CDX1.H12INVITRO.1.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	CDX1.H12INVITRO.1.S.B
Gene (human)	CDX1 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Cdx1
Gene synonyms (mouse)	Cdx-1
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	14
Consensus	nnnTTTATKGSnnn
GC content	38.26%
Information content (bits; total / per base)	11.792 / 0.842
Data sources	HT-SELEX
Aligned words	7909

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.978	0.964	0.947	0.927	0.876	0.855
Overall, 6 experiments	best	0.996	0.993	0.994	0.99	0.975	0.97
Methyl HT-SELEX, 2 experiments	median	0.983	0.973	0.958	0.943	0.902	0.884
Methyl HT-SELEX, 2 experiments	best	0.991	0.984	0.984	0.975	0.949	0.934
Non-Methyl HT-SELEX, 4 experiments	median	0.978	0.964	0.928	0.912	0.814	0.814
Non-Methyl HT-SELEX, 4 experiments	best	0.996	0.993	0.994	0.99	0.975	0.97

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.961	0.751	0.894	0.621
batch 2	0.85	0.753	0.835	0.573

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: 3.1.1.9.1
HGNC	HGNC:1805
MGI	MGI:88360
EntrezGene (human)	GeneID:1044 (SSTAR profile)
EntrezGene (mouse)	GeneID:12590 (SSTAR profile)
UniProt ID (human)	CDX1_HUMAN
UniProt ID (mouse)	CDX1_MOUSE
UniProt AC (human)	P47902 (TFClass)
UniProt AC (mouse)	P18111 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	4
Methyl-HT-SELEX	2

PCM	CDX1.H12INVITRO.1.S.B.pcm
PWM	CDX1.H12INVITRO.1.S.B.pwm
PFM	CDX1.H12INVITRO.1.S.B.pfm
Alignment	CDX1.H12INVITRO.1.S.B.words.tsv
Threshold to P-value map	CDX1.H12INVITRO.1.S.B.thr
Motif in other formats
JASPAR format	CDX1.H12INVITRO.1.S.B_jaspar_format.txt
MEME format	CDX1.H12INVITRO.1.S.B_meme_format.meme
Transfac format	CDX1.H12INVITRO.1.S.B_transfac_format.txt
Homer format	CDX1.H12INVITRO.1.S.B_homer_format_0.001.txt CDX1.H12INVITRO.1.S.B_homer_format_0.0005.txt CDX1.H12INVITRO.1.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1993.75	1908.75	1900.75	2105.75
02	2028.0	1843.0	2831.0	1207.0
03	1408.0	1547.0	2558.0	2396.0
04	211.0	100.0	247.0	7351.0
05	4.0	8.0	0.0	7897.0
06	660.0	0.0	25.0	7224.0
07	7909.0	0.0	0.0	0.0
08	0.0	125.0	0.0	7784.0
09	29.0	9.0	3981.0	3890.0
10	3219.0	6.0	4684.0	0.0
11	252.0	5241.0	1291.0	1125.0
12	1402.0	2572.0	2392.0	1543.0
13	1140.25	2631.25	2384.25	1753.25
14	1420.0	2094.0	1990.0	2405.0

PFM

	A	C	G	T
01	0.252	0.241	0.24	0.266
02	0.256	0.233	0.358	0.153
03	0.178	0.196	0.323	0.303
04	0.027	0.013	0.031	0.929
05	0.001	0.001	0.0	0.998
06	0.083	0.0	0.003	0.913
07	1.0	0.0	0.0	0.0
08	0.0	0.016	0.0	0.984
09	0.004	0.001	0.503	0.492
10	0.407	0.001	0.592	0.0
11	0.032	0.663	0.163	0.142
12	0.177	0.325	0.302	0.195
13	0.144	0.333	0.301	0.222
14	0.18	0.265	0.252	0.304

PWM

	A	C	G	T
01	0.008	-0.035	-0.039	0.063
02	0.025	-0.07	0.359	-0.493
03	-0.339	-0.245	0.257	0.192
04	-2.228	-2.963	-2.072	1.312
05	-5.759	-5.264	-6.782	1.384
06	-1.095	-6.782	-4.286	1.295
07	1.385	-6.782	-6.782	-6.782
08	-6.782	-2.744	-6.782	1.37
09	-4.149	-5.171	0.699	0.676
10	0.487	-5.481	0.862	-6.782
11	-2.052	0.974	-0.426	-0.563
12	-0.343	0.263	0.19	-0.248
13	-0.55	0.285	0.187	-0.12
14	-0.331	0.057	0.006	0.196

Standard thresholds

P-value	Threshold
0.001	3.66361
0.0005	5.04191
0.0001	7.73666