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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 (R6.41) Flybase - Version FB2021_04 Gramates et al - PubMed: 27799470 #1

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 - December 2020 - version 16.0 Mi et al - PubMed: 27899595  

Drosophila

C. elegans

H. sapiens

M. musculus

R. norvegicus

S. cerevisiae

Orthologue and paralogue relationships between these organisms Homologene - September 2021 Agarwala et al - PubMed: 26615191  

Proteins

Drosophila

C. elegans

H. sapiens

M. musculus

R. norvegicus

S. cerevisiae

Protein annotation UniProt - Release 2021_03 UniProt Consortium - PubMed: 27899622  

D. melanogaster

A. gambiae

C. elegans

Protein family and domain assignments to proteins InterPro - Version 86; June 2021 Finn et al - PubMed: 27899635  

Interactions

Drosophila

C. elegans

S. cerevisiae

Molecular interaction datasets IntAct - Version 4.2.17; May 2021 Orchard et al - PubMed:24234451  

D. melanogaster

S. cerevisiae

Interactions from the BioGRID BioGRID - 4.4.201; September 2021" 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 - September 2021 Gene Ontology Consortium - PubMed:10802651  
D. melanogaster InterPro domains to GO annotations InterPro (from Gene Ontology Site) - September 2021 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 December 2020 Tomancak et al - PubMed:17645804  
D. melanogaster Genome-wide RNA_seq Expression Data: raw data produced by modENCODE analysed by FlyBase Flybase - Version FB2021_04 Gelbart and Emmert - 2010FlyBase Report  

Regulation

D. melanogaster Transcriptional cis-regulatory modules (CRMs) REDfly - version 9.5.1; September 2021 Gallo et al - PubMed: 20965965  
D. melanogaster Transcription factor binding sites REDfly - version 9.5.1; September 2021 Bergman et al - PubMed: 20965965  
D. melanogaster Enhancers FlyBase - Version FB2021_04 Gramates et al - PubMed: 27799470  

Phenotypes

D. melanogaster Alleles and phenotypes FlyBase - Version FB2021_04 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 77; June 2021 Fabregat et al - PubMed: 29145629  

Diseases

D. melanogaster Human disease data set OMIM - September 2021 Amberger et al - PubMed: 18842627  

Resources

D. melanogaster Artificial deletions FlyBase - Version FB2021_04 Ryder et al - PubMed: 15238529  
D. melanogaster Insertions Flybase - Version FB2021_04 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 FB2021_04 Gramates et al - PubMed: 27799470  

Drosophila

C. elegans

Gene versus publications NCBI - September 2021