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

Database: dm6 Primary Table: TBP_518_macs Row Count: 10,398 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	586	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	158975	`int(10) unsigned`	range
`chromEnd`	159074	`int(10) unsigned`	range
`name`	dm6_SRR1023763_macs_peak_1	`varchar(255)`	values
`score`	43	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	3.39836	`float`	range
`pValue`	6.61681	`float`	range
`qValue`	4.36386	`float`	range
`peak`	29	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
586	chr2L	158975	159074	dm6_SRR1023763_macs_peak_1	43	.	3.39836	6.61681	4.36386	29
588	chr2L	523658	523810	dm6_SRR1023763_macs_peak_2	44	.	3.41705	6.66111	4.40676	30
590	chr2L	783901	783970	dm6_SRR1023763_macs_peak_3	24	.	2.84	4.54294	2.41428	16
591	chr2L	825858	825927	dm6_SRR1023763_macs_peak_4	36	.	3.19349	5.91646	3.69889	30
591	chr2L	850949	851066	dm6_SRR1023763_macs_peak_5	66	.	4.0825	9.01615	6.65635	72
591	chr2L	901480	901781	dm6_SRR1023763_macs_peak_6	339	.	8.96367	37.3353	33.9967	166
592	chr2L	922772	922840	dm6_SRR1023763_macs_peak_7	59	.	3.905	8.31596	5.98193	29
593	chr2L	1077707	1077854	dm6_SRR1023763_macs_peak_8a	32	.	3.08748	5.4679	3.28155	36
593	chr2L	1077707	1077854	dm6_SRR1023763_macs_peak_8b	32	.	3.0948	5.48468	3.29746	127
593	chr2L	1118904	1119176	dm6_SRR1023763_macs_peak_9	159	.	5.90394	18.6638	15.9952	109

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.