CDX2.H12INVITRO.1.M.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CDX2.H12INVITRO.1.M.C
Gene (human)	CDX2 (GeneCards)
Gene synonyms (human)	CDX3
Gene (mouse)	Cdx2
Gene synonyms (mouse)	Cdx-2
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	C

Motif length	10
Consensus	ndTTACGRbn
GC content	38.51%
Information content (bits; total / per base)	8.873 / 0.887
Data sources	Methyl-HT-SELEX
Aligned words	2358

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)	0.752	0.9	0.598	0.811	0.686	0.848	1.704	2.928	47.409	115.481
Mouse	21 (117)	0.79	0.896	0.659	0.802	0.707	0.829	1.892	2.4	70.0	164.509

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.716	0.668	0.666	0.627	0.621	0.595
Overall, 4 experiments	best	0.847	0.792	0.784	0.732	0.722	0.681
Methyl HT-SELEX, 1 experiments	median	0.847	0.792	0.784	0.732	0.722	0.681
Methyl HT-SELEX, 1 experiments	best	0.847	0.792	0.784	0.732	0.722	0.681
Non-Methyl HT-SELEX, 3 experiments	median	0.642	0.602	0.599	0.572	0.565	0.551
Non-Methyl HT-SELEX, 3 experiments	best	0.79	0.733	0.733	0.682	0.677	0.639

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	2.288	1.415	0.131	0.079

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.H12INVITRO.1.M.C.pcm
PWM	CDX2.H12INVITRO.1.M.C.pwm
PFM	CDX2.H12INVITRO.1.M.C.pfm
Alignment	CDX2.H12INVITRO.1.M.C.words.tsv
Threshold to P-value map	CDX2.H12INVITRO.1.M.C.thr
Motif in other formats
JASPAR format	CDX2.H12INVITRO.1.M.C_jaspar_format.txt
MEME format	CDX2.H12INVITRO.1.M.C_meme_format.meme
Transfac format	CDX2.H12INVITRO.1.M.C_transfac_format.txt
Homer format	CDX2.H12INVITRO.1.M.C_homer_format_0.001.txt CDX2.H12INVITRO.1.M.C_homer_format_0.0005.txt CDX2.H12INVITRO.1.M.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	653.75	650.75	659.75	393.75
02	539.5	139.5	373.5	1305.5
03	72.0	28.0	55.0	2203.0
04	382.0	2.0	0.0	1974.0
05	2354.0	0.0	4.0	0.0
06	0.0	1855.0	10.0	493.0
07	19.0	27.0	2180.0	132.0
08	1586.0	254.0	340.0	178.0
09	178.75	765.75	416.75	996.75
10	594.5	639.5	679.5	444.5

PFM

	A	C	G	T
01	0.277	0.276	0.28	0.167
02	0.229	0.059	0.158	0.554
03	0.031	0.012	0.023	0.934
04	0.162	0.001	0.0	0.837
05	0.998	0.0	0.002	0.0
06	0.0	0.787	0.004	0.209
07	0.008	0.011	0.925	0.056
08	0.673	0.108	0.144	0.075
09	0.076	0.325	0.177	0.423
10	0.252	0.271	0.288	0.189

PWM

	A	C	G	T
01	0.103	0.099	0.112	-0.402
02	-0.088	-1.431	-0.454	0.793
03	-2.079	-2.983	-2.341	1.316
04	-0.432	-5.011	-5.719	1.206
05	1.382	-5.719	-4.601	-5.719
06	-5.719	1.144	-3.903	-0.178
07	-3.341	-3.017	1.305	-1.485
08	0.988	-0.838	-0.548	-1.19
09	-1.186	0.261	-0.345	0.524
10	0.008	0.081	0.142	-0.281

Standard thresholds

P-value	Threshold
0.001	5.18485
0.0005	5.948105
0.0001	7.311355