Dataset mE1_TFBS_HSA

General Information
Name	mE1_TFBS_HSA	Species	D. melanogaster
Dataset type	genomic sequence feature	FlyBase ID	FBlc0000258
Source & Content
Consists of	Genomic sequences identified by integrative analysis of several ChIP data sets. (The modENCODE Consortium, 2010)
Created by
Available from
Strain
Stage & tissue
Stage Tissue/Position (including subcellular localization) Reference embryonic stage (Negre et al., 2011) Comment:TF binding profiles used in this analysis were assayed at early embryo stages.
Cell Line
Recent Updates
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FB2013_03
FB2013_02
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Description & Members
Description	Genomic sequences identified as unique regions of transcription factor (TF) binding using HOT spot analysis (HSA); one or many TFs may bind in a given region. A synthesis of ChIP data sets for 41 different transcription factors. (The modENCODE Consortium, 2010)
Parent collections
Component collection(s)	mE1_TFBS_bab1 BDTNP1_TFBS_bcd mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_cnc mE1_TFBS_D BDTNP1_TFBS_da mE1_TFBS_disco BDTNP1_TFBS_dl mE1_TFBS_Dll mE1_TFBS_en mE1_TFBS_eve BDTNP1_TFBS_ftz mE1_TFBS_ftz-f1 mE1_TFBS_GATAe BDTNP1_TFBS_gt mE1_TFBS_h BDTNP1_TFBS_hb mE1_TFBS_hkb mE1_TFBS_inv mE1_TFBS_jumu mE1_TFBS_kn BDTNP1_TFBS_kni mE1_TFBS_Kr BDTNP1_TFBS_Mad BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_run mE1_TFBS_sbb mE1_TFBS_sens BDTNP1_TFBS_shn BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna mE1_TFBS_Stat92E BDTNP1_TFBS_tll mE1_TFBS_Trl mE1_TFBS_ttk BDTNP1_TFBS_twi mE1_TFBS_Ubx BDTNP1_TFBS_z mE1_TFBS_zfh1
Number in collection
Comment on number in collection
Members
Experimental protocol
Vector
Sample preparation	See component collections for details. (The modENCODE Consortium, 2010)
Collection preparation	See component collections for details. (The modENCODE Consortium, 2010)
Mode of assay	ChIP-chip (The modENCODE Consortium, 2010)
Assay platform	See component collections for details. (The modENCODE Consortium, 2010)
Data analysis	To investigate the co-localization of transcription factors, modENCODE ChIP-chip data sets for 25 factors were integrated with ChIP-chip data sets for an 16 additional factors produced by the Berkeley Drosophila Transcription Network Project (BDTNP, FBrf0192397, FBrf0205197, FBrf0205197). Data sets generated for the same factor were merged and the union was used for further analysis. Highly occupied target (HOT) regions were identified using a Gaussian kernel density estimation across the genome with a bandwidth of 300 bp, using the centers of each of the TF binding peaks as points. The density was then scanned for peaks, and each peak was denoted a HOT region. To determine the complexity of the HOT region, the sum of the Gaussian kernalized distance from the peak to each transcription factor that contributed at least 0.1 to peak's strength was calculated. The reported window around each HOT peak was derived by finding the maximum distance (in bp) from the HOT peak to a contributing TF, and then adding 150 bp (one half of the bandwidth). Each window is centered on the HOT peak. In those analyses in this paper which required a complexity cutoff, those binding sites with TFBS complexity more than 8 were defined as HOT regions. (The modENCODE Consortium, 2010)
Additional data

Associated files
Additional sites
Comments
	HOT regions are primarily associated with open chromatin but they do not always demarcate cis-regulatory elements. (Nègre et al., 2011) Binding profiles of 41 TFs in early embryo development were used to assign a TF complexity score to each of 38,562 distinct TF binding sites, corresponding to the number of distinct TFs bound (from 1 to ~21). Of these distinct TF binding sites, a subset of 1,962 hot regions (hotspots) had a TF complexity of eight or greater, corresponding to ~10 overlapping factors bound. (modENCODE Consortium et al., 2010) HOT spots of increasing TF complexity were strongly correlated to regions of decreased nucleosome density and increased nucleosome turnover. (modENCODE Consortium et al., 2010) This data set is available at http://www.modencode.org/publications/integrative_fly_2010/. (The modENCODE Consortium, 2010)
Synonyms & Secondary IDs
Reported As
Symbol Synonym	combined TFBS (Negre et al., 2011) HOT regions analysis (The modENCODE Consortium, 2010) HOT spot analysis (The modENCODE Consortium, 2010) mE1_TFBS_HSA mE_Transcription_Factor_Binding_Site_Complexity unique binding sites (Nègre et al., 2011) unique TFBSs (The modENCODE Consortium, 2010, Ma, 2011.6.8)
Secondary FlyBase IDs

References ( 7 )
Research paper	Nègre et al., 2011, Nature 471(7339): 527--531 A cis-regulatory map of the Drosophila genome. [FBrf0213303] modENCODE Consortium et al., 2010, Science 330(6012): 1787--1797 Identification of functional elements and regulatory circuits by Drosophila modENCODE. [FBrf0212741]
Supplementary material	Negre et al., 2011, Nature 471(7339): Supplementary Information. [FBrf0213507] The modENCODE Consortium, 2010, Science 330(6012): Supporting Online Material for Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE. [FBrf0213506] The modENCODE Consortium, 2010, Science 330(6012): DataS8: HOT regions. [FBrf0213505] The modENCODE Consortium, 2010, Science 330(6012): DataS7: Predicted TFBS. [FBrf0213603]
Personal communication to FlyBase	Ma, 2011.6.8, HOT spots analysis (Data Set S8) and 41 TFBS GFF files (Data Set S7). HOT spots analysis (Data Set S8) and 41 TFBS GFF files (Data Set S7). [FBrf0213928]