0.665	0.029
14	0.35	0.199	0.341	0.111
15	0.313	0.272	0.241	0.174

PWM

	A	C	G	T
01	0.64	-0.6	-0.224	-0.279
02	0.609	0.021	-0.059	-1.622
03	-0.298	0.938	-1.076	-1.015
04	-0.379	1.019	-0.903	-1.964
05	1.287	-2.131	-2.193	-1.914
06	-1.697	1.101	-0.251	-3.417
07	1.154	-1.867	-3.22	-0.455
08	-0.368	-1.822	-0.885	1.006
09	-1.164	1.016	-0.251	-1.914
10	1.275	-2.489	-3.417	-1.187
11	1.096	-0.682	-0.755	-3.417
12	1.228	-2.489	-1.235	-1.552
13	-0.338	-0.654	0.971	-2.072
14	0.332	-0.224	0.306	-0.802
15	0.224	0.082	-0.036	-0.358

Standard thresholds

P-value	Threshold
0.001	4.51516
0.0005	5.36826
0.0001	7.14486