Schema for Basal Transcription Factors ChIP-Seq - Basal Transcription Factors ChIP-Seq

Database: dm6 Primary Table: TBP_517_macs Row Count: 13,514 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	832	`int(10) unsigned`	range
`chromEnd`	907	`int(10) unsigned`	range
`name`	dm6_SRR1023762_macs_peak_1	`varchar(255)`	values
`score`	57	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.52047	`float`	range
`pValue`	7.85228	`float`	range
`qValue`	5.71366	`float`	range
`peak`	33	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	832	907	dm6_SRR1023762_macs_peak_1	57	.	3.52047	7.85228	5.71366	33
585	chr2L	1271	1345	dm6_SRR1023762_macs_peak_2	75	.	3.96053	9.81582	7.58575	39
585	chr2L	3108	3185	dm6_SRR1023762_macs_peak_3	82	.	4.10721	10.5021	8.24098	35
585	chr2L	18387	18632	dm6_SRR1023762_macs_peak_4	74	.	3.7402	9.71343	7.49634	160
585	chr2L	21221	21461	dm6_SRR1023762_macs_peak_5	98	.	4.29046	12.2072	9.88513	158
585	chr2L	27225	27351	dm6_SRR1023762_macs_peak_6	29	.	2.78704	4.93576	2.98879	83
585	chr2L	47995	48087	dm6_SRR1023762_macs_peak_7	23	.	2.4087	4.23964	2.37785	40
585	chr2L	66877	67046	dm6_SRR1023762_macs_peak_8a	40	.	3.08041	6.04456	4.01074	33
585	chr2L	66877	67046	dm6_SRR1023762_macs_peak_8b	40	.	3.08041	6.04456	4.01074	143
585	chr2L	87347	87482	dm6_SRR1023762_macs_peak_9	34	.	2.93372	5.47996	3.48735	41

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Basal Transcription Factors ChIP-Seq (TFChIPSeq) Track Description

Description

These tracks show the results of the ChIP-Seq analyses of transcription factors that are associated with the core promoter. The peak calls and the log likelihood ratio evidence tracks were produced by MACS.

The ChIP-Seq datasets were obtained from the Gene Expression Omnibus database at NCBI under the following accession numbers:

Accession	Transcription Factors	Reference
GSE46630	M1BP	Li J and Gilmour DS, EMBO J. 2013
GSE40646	GAF, GAF-KD	Fuda NJ et al., PLoS Genet. 2015
GSE38594	GAF (Embryos)	Oh H et al., Cell Rep. 2013
GSE50374	GAF (Embryos; modENCODE)	modENCODE
GSE52029	TBP, TRF2	Wang YL et al., Genes Dev. 2014

Credits

Fuda NJ, Guertin MJ, Sharma S, Danko CG, Martins AL, Siepel A, Lis JT. GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters. PLoS Genet. 2015 Mar 27;11(3):e1005108.

Oh H, Slattery M, Ma L, Crofts A, White KP, Mann RS, Irvine KD. Genome-wide association of Yorkie with chromatin and chromatin-remodeling complexes. Cell Rep. 2013 Feb 21;3(2):309-18.

Landt SG, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep;22(9):1813-31.

Li J, Gilmour DS. Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor. EMBO J. 2013 Jul 3;32(13):1829-41.

Wang YL, Duttke SH, Chen K, Johnston J, Kassavetis GA, Zeitlinger J, Kadonaga JT. TRF2, but not TBP, mediates the transcription of ribosomal protein genes. Genes Dev. 2014 Jul 15;28(14):1550-5.

Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.