Schema for modENCODE Histones ChIP-Seq - modENCODE Chromatin State Mapping Using ChIP-Seq

Database: dm6 Primary Table: L3_H3K9me2_macs Data last updated: 2016-01-26
Big Bed File: /gbdb/dm6/bbi/dm6_H3K9me2.gappedPeak.bb
Item Count: 13,170
Format description: This format is used to provide called regions of signal enrichment based on pooled, normalized (interpreted) data where the regions may be spliced or incorporate gaps in the genomic sequence. It is a BED12+3 format.

field	example	description
`chrom`	chr2L	Reference sequence chromosome or scaffold
`chromStart`	15683894	Pseudogene alignment start position
`chromEnd`	15685220	Pseudogene alignment end position
`name`	dm6_H3K9me2_peak_536	Name of pseudogene
`score`	32	Score of pseudogene with gene (0-1000)
`strand`	.	+ or - or . for unknown
`thickStart`	15683894	Start of where display should be thick (start codon)
`thickEnd`	15685220	End of where display should be thick (stop codon)
`reserved`	0	Always zero for now
`blockCount`	6	Number of blocks
`blockSizes`	1,346,73,82,368,1	Comma separated list of block sizes
`chromStarts`	0,29,659,788,952,1325	Start positions relative to chromStart
`signalValue`	1.55607	Measurement of average enrichment for the region
`pValue`	4.06455	Statistical significance of signal value (-log10). Set to -1 if not used.
`qValue`	3.24792	Statistical significance with multiple-test correction applied (FDR). Set to -1 if not used.

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts	signalValue	pValue	qValue
chr2L	15683894	15685220	dm6_H3K9me2_peak_536	32	.	15683894	15685220	6	1,346,73,82,368,1	0,29,659,788,952,1325	1.55607	4.06455	3.24792
chr2L	15686319	15686654	dm6_H3K9me2_peak_537	11	.	15686319	15686654	2	330,1	0,334	1.22794	1.76662	1.19581
chr2L	15718892	15720181	dm6_H3K9me2_peak_538	14	.	15718892	15720181	6	1,158,131,298,318,1	0,3,253,574,962,1288	1.25761	2.04214	1.45450
chr2L	15720595	15720714	dm6_H3K9me2_peak_539	8	.	15720595	15720714	3	1,115,1	0,3,118	1.12274	1.36929	0.85359
chr2L	15721443	15721649	dm6_H3K9me2_peak_540	13	.	15721443	15721649	2	1,203	0,3	1.26026	1.89715	1.30730
chr2L	15723491	15724056	dm6_H3K9me2_peak_541	14	.	15723491	15724056	4	1,97,180,1	0,64,322,564	1.30666	2.04411	1.42458
chr2L	15726944	15727467	dm6_H3K9me2_peak_542	12	.	15726944	15727467	2	1,1	0,522	1.25264	1.86150	1.27783
chr2L	15751537	15751735	dm6_H3K9me2_peak_543	8	.	15751537	15751735	3	1,134,1	0,63,197	1.15649	1.39153	0.86190
chr2L	15779094	15779373	dm6_H3K9me2_peak_544	22	.	15779094	15779373	2	1,1	0,278	1.46800	2.92008	2.20169
chr2L	15780085	15780548	dm6_H3K9me2_peak_545	16	.	15780085	15780548	3	1,105,1	0,1,462	1.34724	2.28365	1.63618

modENCODE Histones ChIP-Seq (modENCODE_histones_chipseq) Track Description


	Description This track shows the results of the ChIP-Seq analysis of multiple histone modifications at different developmental stages using MACS. The ChIP-Seq data were produced as part of the modENCODE project. Credits Zhang Y et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. Ho JW et al. ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. BMC Genomics. 2011 Feb 28;12:134. The ChIP-Seq datasets are available at the NCBI GEO database under the accession number GSE16013.

Description

Credits