NCVAR

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-	Specificity of TF-binding sites and the DNase sites files downloaded from the UCSC genome browser	+	Supplemental Data Related to:
-	'''TF motif''' '''track''' '''group''' '''cell line''' '''link'''	+	Mu et al. [http://papers.gersteinlab.org/papers/ncvar "Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project,"] NAR (2011)
-	CTCF Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksGm12878CtcfV3.narrowPeak.gz download]	+
-	STAT1 Yale TFBS Regulation Hela-S3 (IFNr 30min) [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3ifngStat1.narrowPeak.gz download]	+
-	NFkB Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa.narrowPeak.gz download]	+
-	c-Myc Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CmycV2.narrowPeak.gz download]	+
-	c-Fos Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CfosV2.narrowPeak.gz download]	+
-	c-Jun Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CjunV2.narrowPeak.gz download]	+
-	JunD Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562JundV2.narrowPeak.gz download]	+
-	PolII	+
-	DNase	+
-	Gene 874 0.87 6.96E-09 0.89	+	Specifications for TF-binding sites and DNase sites files downloaded from the UCSC genome browser
-	CDS 4 0.04 3.47E-24 0.04	+
-	5'UTR Only 92 0.95 3.11E-01 0.95	+	'''TF motif''' '''track''' '''group''' '''cell line''' '''link'''
-	3'UTR Only 10 0.46 6.16E-03 0.50	+	DNase Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksGm12878V3.narrowPeak.gz wgEncodeDukeDNaseSeqPeaksGm12878V3]
-	Intron Only 653 0.99 3.57E-01 1.02	+	CTCF Open Chromatin Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksGm12878CtcfV3.narrowPeak.gz wgEncodeUtaChIPseqPeaksGm12878CtcfV3]
-	Whole CDS(s) 0 0.00 1.24E-14 0.00	+	STAT1 Yale TFBS Regulation Hela-S3 (IFNr 30min) [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksHelas3ifngStat1.narrowPeak.gz wgEncodeYaleChIPseqPeaksHelas3ifngStat1]
-	Partial CDS(s) 4 0.09 1.17E-10 0.09	+	NFkB Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa]
-	Whole Gene(s) 0 0.00 2.34E-01 0.00	+	c-Myc Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CmycV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CmycV2]
-	Partial Gene(s) 874 0.87 7.75E-09 0.89	+	c-Fos Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CfosV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CfosV2]
-	Single whole gene 0 0.00 2.37E-01 0.00	+	c-Jun Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562CjunV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562CjunV2]
-	Multiple whole genes 0 0.00 4.56E-01 0.00	+	JunD Yale TFBS Regulation K562 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksK562JundV2.narrowPeak.gz wgEncodeYaleChIPseqPeaksK562JundV2]
-	2 whole genes 0 0.00 4.58E-01 0.00	+	PolII Yale TFBS Regulation GM12878 [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/wgEncodeYaleChIPseqPeaksGm12878Pol2V2.narrowPeak.gz wgEncodeYaleChIPseqPeaksGm12878Pol2V2]
-	3 whole genes 0 0.00 4.89E-01 0.00	+

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Latest revision as of 02:13, 11 September 2011

Supplemental Data Related to:

Mu et al. "Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project," NAR (2011)

Specifications for TF-binding sites and DNase sites files downloaded from the UCSC genome browser

TF motif	track			group		cell line			link
DNase		Open Chromatin		Regulation	GM12878				wgEncodeDukeDNaseSeqPeaksGm12878V3
CTCF		Open Chromatin		Regulation	GM12878				wgEncodeUtaChIPseqPeaksGm12878CtcfV3
STAT1		Yale TFBS		Regulation	Hela-S3 (IFNr 30min)		wgEncodeYaleChIPseqPeaksHelas3ifngStat1
NFkB		Yale TFBS		Regulation	GM12878				wgEncodeYaleChIPseqPeaksGm12878NfkbTnfa
c-Myc		Yale TFBS		Regulation	K562				wgEncodeYaleChIPseqPeaksK562CmycV2
c-Fos		Yale TFBS		Regulation	K562				wgEncodeYaleChIPseqPeaksK562CfosV2
c-Jun		Yale TFBS		Regulation	K562				wgEncodeYaleChIPseqPeaksK562CjunV2
JunD		Yale TFBS		Regulation	K562				wgEncodeYaleChIPseqPeaksK562JundV2
PolII		Yale TFBS		Regulation	GM12878				wgEncodeYaleChIPseqPeaksGm12878Pol2V2