SIX2.H12INVIVO.2.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SIX2.H12INVIVO.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	11
Consensus	nhvYGATACvn
GC content	49.87%
Information content (bits; total / per base)	9.037 / 0.822
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	2431

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)	0.634	0.664	0.455	0.495	0.586	0.615	1.323	1.418	24.577	35.62
Mouse	8 (52)	0.639	0.669	0.46	0.504	0.586	0.616	1.321	1.465	37.234	51.398

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.887	0.832	0.834	0.78	0.766	0.722
Overall, 4 experiments	best	0.914	0.869	0.86	0.813	0.78	0.745
Methyl HT-SELEX, 2 experiments	median	0.901	0.851	0.851	0.799	0.777	0.737
Methyl HT-SELEX, 2 experiments	best	0.914	0.869	0.86	0.813	0.78	0.745
Non-Methyl HT-SELEX, 2 experiments	median	0.88	0.825	0.826	0.772	0.754	0.714
Non-Methyl HT-SELEX, 2 experiments	best	0.887	0.831	0.827	0.775	0.76	0.715

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	1.561	0.262	0.266	0.029

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.667	0.299	0.494	0.358

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.H12INVIVO.2.SM.B.pcm
PWM	SIX2.H12INVIVO.2.SM.B.pwm
PFM	SIX2.H12INVIVO.2.SM.B.pfm
Alignment	SIX2.H12INVIVO.2.SM.B.words.tsv
Threshold to P-value map	SIX2.H12INVIVO.2.SM.B.thr
Motif in other formats
JASPAR format	SIX2.H12INVIVO.2.SM.B_jaspar_format.txt
MEME format	SIX2.H12INVIVO.2.SM.B_meme_format.meme
Transfac format	SIX2.H12INVIVO.2.SM.B_transfac_format.txt
Homer format	SIX2.H12INVIVO.2.SM.B_homer_format_0.001.txt SIX2.H12INVIVO.2.SM.B_homer_format_0.0005.txt SIX2.H12INVIVO.2.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	782.25	486.25	478.25	684.25
02	594.25	1008.25	411.25	417.25
03	693.0	424.0	931.0	383.0
04	46.0	1138.0	265.0	982.0
05	3.0	56.0	2372.0	0.0
06	1944.0	8.0	1.0	478.0
07	27.0	69.0	0.0	2335.0
08	2348.0	83.0	0.0	0.0
09	25.0	2106.0	136.0	164.0
10	210.75	1062.75	1009.75	147.75
11	403.5	802.5	488.5	736.5

PFM

	A	C	G	T
01	0.322	0.2	0.197	0.281
02	0.244	0.415	0.169	0.172
03	0.285	0.174	0.383	0.158
04	0.019	0.468	0.109	0.404
05	0.001	0.023	0.976	0.0
06	0.8	0.003	0.0	0.197
07	0.011	0.028	0.0	0.961
08	0.966	0.034	0.0	0.0
09	0.01	0.866	0.056	0.067
10	0.087	0.437	0.415	0.061
11	0.166	0.33	0.201	0.303

PWM

	A	C	G	T
01	0.252	-0.222	-0.239	0.118
02	-0.022	0.505	-0.389	-0.375
03	0.131	-0.359	0.425	-0.46
04	-2.543	0.626	-0.826	0.479
05	-4.814	-2.353	1.359	-5.746
06	1.161	-4.115	-5.331	-0.239
07	-3.047	-2.151	-5.746	1.344
08	1.349	-1.971	-5.746	-5.746
09	-3.119	1.241	-1.486	-1.301
10	-1.053	0.557	0.506	-1.404
11	-0.408	0.277	-0.218	0.192

Standard thresholds

P-value	Threshold
0.001	5.08725
0.0005	5.970165
0.0001	7.50814