CDX4.H12INVITRO.0.S.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CDX4.H12INVITRO.0.S.C
Gene (human)	CDX4 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Cdx4
Gene synonyms (mouse)	Cdx-4
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	C

Motif length	14
Consensus	nSTTTTATGAChbb
GC content	39.72%
Information content (bits; total / per base)	16.141 / 1.153
Data sources	HT-SELEX
Aligned words	1601

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.975	0.965	0.914	0.908	0.827	0.838
Overall, 2 experiments	best	0.999	0.998	0.996	0.995	0.984	0.98
Methyl HT-SELEX, 1 experiments	median	0.951	0.933	0.832	0.82	0.671	0.697
Methyl HT-SELEX, 1 experiments	best	0.951	0.933	0.832	0.82	0.671	0.697
Non-Methyl HT-SELEX, 1 experiments	median	0.999	0.998	0.996	0.995	0.984	0.98
Non-Methyl HT-SELEX, 1 experiments	best	0.999	0.998	0.996	0.995	0.984	0.98

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.747	0.555	0.758	0.545

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: 3.1.1.9.3
HGNC	HGNC:1808
MGI	MGI:88362
EntrezGene (human)	GeneID:1046 (SSTAR profile)
EntrezGene (mouse)	GeneID:12592 (SSTAR profile)
UniProt ID (human)	CDX4_HUMAN
UniProt ID (mouse)	CDX4_MOUSE
UniProt AC (human)	O14627 (TFClass)
UniProt AC (mouse)	Q07424 (TFClass)
GRECO-DB-TF	yes

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

PCM	CDX4.H12INVITRO.0.S.C.pcm
PWM	CDX4.H12INVITRO.0.S.C.pwm
PFM	CDX4.H12INVITRO.0.S.C.pfm
Alignment	CDX4.H12INVITRO.0.S.C.words.tsv
Threshold to P-value map	CDX4.H12INVITRO.0.S.C.thr
Motif in other formats
JASPAR format	CDX4.H12INVITRO.0.S.C_jaspar_format.txt
MEME format	CDX4.H12INVITRO.0.S.C_meme_format.meme
Transfac format	CDX4.H12INVITRO.0.S.C_transfac_format.txt
Homer format	CDX4.H12INVITRO.0.S.C_homer_format_0.001.txt CDX4.H12INVITRO.0.S.C_homer_format_0.0005.txt CDX4.H12INVITRO.0.S.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	492.75	434.75	383.75	289.75
02	183.75	361.75	933.75	121.75
03	28.0	19.0	261.0	1293.0
04	0.0	0.0	0.0	1601.0
05	0.0	0.0	0.0	1601.0
06	0.0	0.0	0.0	1601.0
07	1601.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1601.0
09	0.0	0.0	1204.0	397.0
10	893.0	0.0	708.0	0.0
11	0.0	1533.0	8.0	60.0
12	299.0	840.0	213.0	249.0
13	153.25	826.25	328.25	293.25
14	204.5	534.5	314.5	547.5

PFM

	A	C	G	T
01	0.308	0.272	0.24	0.181
02	0.115	0.226	0.583	0.076
03	0.017	0.012	0.163	0.808
04	0.0	0.0	0.0	1.0
05	0.0	0.0	0.0	1.0
06	0.0	0.0	0.0	1.0
07	1.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.0	0.752	0.248
10	0.558	0.0	0.442	0.0
11	0.0	0.958	0.005	0.037
12	0.187	0.525	0.133	0.156
13	0.096	0.516	0.205	0.183
14	0.128	0.334	0.196	0.342

PWM

	A	C	G	T
01	0.207	0.082	-0.042	-0.321
02	-0.773	-0.101	0.844	-1.18
03	-2.601	-2.96	-0.425	1.169
04	-5.384	-5.384	-5.384	1.383
05	-5.384	-5.384	-5.384	1.383
06	-5.384	-5.384	-5.384	1.383
07	1.383	-5.384	-5.384	-5.384
08	-5.384	-5.384	-5.384	1.383
09	-5.384	-5.384	1.098	-0.008
10	0.8	-5.384	0.568	-5.384
11	-5.384	1.339	-3.71	-1.872
12	-0.29	0.739	-0.627	-0.472
13	-0.953	0.722	-0.197	-0.309
14	-0.667	0.288	-0.24	0.312

Standard thresholds

P-value	Threshold
0.001	0.16726
0.0005	2.04866
0.0001	5.241165