PKNX1.H12INVIVO.2.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PKNX1.H12INVIVO.2.SM.B
Gene (human)	PKNOX1 (GeneCards)
Gene synonyms (human)	PREP1
Gene (mouse)	Pknox1
Gene synonyms (mouse)	Prep1
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	B

Motif length	10
Consensus	bTGACAKbbv
GC content	54.26%
Information content (bits; total / per base)	9.452 / 0.945
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	2377

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	5 (35)	0.689	0.777	0.531	0.614	0.663	0.754	1.711	2.085	120.854	208.602
Mouse	5 (35)	0.671	0.726	0.504	0.568	0.68	0.724	1.828	2.086	103.509	197.602

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.873	0.855	0.762	0.758	0.66	0.671
Overall, 6 experiments	best	0.987	0.983	0.956	0.939	0.88	0.863
Methyl HT-SELEX, 2 experiments	median	0.847	0.821	0.756	0.743	0.658	0.664
Methyl HT-SELEX, 2 experiments	best	0.96	0.94	0.894	0.87	0.765	0.761
Non-Methyl HT-SELEX, 4 experiments	median	0.883	0.868	0.791	0.791	0.697	0.709
Non-Methyl HT-SELEX, 4 experiments	best	0.987	0.983	0.956	0.939	0.88	0.863

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.183	9.358	0.192	0.139

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	TALE-type HD {3.1.4} (TFClass)
TF subfamily	PKNOX {3.1.4.5} (TFClass)
TFClass ID	TFClass: 3.1.4.5.1
HGNC	HGNC:9022
MGI	MGI:1201409
EntrezGene (human)	GeneID:5316 (SSTAR profile)
EntrezGene (mouse)	GeneID:18771 (SSTAR profile)
UniProt ID (human)	PKNX1_HUMAN
UniProt ID (mouse)	PKNX1_MOUSE
UniProt AC (human)	P55347 (TFClass)
UniProt AC (mouse)	O70477 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	5 human, 5 mouse
HT-SELEX	4
Methyl-HT-SELEX	2

PCM	PKNX1.H12INVIVO.2.SM.B.pcm
PWM	PKNX1.H12INVIVO.2.SM.B.pwm
PFM	PKNX1.H12INVIVO.2.SM.B.pfm
Alignment	PKNX1.H12INVIVO.2.SM.B.words.tsv
Threshold to P-value map	PKNX1.H12INVIVO.2.SM.B.thr
Motif in other formats
JASPAR format	PKNX1.H12INVIVO.2.SM.B_jaspar_format.txt
MEME format	PKNX1.H12INVIVO.2.SM.B_meme_format.meme
Transfac format	PKNX1.H12INVIVO.2.SM.B_transfac_format.txt
Homer format	PKNX1.H12INVIVO.2.SM.B_homer_format_0.001.txt PKNX1.H12INVIVO.2.SM.B_homer_format_0.0005.txt PKNX1.H12INVIVO.2.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	415.25	437.25	945.25	579.25
02	25.0	289.0	118.0	1945.0
03	18.0	0.0	2337.0	22.0
04	2337.0	0.0	39.0	1.0
05	33.0	2275.0	63.0	6.0
06	2271.0	3.0	92.0	11.0
07	101.0	355.0	1557.0	364.0
08	288.0	719.0	1076.0	294.0
09	336.75	461.75	542.75	1035.75
10	424.75	432.75	1155.75	363.75

PFM

	A	C	G	T
01	0.175	0.184	0.398	0.244
02	0.011	0.122	0.05	0.818
03	0.008	0.0	0.983	0.009
04	0.983	0.0	0.016	0.0
05	0.014	0.957	0.027	0.003
06	0.955	0.001	0.039	0.005
07	0.042	0.149	0.655	0.153
08	0.121	0.302	0.453	0.124
09	0.142	0.194	0.228	0.436
10	0.179	0.182	0.486	0.153

PWM

	A	C	G	T
01	-0.357	-0.306	0.463	-0.025
02	-3.097	-0.717	-1.604	1.183
03	-3.398	-5.726	1.367	-3.215
04	1.367	-5.726	-2.678	-5.311
05	-2.837	1.34	-2.217	-4.318
06	1.338	-4.793	-1.848	-3.83
07	-1.756	-0.513	0.961	-0.488
08	-0.721	0.19	0.592	-0.7
09	-0.565	-0.251	-0.09	0.554
10	-0.334	-0.316	0.664	-0.489

Standard thresholds

P-value	Threshold
0.001	4.99589
0.0005	5.91989
0.0001	7.499935