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What's new

newNormalized gene expression values - the Percent Max or pmax scale

As of DroID v2014_01, DroID includes normalized gene expression values that can be used to filter interaciton data, as described in Murali et al. 2014 (PMID: 24913703). Based on FlyAtlas gene expression data, a gene is expressed in a particular tissue at some percentage of its maximal level across all tissues. In DroID, each gene has a 'percent maximum' or pmax value for each tissue. Likewise, based on modENCODE RNA-seq data, a gene is expressed at a particular developmental time point at some percentage of its maximal level across all time points. Thus, in DroID each gene also has a pmax value for each developmental time point. Filtering interactome data using the pmax values can reveal gene and protein networks that are likely to operate in specific tissues or developmental time points.

Gene expression correlation values updated

As of DroID v2013_02, gene expresion correlation values are calculated based on developmental expresison profiles from modENCODE and tissue expression profiles from FlyAtlas. Both expression data sets can also be used to filter interaction data (see below). The Weighted Correlation valus for each gene pair provides a measure of how fequently the two genes are expressed together across tissues or develomental time. The Weighted Correlation values can be displayed and used to filter lists of gene or protein interactions.

DroID CytoscapePlugin update - version 1.5

The new version (1.5) is compatible with Cytoscape 2.8.2 and provides access to the newer DroID interaction tables (e.g., see below). Available Apri 2012. Download the plugin here.

DPIM co-affinity prufication complex data

Protein interactions determined in large-scale co-affinity purification (co-AP)/MS screens by the Drosophila Protein Interaction Mapping (DPIM) project, a collaboration among the laboratories of Spyros Artavanis-Tsakonsa, Steven Gygi , Susan Celniker, and K. VijayRaghavan (DPIM web site). See DroID database description page for more details.

Functional Genomics of RTK/Ras/ERK Signaling

Protein interaction data and RNAi phenotype data from the Perrimon Lab (Friedman et al., Science Signaling 25 October 2011). Co-affinity purification and MS was used to create a dynamic protein interaction map centered on 15 conserved canonical components of the receptor tyrosine kinase and Ras/ERK signaling pathways under baseline conditions and after insulin or EGF treatment. Genome-wide RNAi screens were also conducted under similar conditions. The interaction network and RNAi data cab be simultaneously searched, visualized, filtered, and combined with other DroID data using a new beta version of IM Browser.

Gene expression data from modENCODE and FlyAtlas

With DroID v2011_02, interaction data can now be searched or filtered using RNA-Seq data from modENCODE or microarray data from FlyAtlas. The quantitative RNA-Seq data is from 30 developmental time points while the FlyAtlas data is from ~25 tissues. See the database description page for more info.

Phenotype and gene expression data from Flybase

With DroID v2011_02, interaction data can also be searched and filtered using phenotype data and RNA and protein expression data. The data are from Flybase and use controlled vocabularies. See the database description page for more info.

Transcription factor - Gene interactions

First added in DroID v2010_08, TF-Gene interactions now include data from REDFly and modENCODE. See the database description page for more info.

miRNA - Gene interactions

First added in DroID v2010_08, miRNA-Gene interactions now include predictions from TargetScanFly, MinoTar, and modENCODE .See the database description page for more info.

 

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