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

Motif	SRF.H12RSNP.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	dYKbCCTTWTWTGGbhW
GC content	39.55%
Information content (bits; total / per base)	15.127 / 0.89
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	307

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)	0.797	0.97	0.795	0.948	0.782	0.967	3.897	5.403	421.678	891.032
Mouse	19 (113)	0.907	0.979	0.888	0.967	0.897	0.978	5.228	7.679	261.538	683.569

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.664	0.692	0.564	0.592	0.526	0.55
Overall, 5 experiments	best	0.983	0.97	0.97	0.954	0.919	0.901
Methyl HT-SELEX, 1 experiments	median	0.983	0.97	0.97	0.954	0.919	0.901
Methyl HT-SELEX, 1 experiments	best	0.983	0.97	0.97	0.954	0.919	0.901
Non-Methyl HT-SELEX, 4 experiments	median	0.624	0.646	0.553	0.57	0.523	0.539
Non-Methyl HT-SELEX, 4 experiments	best	0.975	0.955	0.958	0.934	0.904	0.88

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	4.842	5.636	0.427	0.243

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.876	0.128	0.795	0.295

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

PCM

	A	C	G	T
01	133.0	54.0	63.0	57.0
02	27.0	56.0	26.0	198.0
03	21.0	27.0	66.0	193.0
04	30.0	85.0	83.0	109.0
05	5.0	287.0	5.0	10.0
06	3.0	272.0	0.0	32.0
07	78.0	5.0	2.0	222.0
08	28.0	1.0	3.0	275.0
09	213.0	6.0	10.0	78.0
10	16.0	6.0	0.0	285.0
11	133.0	5.0	5.0	164.0
12	41.0	4.0	12.0	250.0
13	21.0	4.0	277.0	5.0
14	6.0	2.0	285.0	14.0
15	43.0	139.0	67.0	58.0
16	95.0	147.0	15.0	50.0
17	196.0	10.0	35.0	66.0

PFM

	A	C	G	T
01	0.433	0.176	0.205	0.186
02	0.088	0.182	0.085	0.645
03	0.068	0.088	0.215	0.629
04	0.098	0.277	0.27	0.355
05	0.016	0.935	0.016	0.033
06	0.01	0.886	0.0	0.104
07	0.254	0.016	0.007	0.723
08	0.091	0.003	0.01	0.896
09	0.694	0.02	0.033	0.254
10	0.052	0.02	0.0	0.928
11	0.433	0.016	0.016	0.534
12	0.134	0.013	0.039	0.814
13	0.068	0.013	0.902	0.016
14	0.02	0.007	0.928	0.046
15	0.14	0.453	0.218	0.189
16	0.309	0.479	0.049	0.163
17	0.638	0.033	0.114	0.215

PWM

	A	C	G	T
01	0.542	-0.344	-0.193	-0.291
02	-1.012	-0.308	-1.047	0.936
03	-1.249	-1.012	-0.148	0.911
04	-0.911	0.1	0.077	0.345
05	-2.498	1.305	-2.498	-1.923
06	-2.87	1.252	-4.0	-0.85
07	0.016	-2.498	-3.126	1.05
08	-0.977	-3.47	-2.87	1.263
09	1.009	-2.353	-1.923	0.016
10	-1.501	-2.353	-4.0	1.298
11	0.542	-2.498	-2.498	0.75
12	-0.611	-2.667	-1.761	1.168
13	-1.249	-2.667	1.27	-2.498
14	-2.353	-3.126	1.298	-1.623
15	-0.565	0.586	-0.133	-0.274
16	0.21	0.641	-1.56	-0.419
17	0.926	-1.923	-0.764	-0.148

Standard thresholds

P-value	Threshold
0.001	3.29491
0.0005	4.38036
0.0001	6.65796