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

Database: dm6 Primary Table: TRF2_274_macs Row Count: 12,158 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	3571	`int(10) unsigned`	range
`chromEnd`	3635	`int(10) unsigned`	range
`name`	dm6_SRR1023764_macs_peak_1	`varchar(255)`	values
`score`	87	`int(10) unsigned`	range
`strand`	.	`char(1)`	values
`signalValue`	4.35094	`float`	range
`pValue`	11.1688	`float`	range
`qValue`	8.76965	`float`	range
`peak`	37	`int(11)`	range

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	signalValue	pValue	qValue	peak
585	chr2L	3571	3635	dm6_SRR1023764_macs_peak_1	87	.	4.35094	11.1688	8.76965	37
585	chr2L	4948	5008	dm6_SRR1023764_macs_peak_2	85	.	4.27051	10.9511	8.56556	29
585	chr2L	18485	18592	dm6_SRR1023764_macs_peak_3	54	.	3.57399	7.75264	5.48168	45
585	chr2L	21300	21378	dm6_SRR1023764_macs_peak_4	48	.	3.4186	7.12081	4.87948	26
585	chr2L	87334	87430	dm6_SRR1023764_macs_peak_5	87	.	4.35094	11.1688	8.76965	58
586	chr2L	158900	159119	dm6_SRR1023764_macs_peak_6	151	.	5.58474	17.7574	15.1531	87
586	chr2L	221935	222037	dm6_SRR1023764_macs_peak_7	21	.	2.58123	4.11914	2.10857	10
587	chr2L	277493	277627	dm6_SRR1023764_macs_peak_8	74	.	3.86079	9.8058	7.45384	91
587	chr2L	295055	295201	dm6_SRR1023764_macs_peak_9	100	.	4.58926	12.4453	10.0117	86
588	chr2L	419898	419979	dm6_SRR1023764_macs_peak_10	43	.	3.20224	6.56382	4.35312	52

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.