SRF.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SRF.H12INVITRO.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	14
Consensus	nbnCCWTRYWhGKn
GC content	48.36%
Information content (bits; total / per base)	11.453 / 0.818
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9963

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)	0.824	0.961	0.792	0.931	0.772	0.934	3.412	4.64	405.125	793.959
Mouse	19 (113)	0.893	0.963	0.858	0.928	0.851	0.952	3.794	5.148	226.658	614.854

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.667	0.695	0.568	0.595	0.531	0.553
Overall, 5 experiments	best	0.993	0.987	0.986	0.978	0.961	0.949
Methyl HT-SELEX, 1 experiments	median	0.993	0.987	0.986	0.978	0.961	0.949
Methyl HT-SELEX, 1 experiments	best	0.993	0.987	0.986	0.978	0.961	0.949
Non-Methyl HT-SELEX, 4 experiments	median	0.648	0.665	0.563	0.582	0.531	0.546
Non-Methyl HT-SELEX, 4 experiments	best	0.986	0.974	0.975	0.96	0.932	0.914

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.786	4.389	0.396	0.222

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.819	0.118	0.667	0.314

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.H12INVITRO.0.PSM.A.pcm
PWM	SRF.H12INVITRO.0.PSM.A.pwm
PFM	SRF.H12INVITRO.0.PSM.A.pfm
Alignment	SRF.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	SRF.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	SRF.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	SRF.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	SRF.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	SRF.H12INVITRO.0.PSM.A_homer_format_0.001.txt SRF.H12INVITRO.0.PSM.A_homer_format_0.0005.txt SRF.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2034.25	3108.25	1595.25	3225.25
02	663.75	2711.75	3774.75	2812.75
03	3214.0	1423.0	2965.0	2361.0
04	36.0	9909.0	14.0	4.0
05	1.0	9949.0	1.0	12.0
06	3922.0	206.0	175.0	5660.0
07	219.0	43.0	0.0	9701.0
08	6160.0	391.0	2363.0	1049.0
09	786.0	1868.0	212.0	7097.0
10	7548.0	215.0	692.0	1508.0
11	2043.0	2138.0	1162.0	4620.0
12	799.0	139.0	8918.0	107.0
13	499.75	786.75	7334.75	1341.75
14	2358.25	3178.25	2186.25	2240.25

PFM

	A	C	G	T
01	0.204	0.312	0.16	0.324
02	0.067	0.272	0.379	0.282
03	0.323	0.143	0.298	0.237
04	0.004	0.995	0.001	0.0
05	0.0	0.999	0.0	0.001
06	0.394	0.021	0.018	0.568
07	0.022	0.004	0.0	0.974
08	0.618	0.039	0.237	0.105
09	0.079	0.187	0.021	0.712
10	0.758	0.022	0.069	0.151
11	0.205	0.215	0.117	0.464
12	0.08	0.014	0.895	0.011
13	0.05	0.079	0.736	0.135
14	0.237	0.319	0.219	0.225

PWM

	A	C	G	T
01	-0.202	0.221	-0.445	0.258
02	-1.32	0.085	0.415	0.121
03	0.255	-0.559	0.174	-0.053
04	-4.176	1.38	-5.03	-5.98
05	-6.627	1.384	-6.627	-5.161
06	0.454	-2.482	-2.643	0.82
07	-2.422	-4.008	-6.988	1.359
08	0.905	-1.847	-0.053	-0.863
09	-1.151	-0.287	-2.454	1.046
10	1.108	-2.44	-1.278	-0.501
11	-0.198	-0.153	-0.761	0.617
12	-1.135	-2.87	1.275	-3.127
13	-1.603	-1.15	1.079	-0.618
14	-0.055	0.244	-0.13	-0.106

Standard thresholds

P-value	Threshold
0.001	4.28991
0.0005	5.35071
0.0001	7.38086