HTF4.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HTF4.H12RSNP.0.PSM.A
Gene (human)	TCF12 (GeneCards)
Gene synonyms (human)	BHLHB20, HEB, HTF4
Gene (mouse)	Tcf12
Gene synonyms (mouse)	Alf1, Meb
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	9
Consensus	RRCAGSTGb
GC content	64.71%
Information content (bits; total / per base)	10.574 / 1.175
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1000

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	8 (55)	0.84	0.883	0.698	0.752	0.793	0.88	2.169	2.795	108.26	285.0
Mouse	4 (28)	0.794	0.837	0.661	0.722	0.726	0.787	1.982	2.246	107.891	170.051

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.959	0.926	0.953	0.919	0.896	0.866
Overall, 4 experiments	best	0.96	0.929	0.958	0.925	0.921	0.89
Methyl HT-SELEX, 2 experiments	median	0.959	0.927	0.956	0.922	0.911	0.881
Methyl HT-SELEX, 2 experiments	best	0.96	0.929	0.958	0.925	0.921	0.89
Non-Methyl HT-SELEX, 2 experiments	median	0.947	0.908	0.926	0.887	0.852	0.821
Non-Methyl HT-SELEX, 2 experiments	best	0.959	0.926	0.952	0.918	0.89	0.862

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.681	2.639	0.113	0.065

TF superclass	Basic domains {1} (TFClass)
TF class	Basic helix-loop-helix factors (bHLH) {1.2} (TFClass)
TF family	E2A {1.2.1} (TFClass)
TF subfamily	E2A-like {1.2.1.0} (TFClass)
TFClass ID	TFClass: 1.2.1.0.3
HGNC	HGNC:11623
MGI	MGI:101877
EntrezGene (human)	GeneID:6938 (SSTAR profile)
EntrezGene (mouse)	GeneID:21406 (SSTAR profile)
UniProt ID (human)	HTF4_HUMAN
UniProt ID (mouse)	HTF4_MOUSE
UniProt AC (human)	Q99081 (TFClass)
UniProt AC (mouse)	Q61286 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	8 human, 4 mouse
HT-SELEX	2
Methyl-HT-SELEX	2

PCM	HTF4.H12RSNP.0.PSM.A.pcm
PWM	HTF4.H12RSNP.0.PSM.A.pwm
PFM	HTF4.H12RSNP.0.PSM.A.pfm
Alignment	HTF4.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	HTF4.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	HTF4.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	HTF4.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	HTF4.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	HTF4.H12RSNP.0.PSM.A_homer_format_0.001.txt HTF4.H12RSNP.0.PSM.A_homer_format_0.0005.txt HTF4.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	481.0	59.0	376.0	84.0
02	193.0	161.0	628.0	18.0
03	10.0	956.0	28.0	6.0
04	981.0	4.0	7.0	8.0
05	4.0	2.0	991.0	3.0
06	87.0	335.0	574.0	4.0
07	21.0	37.0	37.0	905.0
08	2.0	3.0	981.0	14.0
09	49.0	348.0	297.0	306.0

PFM

	A	C	G	T
01	0.481	0.059	0.376	0.084
02	0.193	0.161	0.628	0.018
03	0.01	0.956	0.028	0.006
04	0.981	0.004	0.007	0.008
05	0.004	0.002	0.991	0.003
06	0.087	0.335	0.574	0.004
07	0.021	0.037	0.037	0.905
08	0.002	0.003	0.981	0.014
09	0.049	0.348	0.297	0.306

PWM

	A	C	G	T
01	0.651	-1.422	0.406	-1.077
02	-0.257	-0.436	0.917	-2.546
03	-3.066	1.336	-2.136	-3.484
04	1.362	-3.783	-3.362	-3.253
05	-3.783	-4.213	1.372	-3.975
06	-1.043	0.291	0.827	-3.783
07	-2.405	-1.872	-1.872	1.281
08	-4.213	-3.975	1.362	-2.773
09	-1.602	0.329	0.171	0.201

Standard thresholds

P-value	Threshold
0.001	4.408015
0.0005	5.577535
0.0001	7.596255