SRF.H12CORE.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SRF.H12CORE.0.PSM.A
Gene (human)	SRF (GeneCards)
Gene synonyms (human)
Gene (mouse)	Srf
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	17
Consensus	hbnCCWTWTWTGGnhdd
GC content	41.52%
Information content (bits; total / per base)	14.735 / 0.867
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	948

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	21 (147)	0.823	0.986	0.821	0.973	0.793	0.979	4.267	6.2	441.432	960.367
Mouse	19 (113)	0.914	0.98	0.902	0.966	0.891	0.975	4.869	6.587	274.051	697.62

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.656	0.69	0.556	0.589	0.517	0.546
Overall, 5 experiments	best	0.988	0.978	0.982	0.969	0.944	0.93
Methyl HT-SELEX, 1 experiments	median	0.988	0.978	0.982	0.969	0.944	0.93
Methyl HT-SELEX, 1 experiments	best	0.988	0.978	0.982	0.969	0.944	0.93
Non-Methyl HT-SELEX, 4 experiments	median	0.619	0.643	0.545	0.568	0.516	0.536
Non-Methyl HT-SELEX, 4 experiments	best	0.981	0.964	0.971	0.953	0.931	0.91

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	5.769	6.179	0.409	0.262

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.821	0.08	0.75	0.333

TF superclass	alpha-Helices exposed by beta-structures {5} (TFClass)
TF class	MADS box factors {5.1} (TFClass)
TF family	Responders to external signals {5.1.2} (TFClass)
TF subfamily	{5.1.2.0} (TFClass)
TFClass ID	TFClass: 5.1.2.0.1
HGNC	HGNC:11291
MGI	MGI:106658
EntrezGene (human)	GeneID:6722 (SSTAR profile)
EntrezGene (mouse)	GeneID:20807 (SSTAR profile)
UniProt ID (human)	SRF_HUMAN
UniProt ID (mouse)	SRF_MOUSE
UniProt AC (human)	P11831 (TFClass)
UniProt AC (mouse)	Q9JM73 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	21 human, 19 mouse
HT-SELEX	4
Methyl-HT-SELEX	1

PCM	SRF.H12CORE.0.PSM.A.pcm
PWM	SRF.H12CORE.0.PSM.A.pwm
PFM	SRF.H12CORE.0.PSM.A.pfm
Alignment	SRF.H12CORE.0.PSM.A.words.tsv
Threshold to P-value map	SRF.H12CORE.0.PSM.A.thr
Motif in other formats
JASPAR format	SRF.H12CORE.0.PSM.A_jaspar_format.txt
MEME format	SRF.H12CORE.0.PSM.A_meme_format.meme
Transfac format	SRF.H12CORE.0.PSM.A_transfac_format.txt
Homer format	SRF.H12CORE.0.PSM.A_homer_format_0.001.txt SRF.H12CORE.0.PSM.A_homer_format_0.0005.txt SRF.H12CORE.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	142.0	163.0	85.0	558.0
02	73.0	134.0	200.0	541.0
03	218.0	155.0	292.0	283.0
04	10.0	921.0	11.0	6.0
05	0.0	906.0	0.0	42.0
06	267.0	143.0	17.0	521.0
07	100.0	31.0	20.0	797.0
08	682.0	16.0	39.0	211.0
09	17.0	28.0	10.0	893.0
10	594.0	20.0	9.0	325.0
11	100.0	12.0	15.0	821.0
12	92.0	0.0	855.0	1.0
13	8.0	10.0	919.0	11.0
14	117.0	276.0	279.0	276.0
15	176.0	539.0	92.0	141.0
16	409.0	88.0	114.0	337.0
17	262.0	129.0	163.0	394.0

PFM

	A	C	G	T
01	0.15	0.172	0.09	0.589
02	0.077	0.141	0.211	0.571
03	0.23	0.164	0.308	0.299
04	0.011	0.972	0.012	0.006
05	0.0	0.956	0.0	0.044
06	0.282	0.151	0.018	0.55
07	0.105	0.033	0.021	0.841
08	0.719	0.017	0.041	0.223
09	0.018	0.03	0.011	0.942
10	0.627	0.021	0.009	0.343
11	0.105	0.013	0.016	0.866
12	0.097	0.0	0.902	0.001
13	0.008	0.011	0.969	0.012
14	0.123	0.291	0.294	0.291
15	0.186	0.569	0.097	0.149
16	0.431	0.093	0.12	0.355
17	0.276	0.136	0.172	0.416

PWM

	A	C	G	T
01	-0.507	-0.371	-1.013	0.852
02	-1.162	-0.565	-0.168	0.821
03	-0.083	-0.421	0.207	0.176
04	-3.015	1.352	-2.933	-3.432
05	-4.937	1.336	-4.937	-1.698
06	0.118	-0.501	-2.546	0.784
07	-0.853	-1.987	-2.397	1.208
08	1.052	-2.601	-1.769	-0.115
09	-2.546	-2.084	-3.015	1.321
10	0.914	-2.397	-3.104	0.314
11	-0.853	-2.857	-2.659	1.237
12	-0.935	-4.937	1.278	-4.477
13	-3.202	-3.015	1.35	-2.933
14	-0.699	0.151	0.162	0.151
15	-0.295	0.818	-0.935	-0.514
16	0.543	-0.979	-0.724	0.35
17	0.1	-0.602	-0.371	0.505

Standard thresholds

P-value	Threshold
0.001	3.08091
0.0005	4.24131
0.0001	6.65706