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

Database: dm6 Primary Table: L3_H3K27me3_macs Data last updated: 2016-01-26
Big Bed File: /gbdb/dm6/bbi/dm6_H3K27me3.gappedPeak.bb
Item Count: 8,441
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`	15687479	Pseudogene alignment start position
`chromEnd`	15688057	Pseudogene alignment end position
`name`	dm6_H3K27me3_peak_1126	Name of pseudogene
`score`	121	Score of pseudogene with gene (0-1000)
`strand`	.	+ or - or . for unknown
`thickStart`	15687479	Start of where display should be thick (start codon)
`thickEnd`	15688057	End of where display should be thick (stop codon)
`reserved`	0	Always zero for now
`blockCount`	3	Number of blocks
`blockSizes`	1,73,1	Comma separated list of block sizes
`chromStarts`	0,504,577	Start positions relative to chromStart
`signalValue`	3.75019	Measurement of average enrichment for the region
`pValue`	14.03178	Statistical significance of signal value (-log10). Set to -1 if not used.
`qValue`	12.14800	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	15687479	15688057	dm6_H3K27me3_peak_1126	121	.	15687479	15688057	3	1,73,1	0,504,577	3.75019	14.03178	12.14800
chr2L	15839656	15839771	dm6_H3K27me3_peak_1127	140	.	15839656	15839771	2	1,1	0,114	4.18203	16.07011	14.08857
chr2L	15901860	15902133	dm6_H3K27me3_peak_1128	119	.	15901860	15902133	2	1,1	0,272	3.72278	13.85866	11.98494
chr2L	15921282	15921361	dm6_H3K27me3_peak_1129	128	.	15921282	15921361	2	1,1	0,78	3.85748	14.77527	12.86044
chr2L	16233918	16234005	dm6_H3K27me3_peak_1130	133	.	16233918	16234005	2	1,1	0,86	4.04306	15.32299	13.38365
chr2L	16357753	16357923	dm6_H3K27me3_peak_1131	118	.	16357753	16357923	2	1,1	0,169	3.72662	13.65487	11.80831
chr2L	16358998	16359425	dm6_H3K27me3_peak_1132	143	.	16358998	16359425	4	1,231,121,1	0,11,299,426	4.26720	16.34644	14.35524
chr2L	16360302	16360521	dm6_H3K27me3_peak_1133	113	.	16360302	16360521	2	1,1	0,218	3.62614	13.11664	11.30402
chr2L	16361563	16361979	dm6_H3K27me3_peak_1134	133	.	16361563	16361979	3	1,135,1	0,277,415	4.07186	15.25319	13.31285
chr2L	16362602	16362682	dm6_H3K27me3_peak_1135	161	.	16362602	16362682	2	1,1	0,79	4.56209	18.27955	16.19261

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