MEIS2.H12RSNP.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	MEIS2.H12RSNP.1.PSM.A
Gene (human)	MEIS2 (GeneCards)
Gene synonyms (human)	MRG1
Gene (mouse)	Meis2
Gene synonyms (mouse)	Mrg1, Stra10
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	9
Consensus	nTGACASbb
GC content	51.05%
Information content (bits; total / per base)	10.175 / 1.131
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	2129

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)	0.713	0.722	0.567	0.582	0.672	0.682	1.673	1.734	103.0	164.252

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.965	0.949	0.921	0.896	0.824	0.807
Overall, 8 experiments	best	0.998	0.997	0.995	0.992	0.989	0.984
Methyl HT-SELEX, 2 experiments	median	0.965	0.949	0.921	0.896	0.824	0.807
Methyl HT-SELEX, 2 experiments	best	0.974	0.962	0.933	0.913	0.828	0.813
Non-Methyl HT-SELEX, 6 experiments	median	0.937	0.91	0.882	0.856	0.785	0.775
Non-Methyl HT-SELEX, 6 experiments	best	0.998	0.997	0.995	0.992	0.989	0.984

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.824	2.559	0.184	0.184

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.726	0.372	0.46	0.232

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.1.PSM.A.pcm
PWM	MEIS2.H12RSNP.1.PSM.A.pwm
PFM	MEIS2.H12RSNP.1.PSM.A.pfm
Alignment	MEIS2.H12RSNP.1.PSM.A.words.tsv
Threshold to P-value map	MEIS2.H12RSNP.1.PSM.A.thr
Motif in other formats
JASPAR format	MEIS2.H12RSNP.1.PSM.A_jaspar_format.txt
MEME format	MEIS2.H12RSNP.1.PSM.A_meme_format.meme
Transfac format	MEIS2.H12RSNP.1.PSM.A_transfac_format.txt
Homer format	MEIS2.H12RSNP.1.PSM.A_homer_format_0.001.txt MEIS2.H12RSNP.1.PSM.A_homer_format_0.0005.txt MEIS2.H12RSNP.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	489.75	386.75	547.75	704.75
02	60.25	81.25	159.25	1828.25
03	22.0	4.0	2095.0	8.0
04	2126.0	0.0	3.0	0.0
05	0.0	2125.0	3.0	1.0
06	2108.0	0.0	21.0	0.0
07	54.0	252.0	1595.0	228.0
08	216.25	792.25	845.25	275.25
09	332.5	413.5	458.5	924.5

PFM

	A	C	G	T
01	0.23	0.182	0.257	0.331
02	0.028	0.038	0.075	0.859
03	0.01	0.002	0.984	0.004
04	0.999	0.0	0.001	0.0
05	0.0	0.998	0.001	0.0
06	0.99	0.0	0.01	0.0
07	0.025	0.118	0.749	0.107
08	0.102	0.372	0.397	0.129
09	0.156	0.194	0.215	0.434

PWM

	A	C	G	T
01	-0.083	-0.318	0.029	0.28
02	-2.151	-1.86	-1.198	1.231
03	-3.106	-4.503	1.368	-3.987
04	1.382	-5.631	-4.688	-5.631
05	-5.631	1.382	-4.688	-5.211
06	1.374	-5.631	-3.149	-5.631
07	-2.257	-0.744	1.095	-0.843
08	-0.895	0.397	0.461	-0.656
09	-0.468	-0.251	-0.149	0.551

Standard thresholds

P-value	Threshold
0.001	4.7791
0.0005	5.88924
0.0001	7.76604