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Summary of data sources available in release 6.0 of FlyMine |
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| Data |
Organism |
Source |
Reference |
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| 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 |
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| 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] |
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*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). | |||
Lyne et al. Genome Biology 2007 8:R129 doi:10.1186/gb-2007-8-7-r129 |
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