TCF21.H12RSNP.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	TCF21.H12RSNP.1.SM.B
Gene (human)	TCF21 (GeneCards)
Gene synonyms (human)	BHLHA23, POD1
Gene (mouse)	Tcf21
Gene synonyms (mouse)	Pod1
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	13
Consensus	nRvCATATGGYvn
GC content	45.75%
Information content (bits; total / per base)	14.106 / 1.085
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	2163

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	3 (9)	0.763	0.77	0.537	0.555	0.646	0.654	1.437	1.482	64.42	72.553

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.855	0.809	0.773	0.732	0.681	0.663
Overall, 5 experiments	best	0.995	0.993	0.938	0.93	0.794	0.804
Methyl HT-SELEX, 1 experiments	median	0.995	0.993	0.938	0.93	0.794	0.804
Methyl HT-SELEX, 1 experiments	best	0.995	0.993	0.938	0.93	0.794	0.804
Non-Methyl HT-SELEX, 4 experiments	median	0.793	0.76	0.701	0.678	0.626	0.62
Non-Methyl HT-SELEX, 4 experiments	best	0.968	0.957	0.901	0.88	0.784	0.777

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.794	0.276	0.808	0.488

TF superclass	Basic domains {1} (TFClass)
TF class	Basic helix-loop-helix factors (bHLH) {1.2} (TFClass)
TF family	Tal-related {1.2.3} (TFClass)
TF subfamily	MESP {1.2.3.3} (TFClass)
TFClass ID	TFClass: 1.2.3.3.5
HGNC	HGNC:11632
MGI	MGI:1202715
EntrezGene (human)	GeneID:6943 (SSTAR profile)
EntrezGene (mouse)	GeneID:21412 (SSTAR profile)
UniProt ID (human)	TCF21_HUMAN
UniProt ID (mouse)	TCF21_MOUSE
UniProt AC (human)	O43680 (TFClass)
UniProt AC (mouse)	O35437 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	3 human, 0 mouse
HT-SELEX	4
Methyl-HT-SELEX	1

PCM	TCF21.H12RSNP.1.SM.B.pcm
PWM	TCF21.H12RSNP.1.SM.B.pwm
PFM	TCF21.H12RSNP.1.SM.B.pfm
Alignment	TCF21.H12RSNP.1.SM.B.words.tsv
Threshold to P-value map	TCF21.H12RSNP.1.SM.B.thr
Motif in other formats
JASPAR format	TCF21.H12RSNP.1.SM.B_jaspar_format.txt
MEME format	TCF21.H12RSNP.1.SM.B_meme_format.meme
Transfac format	TCF21.H12RSNP.1.SM.B_transfac_format.txt
Homer format	TCF21.H12RSNP.1.SM.B_homer_format_0.001.txt TCF21.H12RSNP.1.SM.B_homer_format_0.0005.txt TCF21.H12RSNP.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	491.75	514.75	655.75	500.75
02	1353.25	221.25	357.25	231.25
03	741.0	907.0	454.0	61.0
04	7.0	2149.0	7.0	0.0
05	2071.0	0.0	92.0	0.0
06	0.0	1.0	68.0	2094.0
07	2098.0	64.0	1.0	0.0
08	2.0	0.0	0.0	2161.0
09	0.0	0.0	2161.0	2.0
10	2.0	15.0	1839.0	307.0
11	231.0	1034.0	30.0	868.0
12	702.75	387.75	858.75	213.75
13	540.0	553.0	493.0	577.0

PFM

	A	C	G	T
01	0.227	0.238	0.303	0.232
02	0.626	0.102	0.165	0.107
03	0.343	0.419	0.21	0.028
04	0.003	0.994	0.003	0.0
05	0.957	0.0	0.043	0.0
06	0.0	0.0	0.031	0.968
07	0.97	0.03	0.0	0.0
08	0.001	0.0	0.0	0.999
09	0.0	0.0	0.999	0.001
10	0.001	0.007	0.85	0.142
11	0.107	0.478	0.014	0.401
12	0.325	0.179	0.397	0.099
13	0.25	0.256	0.228	0.267

PWM

	A	C	G	T
01	-0.095	-0.049	0.192	-0.077
02	0.915	-0.889	-0.413	-0.845
03	0.314	0.516	-0.174	-2.155
04	-4.108	1.377	-4.108	-5.644
05	1.34	-5.644	-1.754	-5.644
06	-5.644	-5.225	-2.049	1.351
07	1.353	-2.108	-5.225	-5.644
08	-4.93	-5.644	-5.644	1.383
09	-5.644	-5.644	1.383	-4.93
10	-4.93	-3.468	1.222	-0.563
11	-0.846	0.647	-2.833	0.472
12	0.261	-0.331	0.461	-0.923
13	-0.001	0.022	-0.092	0.065

Standard thresholds

P-value	Threshold
0.001	2.21181
0.0005	3.591265
0.0001	6.71423