RFX5.H12INVITRO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RFX5.H12INVITRO.0.P.B
Gene (human)	RFX5 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Rfx5
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	18
Consensus	bvbbdGTYRCYRKGvvvv
GC content	55.62%
Information content (bits; total / per base)	11.355 / 0.631
Data sources	ChIP-Seq
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	6 (41)	0.873	0.933	0.818	0.908	0.852	0.917	3.992	5.05	258.301	498.222

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.99	0.983	0.935	0.93	0.825	0.836
Overall, 4 experiments	best	0.995	0.992	0.991	0.986	0.98	0.972
Methyl HT-SELEX, 1 experiments	median	0.988	0.979	0.977	0.965	0.945	0.928
Methyl HT-SELEX, 1 experiments	best	0.988	0.979	0.977	0.965	0.945	0.928
Non-Methyl HT-SELEX, 3 experiments	median	0.992	0.988	0.893	0.894	0.705	0.743
Non-Methyl HT-SELEX, 3 experiments	best	0.995	0.992	0.991	0.986	0.98	0.972

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.92	1.748	0.091	0.012

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.679	0.265	0.6	0.396

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Fork head/winged helix factors {3.3} (TFClass)
TF family	RFX {3.3.3} (TFClass)
TF subfamily	{3.3.3.0} (TFClass)
TFClass ID	TFClass: 3.3.3.0.5
HGNC	HGNC:9986
MGI	MGI:1858421
EntrezGene (human)	GeneID:5993 (SSTAR profile)
EntrezGene (mouse)	GeneID:53970 (SSTAR profile)
UniProt ID (human)	RFX5_HUMAN
UniProt ID (mouse)	RFX5_MOUSE
UniProt AC (human)	P48382 (TFClass)
UniProt AC (mouse)	Q9JL61 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	6 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	RFX5.H12INVITRO.0.P.B.pcm
PWM	RFX5.H12INVITRO.0.P.B.pwm
PFM	RFX5.H12INVITRO.0.P.B.pfm
Alignment	RFX5.H12INVITRO.0.P.B.words.tsv
Threshold to P-value map	RFX5.H12INVITRO.0.P.B.thr
Motif in other formats
JASPAR format	RFX5.H12INVITRO.0.P.B_jaspar_format.txt
MEME format	RFX5.H12INVITRO.0.P.B_meme_format.meme
Transfac format	RFX5.H12INVITRO.0.P.B_transfac_format.txt
Homer format	RFX5.H12INVITRO.0.P.B_homer_format_0.001.txt RFX5.H12INVITRO.0.P.B_homer_format_0.0005.txt RFX5.H12INVITRO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	127.0	583.0	156.0	134.0
02	491.0	197.0	186.0	126.0
03	98.0	276.0	347.0	279.0
04	57.0	541.0	133.0	269.0
05	242.0	89.0	233.0	436.0
06	51.0	15.0	924.0	10.0
07	22.0	56.0	29.0	893.0
08	63.0	176.0	29.0	732.0
09	184.0	26.0	681.0	109.0
10	12.0	891.0	29.0	68.0
11	15.0	485.0	21.0	479.0
12	679.0	27.0	251.0	43.0
13	147.0	29.0	598.0	226.0
14	43.0	44.0	878.0	35.0
15	137.0	322.0	430.0	111.0
16	489.0	189.0	227.0	95.0
17	332.0	114.0	471.0	83.0
18	528.0	155.0	174.0	143.0

PFM

	A	C	G	T
01	0.127	0.583	0.156	0.134
02	0.491	0.197	0.186	0.126
03	0.098	0.276	0.347	0.279
04	0.057	0.541	0.133	0.269
05	0.242	0.089	0.233	0.436
06	0.051	0.015	0.924	0.01
07	0.022	0.056	0.029	0.893
08	0.063	0.176	0.029	0.732
09	0.184	0.026	0.681	0.109
10	0.012	0.891	0.029	0.068
11	0.015	0.485	0.021	0.479
12	0.679	0.027	0.251	0.043
13	0.147	0.029	0.598	0.226
14	0.043	0.044	0.878	0.035
15	0.137	0.322	0.43	0.111
16	0.489	0.189	0.227	0.095
17	0.332	0.114	0.471	0.083
18	0.528	0.155	0.174	0.143

PWM

	A	C	G	T
01	-0.671	0.843	-0.467	-0.618
02	0.672	-0.236	-0.293	-0.678
03	-0.926	0.098	0.326	0.109
04	-1.455	0.768	-0.625	0.073
05	-0.032	-1.02	-0.07	0.553
06	-1.563	-2.711	1.302	-3.066
07	-2.362	-1.473	-2.103	1.268
08	-1.358	-0.348	-2.103	1.07
09	-0.304	-2.206	0.998	-0.821
10	-2.909	1.266	-2.103	-1.284
11	-2.711	0.659	-2.405	0.647
12	0.995	-2.171	0.004	-1.728
13	-0.526	-2.103	0.868	-0.1
14	-1.728	-1.706	1.251	-1.925
15	-0.596	0.252	0.539	-0.803
16	0.668	-0.278	-0.096	-0.956
17	0.282	-0.777	0.63	-1.089
18	0.744	-0.474	-0.359	-0.553

Standard thresholds

P-value	Threshold
0.001	4.40651
0.0005	5.28366
0.0001	7.11701