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Data

This page lists all data sources loaded along with the date the data was downloaded and related publication. NOTE: All external links open in a new window.

Data Category Organism Data Source PubMed Note

Genes

Drosophila Genome annotation for D. melanogaster (R6.27), D. ananassae (R1.06), D. erecta (R1.05), D. grimshawi (R1.05), D. mojavensis (R1.04), D. persimilis (R1.3), D. pseudoobscura (R3.04), D. sechellia (R1.3), D. simulans (R2.02), D. virilis (R1.07), D. willistoni (R1.05) and D. yakuba (R1.05). Flybase - Version FB2019_02 Gramates et al - PubMed: 27799470 #1

Homology

Drosophila Orthologues and paralogues between the 12 Drosophila genomes. Flybase - Version FB2018_03 Gramates et al - PubMed: 27799470  

D. melanogaster

D. rerio

C. elegans

M. musculus

R. norvegicus

H. sapiens

S. cerevisiae

Orthologue and paralogue relationships between these organisms Treefam - release 9.0 Ruan et al - PubMed: 18056084  

D. melanogaster

D. rerio

C. elegans

M. musculus

R. norvegicus

H. sapiens

S. cerevisiae

Orthologue and paralogue relationships between these organisms Panther - 14.1 Mi et al - PubMed: 27899595  

Drosophila

C. elegans

H. sapiens

M. musculus

R. norvegicus

S. cerevisiae

Orthologue and paralogue relationships between these organisms Homologene - 9th April 2019 Agarwala et al - PubMed: 26615191  

Proteins

Drosophila

C. elegans

H. sapiens

M. musculus

R. norvegicus

S. cerevisiae

Protein annotation UniProt - Release 2019_02 UniProt Consortium - PubMed: 27899622  

D. melanogaster

A. gambiae

C. elegans

Protein family and domain assignments to proteins InterPro9th April 2019 Finn et al - PubMed: 27899635  

Interactions

Drosophila

C. elegans

S. cerevisiae

Molecular interaction datasets IntAct23rd March 2019 Orchard et al - PubMed:24234451  

D. melanogaster

S. cerevisiae

Interactions from the BioGRID BioGRID - Version 3.5.169 Chatr-Aryamontri et al - PubMed:27980099  
D. melanogaster miRNA target predictions from miRBase miRBase - Version 5 Enright et al - PubMed:14709173  

Gene Ontology

D. melanogaster GO annotations Gene Ontology Site - 9th April 2019 Gene Ontology Consortium - PubMed:10802651  
D. melanogaster InterPro domains to GO annotations InterPro (from Gene Ontology Site) - 9th April 2019 Gene Ontology Consortium - PubMed:10802651, Mulder et al - PubMed: 17202162  

Expression

D. melanogaster Microarray-based gene expression data for the life cycle of D. melanogaster ArrayExpress - Experiment E-FLYC-6 Arbeitman et al - PubMed: 12351791  
D. melanogaster Affymetrix microarray-based atlas of gene expression in larval and adult tissues FlyAtlas - 13th June 2011 Chintapalli et al - PubMed: 17534367  
D. melanogaster Expression patterns of mRNAs at the subcellular level during early embryogenesis Fly-FISH - 22nd July 2013 Lecuyer et al - PubMed: 17923096  
D. melanogaster Expression patterns of mRNAs during embryogenesis BDGP - Release 3.0 June 2018 Tomancak et al - PubMed:17645804  
D. melanogaster Genome-wide RNA_seq Expression Data: raw data produced by modENCODE analysed by FlyBase Flybase - Version FB2019_02 Gelbart and Emmert - 2010FlyBase Report  

Regulation

D. melanogaster Transcriptional cis-regulatory modules (CRMs) REDfly - 5.5.2 April 2019 Gallo et al - PubMed: 20965965  
D. melanogaster Transcription factor binding sites REDfly - 5.5.2 April 2019 Bergman et al - PubMed: 20965965  
D. melanogaster Enhancers FlyBase - Version FB2019_02 Gramates et al - PubMed: 27799470  

Phenotypes

D. melanogaster Alleles and phenotypes FlyBase - Version FB2019_02 Gramates et al - PubMed: 27799470  
D. melanogaster High-throughput cell-based RNAi screens GenomeRNAi - Version 17.0 Schmidt et al - PubMed: 23193271  

Pathways

D. melanogaster

Curated pathway information and the genes involved in them KEGG - Release 58, 31 May 2011 Kanehisa et al - PubMed: 16381885  

D. melanogaster

Pathway information and the genes involved in them, inferred through orthologues from Human curated pathways Reactome - version 68 Fabregat et al - PubMed: 29145629    

Diseases

D. melanogaster Human disease data set OMIM - April 2019 Amberger et al - PubMed: 18842627  

Resources

D. melanogaster DrosDel artificial deletions FlyBase - Version FB2019_02 Ryder et al - PubMed: 15238529  
D. melanogaster Insertions (including DrosDel and Exelixis) Flybase - Version FB2019_02 Gramates et al - PubMed: 27799470  
D. melanogaster Probe sets from the Affymetrix GeneChip Drosophila Genome 1.0 Array Ensembl - Release 50    
D. melanogaster Probe sets from the Affymetrix GeneChip Drosophila Genome 2.0 Array Ensembl - Release 50    
D. melanogaster INDAC Microarray oligo set - Version 1.0 International Drosophila Array Consortium    

Publications

Drosophila Gene versus publications Flybase - Version FB2019_02 Gramates et al - PubMed: 27799470  

Drosophila

C. elegans

Gene versus publications NCBI - April 2019