MEIS2.H12RSNP.0.P.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	MEIS2.H12RSNP.0.P.C
Gene (human)	MEIS2 (GeneCards)
Gene synonyms (human)	MRG1
Gene (mouse)	Meis2
Gene synonyms (mouse)	Mrg1, Stra10
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	C

Motif length	10
Consensus	TGAbWdRYdd
GC content	35.33%
Information content (bits; total / per base)	7.959 / 0.796
Data sources	ChIP-Seq
Aligned words	873

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	1 (7)	0.777	0.826	0.684	0.718	0.751	0.809	2.429	2.828	258.959	313.523

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.745	0.662	0.716	0.647	0.66	0.616
Overall, 8 experiments	best	0.895	0.825	0.89	0.821	0.873	0.807
Methyl HT-SELEX, 2 experiments	median	0.745	0.662	0.716	0.647	0.66	0.616
Methyl HT-SELEX, 2 experiments	best	0.747	0.663	0.722	0.651	0.664	0.62
Non-Methyl HT-SELEX, 6 experiments	median	0.713	0.648	0.685	0.63	0.64	0.604
Non-Methyl HT-SELEX, 6 experiments	best	0.895	0.825	0.89	0.821	0.873	0.807

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	5.398	3.533	0.137	0.165

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.521	0.081	0.209	0.05

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	TALE-type HD {3.1.4} (TFClass)
TF subfamily	MEIS {3.1.4.2} (TFClass)
TFClass ID	TFClass: 3.1.4.2.2
HGNC	HGNC:7001
MGI	MGI:108564
EntrezGene (human)	GeneID:4212 (SSTAR profile)
EntrezGene (mouse)	GeneID:17536 (SSTAR profile)
UniProt ID (human)	MEIS2_HUMAN
UniProt ID (mouse)	MEIS2_MOUSE
UniProt AC (human)	O14770 (TFClass)
UniProt AC (mouse)	P97367 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 0 mouse
HT-SELEX	6
Methyl-HT-SELEX	2

PCM	MEIS2.H12RSNP.0.P.C.pcm
PWM	MEIS2.H12RSNP.0.P.C.pwm
PFM	MEIS2.H12RSNP.0.P.C.pfm
Alignment	MEIS2.H12RSNP.0.P.C.words.tsv
Threshold to P-value map	MEIS2.H12RSNP.0.P.C.thr
Motif in other formats
JASPAR format	MEIS2.H12RSNP.0.P.C_jaspar_format.txt
MEME format	MEIS2.H12RSNP.0.P.C_meme_format.meme
Transfac format	MEIS2.H12RSNP.0.P.C_transfac_format.txt
Homer format	MEIS2.H12RSNP.0.P.C_homer_format_0.001.txt MEIS2.H12RSNP.0.P.C_homer_format_0.0005.txt MEIS2.H12RSNP.0.P.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	75.0	1.0	15.0	782.0
02	18.0	2.0	844.0	9.0
03	805.0	28.0	26.0	14.0
04	38.0	257.0	118.0	460.0
05	298.0	16.0	80.0	479.0
06	156.0	72.0	354.0	291.0
07	691.0	69.0	85.0	28.0
08	79.0	152.0	51.0	591.0
09	187.0	37.0	425.0	224.0
10	255.0	77.0	375.0	166.0

PFM

	A	C	G	T
01	0.086	0.001	0.017	0.896
02	0.021	0.002	0.967	0.01
03	0.922	0.032	0.03	0.016
04	0.044	0.294	0.135	0.527
05	0.341	0.018	0.092	0.549
06	0.179	0.082	0.405	0.333
07	0.792	0.079	0.097	0.032
08	0.09	0.174	0.058	0.677
09	0.214	0.042	0.487	0.257
10	0.292	0.088	0.43	0.19

PWM

	A	C	G	T
01	-1.054	-4.403	-2.578	1.271
02	-2.413	-4.087	1.347	-3.024
03	1.3	-2.002	-2.072	-2.64
04	-1.712	0.162	-0.608	0.742
05	0.309	-2.52	-0.99	0.782
06	-0.333	-1.093	0.481	0.286
07	1.147	-1.135	-0.931	-2.002
08	-1.003	-0.358	-1.429	0.991
09	-0.153	-1.738	0.663	0.026
10	0.155	-1.028	0.538	-0.271

Standard thresholds

P-value	Threshold
0.001	5.08359
0.0005	5.78063
0.0001	7.10673