PKNX1.H12INVITRO.1.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PKNX1.H12INVITRO.1.P.B
Gene (human)	PKNOX1 (GeneCards)
Gene synonyms (human)	PREP1
Gene (mouse)	Pknox1
Gene synonyms (mouse)	Prep1
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	10
Consensus	dRRbWGRMWK
GC content	49.83%
Information content (bits; total / per base)	7.795 / 0.779
Data sources	ChIP-Seq
Aligned words	990

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)	0.822	0.855	0.732	0.786	0.825	0.856	3.21	3.646	258.569	435.432
Mouse	5 (35)	0.819	0.84	0.724	0.767	0.839	0.86	3.443	3.665	291.018	442.0

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.748	0.706	0.674	0.646	0.614	0.601
Overall, 6 experiments	best	0.923	0.885	0.873	0.829	0.793	0.76
Methyl HT-SELEX, 2 experiments	median	0.714	0.68	0.652	0.629	0.6	0.589
Methyl HT-SELEX, 2 experiments	best	0.846	0.796	0.761	0.72	0.678	0.657
Non-Methyl HT-SELEX, 4 experiments	median	0.778	0.739	0.715	0.685	0.651	0.635
Non-Methyl HT-SELEX, 4 experiments	best	0.923	0.885	0.873	0.829	0.793	0.76

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	7.034	21.181	0.249	0.177

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.H12INVITRO.1.P.B.pcm
PWM	PKNX1.H12INVITRO.1.P.B.pwm
PFM	PKNX1.H12INVITRO.1.P.B.pfm
Alignment	PKNX1.H12INVITRO.1.P.B.words.tsv
Threshold to P-value map	PKNX1.H12INVITRO.1.P.B.thr
Motif in other formats
JASPAR format	PKNX1.H12INVITRO.1.P.B_jaspar_format.txt
MEME format	PKNX1.H12INVITRO.1.P.B_meme_format.meme
Transfac format	PKNX1.H12INVITRO.1.P.B_transfac_format.txt
Homer format	PKNX1.H12INVITRO.1.P.B_homer_format_0.001.txt PKNX1.H12INVITRO.1.P.B_homer_format_0.0005.txt PKNX1.H12INVITRO.1.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	252.0	44.0	163.0	531.0
02	141.0	131.0	678.0	40.0
03	758.0	45.0	107.0	80.0
04	96.0	201.0	456.0	237.0
05	145.0	17.0	108.0	720.0
06	9.0	4.0	967.0	10.0
07	656.0	11.0	285.0	38.0
08	91.0	765.0	55.0	79.0
09	724.0	2.0	124.0	140.0
10	52.0	158.0	612.0	168.0

PFM

	A	C	G	T
01	0.255	0.044	0.165	0.536
02	0.142	0.132	0.685	0.04
03	0.766	0.045	0.108	0.081
04	0.097	0.203	0.461	0.239
05	0.146	0.017	0.109	0.727
06	0.009	0.004	0.977	0.01
07	0.663	0.011	0.288	0.038
08	0.092	0.773	0.056	0.08
09	0.731	0.002	0.125	0.141
10	0.053	0.16	0.618	0.17

PWM

	A	C	G	T
01	0.018	-1.696	-0.414	0.76
02	-0.557	-0.63	1.003	-1.787
03	1.115	-1.674	-0.83	-1.115
04	-0.936	-0.207	0.608	-0.043
05	-0.53	-2.589	-0.82	1.063
06	-3.146	-3.774	1.358	-3.057
07	0.97	-2.975	0.14	-1.836
08	-0.989	1.124	-1.48	-1.127
09	1.069	-4.203	-0.684	-0.564
10	-1.534	-0.445	0.901	-0.384

Standard thresholds

P-value	Threshold
0.001	5.022235
0.0005	5.64808
0.0001	7.030885