PPARD.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PPARD.H12INVITRO.0.PSM.A
Gene (human)	PPARD (GeneCards)
Gene synonyms (human)	NR1C2, PPARB
Gene (mouse)	Ppard
Gene synonyms (mouse)	Nr1c2, Pparb
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	17
Consensus	nRRGGTSAAAGGTCRnv
GC content	54.39%
Information content (bits; total / per base)	15.942 / 0.938
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9828

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
Mouse	2 (12)	0.797	0.819	0.664	0.698	0.795	0.818	2.618	2.773	111.189	148.187

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.973	0.973	0.791	0.805	0.664	0.69
Overall, 2 experiments	best	0.991	0.99	0.819	0.83	0.689	0.71
Methyl HT-SELEX, 1 experiments	median	0.991	0.99	0.819	0.83	0.689	0.71
Methyl HT-SELEX, 1 experiments	best	0.991	0.99	0.819	0.83	0.689	0.71
Non-Methyl HT-SELEX, 1 experiments	median	0.954	0.956	0.763	0.779	0.639	0.669
Non-Methyl HT-SELEX, 1 experiments	best	0.954	0.956	0.763	0.779	0.639	0.669

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	Nuclear receptors with C4 zinc fingers {2.1} (TFClass)
TF family	Thyroid hormone receptor-related {2.1.2} (TFClass)
TF subfamily	PPAR (NR1C) {2.1.2.5} (TFClass)
TFClass ID	TFClass: 2.1.2.5.2
HGNC	HGNC:9235
MGI	MGI:101884
EntrezGene (human)	GeneID:5467 (SSTAR profile)
EntrezGene (mouse)	GeneID:19015 (SSTAR profile)
UniProt ID (human)	PPARD_HUMAN
UniProt ID (mouse)	PPARD_MOUSE
UniProt AC (human)	Q03181 (TFClass)
UniProt AC (mouse)	P35396 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 2 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	PPARD.H12INVITRO.0.PSM.A.pcm
PWM	PPARD.H12INVITRO.0.PSM.A.pwm
PFM	PPARD.H12INVITRO.0.PSM.A.pfm
Alignment	PPARD.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	PPARD.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	PPARD.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	PPARD.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	PPARD.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	PPARD.H12INVITRO.0.PSM.A_homer_format_0.001.txt PPARD.H12INVITRO.0.PSM.A_homer_format_0.0005.txt PPARD.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3165.75	1742.75	2774.75	2144.75
02	2642.75	751.75	5555.75	877.75
03	3837.0	368.0	5296.0	327.0
04	331.0	370.0	8747.0	380.0
05	374.0	350.0	8103.0	1001.0
06	396.0	412.0	1120.0	7900.0
07	337.0	6794.0	1534.0	1163.0
08	7898.0	223.0	1439.0	268.0
09	7824.0	138.0	1473.0	393.0
10	8613.0	32.0	1077.0	106.0
11	26.0	22.0	9745.0	35.0
12	44.0	34.0	9276.0	474.0
13	77.0	59.0	620.0	9072.0
14	201.0	7877.0	939.0	811.0
15	6319.0	101.0	3288.0	120.0
16	2659.0	2615.0	1952.0	2602.0
17	2338.0	1548.0	4493.0	1449.0

PFM

	A	C	G	T
01	0.322	0.177	0.282	0.218
02	0.269	0.076	0.565	0.089
03	0.39	0.037	0.539	0.033
04	0.034	0.038	0.89	0.039
05	0.038	0.036	0.824	0.102
06	0.04	0.042	0.114	0.804
07	0.034	0.691	0.156	0.118
08	0.804	0.023	0.146	0.027
09	0.796	0.014	0.15	0.04
10	0.876	0.003	0.11	0.011
11	0.003	0.002	0.992	0.004
12	0.004	0.003	0.944	0.048
13	0.008	0.006	0.063	0.923
14	0.02	0.801	0.096	0.083
15	0.643	0.01	0.335	0.012
16	0.271	0.266	0.199	0.265
17	0.238	0.158	0.457	0.147

PWM

	A	C	G	T
01	0.253	-0.343	0.122	-0.136
02	0.073	-1.182	0.815	-1.028
03	0.445	-1.893	0.768	-2.011
04	-1.999	-1.888	1.269	-1.861
05	-1.877	-1.943	1.193	-0.897
06	-1.82	-1.781	-0.784	1.167
07	-1.981	1.017	-0.471	-0.747
08	1.167	-2.39	-0.534	-2.208
09	1.158	-2.864	-0.511	-1.828
10	1.254	-4.273	-0.824	-3.123
11	-4.465	-4.617	1.377	-4.189
12	-3.973	-4.216	1.328	-1.642
13	-3.434	-3.692	-1.374	1.306
14	-2.493	1.164	-0.96	-1.107
15	0.944	-3.17	0.291	-3.001
16	0.079	0.062	-0.23	0.057
17	-0.05	-0.461	0.603	-0.527

Standard thresholds

P-value	Threshold
0.001	2.55971
0.0005	3.76351
0.0001	6.27811