KDM2A.H13INVITRO.0.PSGB.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	KDM2A.H13INVITRO.0.PSGB.A
Gene (human)	KDM2A (GeneCards)
Gene synonyms (human)	CXXC8, FBL11, FBL7, FBXL11, JHDM1A, KIAA1004
Gene (mouse)	Kdm2a
Gene synonyms (mouse)	Fbl11, Fbxl11, Jhdm1a, Kiaa1004
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	9
Consensus	nhTdCGYdn
GC content	52.29%
Information content (bits; total / per base)	6.744 / 0.749
Data sources	ChIP-Seq + HT-SELEX + Genomic HT-SELEX + PBM
Aligned words	797
Previous names

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	Centrality, median	Centrality, best
Overall	2 (4)	0.637	0.646	0.418	0.433	0.423	0.458	0.0	0.131

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
overall, 2 experiments	median	0.814	0.773	0.777	0.738	0.734	0.703
overall, 2 experiments	best	0.949	0.918	0.92	0.882	0.877	0.836
Lysate, 1 experiments	median	0.949	0.918	0.92	0.882	0.877	0.836
Lysate, 1 experiments	best	0.949	0.918	0.92	0.882	0.877	0.836
GFPIVT, 1 experiments	median	0.678	0.627	0.634	0.595	0.592	0.57
GFPIVT, 1 experiments	best	0.678	0.627	0.634	0.595	0.592	0.57

Genomic HT-SELEX benchmarking		Centrality	pseudo-auROC	auROC	auPR
Lysate, 1 experiments	median	8.229	0.445	0.775	0.604
Lysate, 1 experiments	best	8.229	0.445	0.775	0.604

PBM benchmarking		auROC, QNZS	auPR, QNZS	auROC, SD	auPR, SD
Overall, 4 experiments	median	0.837	0.024	0.775	0.023
Overall, 4 experiments	best	0.846	0.031	0.871	0.026

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	CXXC zinc finger factors {2.6} (TFClass)
TF family	CpG-binding {2.6.1} (TFClass)
TF subfamily	{2.6.1.0} (TFClass)
TFClass ID	TFClass: 2.6.1.0.5
HGNC	HGNC:13606
MGI	MGI:1354736
EntrezGene (human)	GeneID:22992 (SSTAR profile)
EntrezGene (mouse)	GeneID:225876 (SSTAR profile)
UniProt ID (human)	KDM2A_HUMAN
UniProt ID (mouse)	KDM2A_MOUSE
UniProt AC (human)	Q9Y2K7 (TFClass)
UniProt AC (mouse)	P59997 (TFClass)
GRECO-DB-TF	no

ChIP-Seq	2 human, 0 mouse
HT-SELEX	2 overall: 1 Lysate, 0 IVT, 1 GFPIVT
Genomic HT-SELEX	1 overall: 1 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	4

PCM	KDM2A.H13INVITRO.0.PSGB.A.pcm
PWM	KDM2A.H13INVITRO.0.PSGB.A.pwm
PFM	KDM2A.H13INVITRO.0.PSGB.A.pfm
Threshold to P-value map	KDM2A.H13INVITRO.0.PSGB.A.thr
Motif in other formats
JASPAR format	KDM2A.H13INVITRO.0.PSGB.A_jaspar_format.txt
MEME format	KDM2A.H13INVITRO.0.PSGB.A_meme_format.meme
Transfac format	KDM2A.H13INVITRO.0.PSGB.A_transfac_format.txt
Homer format	KDM2A.H13INVITRO.0.PSGB.A_homer_format_0.001.txt KDM2A.H13INVITRO.0.PSGB.A_homer_format_0.0005.txt KDM2A.H13INVITRO.0.PSGB.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	253.0	125.0	196.0	223.0
02	199.0	127.0	76.0	395.0
03	170.0	0.0	19.0	608.0
04	336.0	139.0	166.0	156.0
05	0.0	797.0	0.0	0.0
06	2.0	0.0	795.0	0.0
07	4.0	415.0	1.0	377.0
08	168.0	75.0	424.0	130.0
09	186.0	252.0	144.0	215.0

PFM

	A	C	G	T
01	0.317	0.157	0.246	0.28
02	0.25	0.159	0.095	0.496
03	0.213	0.0	0.024	0.763
04	0.422	0.174	0.208	0.196
05	0.0	1.0	0.0	0.0
06	0.003	0.0	0.997	0.0
07	0.005	0.521	0.001	0.473
08	0.211	0.094	0.532	0.163
09	0.233	0.316	0.181	0.27

PWM

	A	C	G	T
01	0.237	-0.461	-0.016	0.112
02	-0.001	-0.446	-0.95	0.68
03	-0.157	-4.79	-2.274	1.11
04	0.519	-0.356	-0.181	-0.242
05	-4.79	1.38	-4.79	-4.79
06	-4.003	-4.79	1.378	-4.79
07	-3.568	0.729	-4.321	0.634
08	-0.169	-0.963	0.751	-0.423
09	-0.068	0.233	-0.322	0.075

Standard thresholds

P-value	Threshold
0.001	5.23932
0.0005	5.639085
0.0001	6.23312