SIX2.H12INVITRO.2.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SIX2.H12INVITRO.2.SM.B
Gene (human)	SIX2 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Six2
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	B

Motif length	9
Consensus	nbGATACvn
GC content	48.47%
Information content (bits; total / per base)	8.307 / 0.923
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9559

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 (34)	0.625	0.651	0.436	0.473	0.58	0.605	1.266	1.334	25.296	35.553
Mouse	8 (52)	0.619	0.649	0.436	0.487	0.571	0.607	1.249	1.39	31.747	47.071

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.891	0.842	0.836	0.785	0.769	0.724
Overall, 4 experiments	best	0.921	0.881	0.869	0.825	0.789	0.755
Methyl HT-SELEX, 2 experiments	median	0.903	0.858	0.854	0.805	0.782	0.742
Methyl HT-SELEX, 2 experiments	best	0.921	0.881	0.869	0.825	0.789	0.755
Non-Methyl HT-SELEX, 2 experiments	median	0.885	0.833	0.828	0.777	0.758	0.718
Non-Methyl HT-SELEX, 2 experiments	best	0.896	0.85	0.833	0.786	0.763	0.719

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	1.059	-0.0	0.342	0.109

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.681	0.31	0.54	0.409

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	HD-SINE {3.1.6} (TFClass)
TF subfamily	SIX1-like {3.1.6.1} (TFClass)
TFClass ID	TFClass: 3.1.6.1.2
HGNC	HGNC:10888
MGI	MGI:102778
EntrezGene (human)	GeneID:10736 (SSTAR profile)
EntrezGene (mouse)	GeneID:20472 (SSTAR profile)
UniProt ID (human)	SIX2_HUMAN
UniProt ID (mouse)	SIX2_MOUSE
UniProt AC (human)	Q9NPC8 (TFClass)
UniProt AC (mouse)	Q62232 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	5 human, 8 mouse
HT-SELEX	2
Methyl-HT-SELEX	2

PCM	SIX2.H12INVITRO.2.SM.B.pcm
PWM	SIX2.H12INVITRO.2.SM.B.pwm
PFM	SIX2.H12INVITRO.2.SM.B.pfm
Alignment	SIX2.H12INVITRO.2.SM.B.words.tsv
Threshold to P-value map	SIX2.H12INVITRO.2.SM.B.thr
Motif in other formats
JASPAR format	SIX2.H12INVITRO.2.SM.B_jaspar_format.txt
MEME format	SIX2.H12INVITRO.2.SM.B_meme_format.meme
Transfac format	SIX2.H12INVITRO.2.SM.B_transfac_format.txt
Homer format	SIX2.H12INVITRO.2.SM.B_homer_format_0.001.txt SIX2.H12INVITRO.2.SM.B_homer_format_0.0005.txt SIX2.H12INVITRO.2.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2726.0	1920.0	3162.0	1751.0
02	414.5	4170.5	1120.5	3853.5
03	106.0	150.0	9291.0	12.0
04	7539.0	0.0	0.0	2020.0
05	97.0	496.0	0.0	8966.0
06	9263.0	296.0	0.0	0.0
07	44.0	7761.0	627.0	1127.0
08	1102.75	3630.75	3989.75	835.75
09	1627.25	2892.25	2195.25	2844.25

PFM

	A	C	G	T
01	0.285	0.201	0.331	0.183
02	0.043	0.436	0.117	0.403
03	0.011	0.016	0.972	0.001
04	0.789	0.0	0.0	0.211
05	0.01	0.052	0.0	0.938
06	0.969	0.031	0.0	0.0
07	0.005	0.812	0.066	0.118
08	0.115	0.38	0.417	0.087
09	0.17	0.303	0.23	0.298

PWM

	A	C	G	T
01	0.132	-0.219	0.28	-0.311
02	-1.747	0.556	-0.756	0.477
03	-3.095	-2.754	1.357	-5.12
04	1.148	-6.951	-6.951	-0.168
05	-3.182	-1.569	-6.951	1.322
06	1.354	-2.082	-6.951	-6.951
07	-3.945	1.177	-1.335	-0.751
08	-0.772	0.418	0.512	-1.049
09	-0.384	0.191	-0.085	0.174

Standard thresholds

P-value	Threshold
0.001	5.310345
0.0005	6.00888
0.0001	7.314695