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Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset
TLDR
A best-route combination of analysis methods is presented that allows detection of approximately 70% of true positives before reaching a 10% false-discovery rate, and highlights areas in need of improvement, including better estimate of false-Discovery rates and decreased false-negative rates.
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila
TLDR
The third major release of the REDfly database of Drosophila transcriptional cis-regulatory elements extends the utility of REDfly as a powerful tool for both computational and experimental studies of transcription regulation.
REDfly: a Regulatory Element Database for Drosophila
TLDR
A database of Drosophila CRMs curated from the literature complete with both DNA sequence and a searchable description of the gene expression pattern regulated by each CRM is presented.
ORegAnno: an open-access community-driven resource for regulatory annotation
TLDR
The current release of ORegAnno comprises 30 145 records curated from 922 publications and describing regulatory sequences for over 3853 genes and 465 transcription factors from 19 species.
New fluorescent protein reporters for use with the drosophila gal4 expression system and for vital detection of balancer chromosomes
TLDR
A set of dicistronic GFP and YFP reporters constructed for use with the GAL4/UAS expression system are described, which, as a result of their containing two copies of the respective fluorescent protein gene, are significantly brighter and thus more easily and rapidly detectable than currently available UAS-GFP fly stocks.
REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila
TLDR
A one-stop portal for Drosophila cis-regulatory data that will serve as a powerful resource for both computational and experimental studies of transcriptional regulation and enhanced functionality made possible through this integration of TFBS data into REDfly.
An Integrated Strategy for Analyzing the Unique Developmental Programs of Different Myoblast Subtypes
TLDR
An integrated genetic, genomic, and computational strategy is used to comprehensively determine the molecular identities of distinct myoblast subpopulations within the Drosophila embryonic mesoderm at the time that cell fates are initially specified.
Reciprocal regulatory interactions between the Notch and Ras signaling pathways in the Drosophila embryonic mesoderm.
TLDR
The findings reveal that Ras and Notch do not function independently; rather, several modes of cross-talk between these pathways are uncovered, including Ras-mediated upregulation of proximal components of both the epidermal and fibroblast growth factor receptor pathways.
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