CDX2.H12RSNP.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CDX2.H12RSNP.0.PS.A
Gene (human)	CDX2 (GeneCards)
Gene synonyms (human)	CDX3
Gene (mouse)	Cdx2
Gene synonyms (mouse)	Cdx-2
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	dTTTATKRYhbb
GC content	33.89%
Information content (bits; total / per base)	10.398 / 0.866
Data sources	ChIP-Seq + HT-SELEX
Aligned words	1002

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	10 (61)	0.831	0.975	0.702	0.951	0.827	0.973	2.767	4.838	104.337	252.42
Mouse	21 (117)	0.878	0.977	0.825	0.958	0.868	0.968	3.248	4.807	148.387	367.018

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.79	0.746	0.693	0.667	0.619	0.612
Overall, 4 experiments	best	0.84	0.783	0.764	0.717	0.678	0.655
Methyl HT-SELEX, 1 experiments	median	0.815	0.749	0.748	0.695	0.674	0.643
Methyl HT-SELEX, 1 experiments	best	0.815	0.749	0.748	0.695	0.674	0.643
Non-Methyl HT-SELEX, 3 experiments	median	0.765	0.743	0.637	0.639	0.565	0.581
Non-Methyl HT-SELEX, 3 experiments	best	0.84	0.783	0.764	0.717	0.678	0.655

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	8.191	6.095	0.326	0.224

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	HOX-related {3.1.1} (TFClass)
TF subfamily	CDX {3.1.1.9} (TFClass)
TFClass ID	TFClass: 3.1.1.9.2
HGNC	HGNC:1806
MGI	MGI:88361
EntrezGene (human)	GeneID:1045 (SSTAR profile)
EntrezGene (mouse)	GeneID:12591 (SSTAR profile)
UniProt ID (human)	CDX2_HUMAN
UniProt ID (mouse)	CDX2_MOUSE
UniProt AC (human)	Q99626 (TFClass)
UniProt AC (mouse)	P43241 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	10 human, 21 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	CDX2.H12RSNP.0.PS.A.pcm
PWM	CDX2.H12RSNP.0.PS.A.pwm
PFM	CDX2.H12RSNP.0.PS.A.pfm
Alignment	CDX2.H12RSNP.0.PS.A.words.tsv
Threshold to P-value map	CDX2.H12RSNP.0.PS.A.thr
Motif in other formats
JASPAR format	CDX2.H12RSNP.0.PS.A_jaspar_format.txt
MEME format	CDX2.H12RSNP.0.PS.A_meme_format.meme
Transfac format	CDX2.H12RSNP.0.PS.A_transfac_format.txt
Homer format	CDX2.H12RSNP.0.PS.A_homer_format_0.001.txt CDX2.H12RSNP.0.PS.A_homer_format_0.0005.txt CDX2.H12RSNP.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	184.0	129.0	211.0	478.0
02	20.0	12.0	17.0	953.0
03	13.0	18.0	5.0	966.0
04	39.0	28.0	123.0	812.0
05	978.0	11.0	10.0	3.0
06	2.0	75.0	8.0	917.0
07	83.0	10.0	441.0	468.0
08	329.0	78.0	583.0	12.0
09	28.0	695.0	118.0	161.0
10	217.0	395.0	80.0	310.0
11	137.0	338.0	174.0	353.0
12	73.0	314.0	202.0	413.0

PFM

	A	C	G	T
01	0.184	0.129	0.211	0.477
02	0.02	0.012	0.017	0.951
03	0.013	0.018	0.005	0.964
04	0.039	0.028	0.123	0.81
05	0.976	0.011	0.01	0.003
06	0.002	0.075	0.008	0.915
07	0.083	0.01	0.44	0.467
08	0.328	0.078	0.582	0.012
09	0.028	0.694	0.118	0.161
10	0.217	0.394	0.08	0.309
11	0.137	0.337	0.174	0.352
12	0.073	0.313	0.202	0.412

PWM

	A	C	G	T
01	-0.306	-0.657	-0.17	0.643
02	-2.452	-2.911	-2.6	1.331
03	-2.841	-2.548	-3.624	1.345
04	-1.823	-2.138	-0.704	1.171
05	1.357	-2.987	-3.068	-3.977
06	-4.215	-1.19	-3.255	1.293
07	-1.091	-3.068	0.563	0.622
08	0.271	-1.152	0.841	-2.911
09	-2.138	1.016	-0.745	-0.438
10	-0.143	0.453	-1.127	0.212
11	-0.598	0.298	-0.361	0.341
12	-1.216	0.225	-0.214	0.497

Standard thresholds

P-value	Threshold
0.001	4.63166
0.0005	5.54267
0.0001	7.412525