FlyMine: an integrated database for Drosophila and Anopheles genomics

Table 1 Summary of data sources available in release 6.0 of FlyMine

Data	Organism	Source	Reference
Genome annotation	D. melanogaster, A. gambiae, D. pseudoobscura, A. mellifera	FlyBase Ensembl	[50,51] [39,40]
Protein annotation	D. melanogaster, D. pseudoobscura, A. gambiae, A. mellifera, C. elegans, S. cerevisiae	UniProtKB version 8.9	[35,36]
Protein family and domain annotation	D. melanogaster, A. gambiae, C. elegans	InterPro version 12.0	[41,42]
Protein-protein interactions	D. melanogaster, C. elegans, S. cerevisiae	IntAct	[65-74]*
RNAi phenotypes	C. elegans D. melanogaster	WormBase Drosophila RNAi screening center	[75-78] [79-85]
Three-dimensional structural domain predictions	D. melanogaster	Kenji Mizuguchi	Personal communication
MicroArray GeneExpression	D. melanogaster	ArrayExpress FlyAtlas	[86] [52]
Orthologues/paralogues	D. melanogaster, A. gambiae, C. elegans, A. mellifera, D. pseudoobscura + others (see [64])	InParanoid	[45,46]
GO annotation and the Gene Ontology	D. melanogaster, C. elegans, A. gambiae + others (see [64])	Gene Ontology site UniProtKB GOA	[87,88] [35,36]
DNAse1 footprints.	D. melanogaster	flyreg version 2.0	[89,90]
Transcriptional cis-regulatory modules	D. melanogaster	REDfly	[91]
Whole genome tiling path	D. melanogaster	Cambridge University
INDAC microarray oligo set	D. melanogaster	INDAC Version 1.0	[92]
P-element insertions and deletions	D. melanogaster	DrosDel	[43,44]
Homophila	Human disease to D. melanogaster	Homophila version 2.1	[93,94]

*In addition, a number of protein interactions and complexes from smaller scale experiments are available (see the Protein Interaction aspect on the FlyMine web site for details).

ISSN: 1474-760X