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FlyFactorSurvey specifications

Information


Unique identifier OMICS_01879
Name FlyFactorSurvey
Restrictions to use None
Database management system MySQL
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/FlyFactorSurvey

Taxon


  • Invertebrates
    • Drosophila melanogaster

Maintainer


  • person_outline Michael H. Brodsky

Publication for FlyFactorSurvey

FlyFactorSurvey citations

 (7)
library_books

Cooption of heat shock regulatory system for anhydrobiosis in the sleeping chironomid Polypedilum vanderplanki

2018
Proc Natl Acad Sci U S A
PMCID: 5877948
PMID: 29463761
DOI: 10.1073/pnas.1719493115

[…] up-regulated genes overlap and form a near-palindromic motif TCTAGAA that closely resembles the binding motif of the D. melanogaster heat shock transcription factor Dmel\Hsf [TOMTOM () search in the FlyFactorSurvey database (); P < 0.0004]. We also found that one of the remaining hexamers, GTTGGC, is similar (P < 0.0001) to the binding motif of D. melanogaster zinc finger protein Dmel\CG4854. Unl […]

library_books

Evolution and multiple roles of the Pancrustacea specific transcription factor zelda in insects

2017
PLoS Genet
PMCID: 5515446
PMID: 28671979
DOI: 10.1371/journal.pgen.1006868

[…] erformed using the DREME software [], part of the MEME suite software toolkit []. The motif with highest identity with Dm-Zld binding site (CAGGTAY) was compared to previously described motifs in the FlyFactorSurvey [] database with TOMTOM. Further, this motif was used to scan 2000 bp upstream of all predicted T. castaneum genes with FIMO [, , ]. Upstream regions and orthology information were ret […]

library_books

Genome wide identification of Drosophila dorso ventral enhancers by differential histone acetylation analysis

2016
Genome Biol
PMCID: 5037609
PMID: 27678375
DOI: 10.1186/s13059-016-1057-2

[…] ltered to include only those where the corresponding transcription factor is expressed in either gd7 or Tl10b (mRNA-seq FPKM greater than 3). Motifs derived from daughterless (da) heterodimers in the FlyFactorSurvey database [] were also excluded. The genomic locations of all remaining motifs were obtained using FIMO [], part of the MEME Suite v4.10.1 [], with the following parameters:fimo --text […]

library_books

Pervasive Variation of Transcription Factor Orthologs Contributes to Regulatory Network Evolution

2015
PLoS Genet
PMCID: 4351887
PMID: 25748510
DOI: 10.1371/journal.pgen.1005011

[…] We initially obtained binding specificity motifs, represented as PWMs, for 62 D. melanogaster poly-ZF genes from the FlyFactorSurvey, JASPAR, and public Transfac databases. There are 96 binding specificity motifs for these 62 genes, as different isoforms or subsets of binding domains may correspond to distinct motif […]

library_books

Coordinated repression and activation of two transcriptional programs stabilizes cell fate during myogenesis

2014
PMCID: 4146391
PMID: 24961800
DOI: 10.1242/dev.101956

[…] ing 200 bp repeat-masked regions centered on the ChIP peak. TOMTOM () was used (default parameters, but AT/GC content was set to 0.3/0.2) to match discovered motifs to known Drosophila PWM databases (FlyFactorSurvey, FlyRegv2, idmmpmm2009 and dmmpmm2009) with P-value ≤0.05. […]

library_books

Computational Identification of Diverse Mechanisms Underlying Transcription Factor DNA Occupancy

2013
PLoS Genet
PMCID: 3731213
PMID: 23935523
DOI: 10.1371/journal.pgen.1003571

[…] e liftOver tool and chain files from the UCSC web site (http://hgdownload.cse.ucsc.edu/downloads.html). We used 614 Drosophila transcription factor motifs, corresponding to 322 distinct TFs, from the FlyFactorSurvey database . The motifs were ranked based on expression of the associated TF gene, using RNA-SEQ data for the appropriate developmental stage. In cases where a TF-ChIP data set correspo […]

Citations

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FlyFactorSurvey institution(s)
Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA

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