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Protocols

FlyMine specifications

Information


Unique identifier OMICS_00534
Name FlyMine
Alternative name FlyTF
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Invertebrates
    • Drosophila melanogaster

Maintainers


  • person_outline Gos Micklem
  • person_outline Boris Adryan

Additional information


http://flytf.gen.cam.ac.uk/flytfmine/begin.do

Publications for FlyMine

FlyMine citations

 (39)
library_books

Atf3 links loss of epithelial polarity to defects in cell differentiation and cytoarchitecture

2018
PLoS Genet
PMCID: 5849342
PMID: 29494583
DOI: 10.1371/journal.pgen.1007241

[…] n []. The positional weight matrix returned by MEME was submitted to TOMTOM (http://meme-suite.org/tools/tomtom) for interspecies motif comparison []. FlyBase gene ontology (GO) terms identified with FlyMine (http://www.flymine.org, RRID: SCR_002694) were used for functional annotation []. […]

library_books

Interplay between trauma and Pseudomonas entomophila infection in flies: a central role of the JNK pathway and of CrebA

2017
Sci Rep
PMCID: 5701226
PMID: 29176735
DOI: 10.1038/s41598-017-14969-7

[…] tool (MeV). Differentially expressed genes were clustered using the unsupervised classification method of the Kmeans. Functional annotation enrichment for Gene Ontology (GO) terms were realized using Flymine database [http://www.flymine.org/]. Benjamini-Hochberg corrected P values of less than 0.05 were considered significant. We also used i-cisTarget tool to look for enrichment in TF (TF) positio […]

library_books

FlyExpress 7: An Integrated Discovery Platform To Study Coexpressed Genes Using in Situ Hybridization Images in Drosophila

2017
PMCID: 5555482
PMID: 28667017
DOI: 10.1534/g3.117.040345

[…] ation Program Interfaces. From a queried gene, users can choose a coexpressed gene to compare upstream gene regions for structural genomic signatures of similarity. The dotplot function first queries FlyMine () for upstream IGRs for each of the pair of genes and uses the returned coordinates to fetch the corresponding sequence from a genomic sequence preloaded from FlyBase (). An evolutionary filt […]

library_books

Drosophila melanogaster positive transcriptional elongation factors regulate metabolic and sex biased expression in adults

2017
BMC Genomics
PMCID: 5436443
PMID: 28521739
DOI: 10.1186/s12864-017-3755-x

[…] l using 1 = “enriched”, 0 = “not different”, and -1 = “depleted” as compared to the signal in the whole body. We defined enriched expression as mean > 0. Gene Ontology (GO) [] tests were conducted in FlyMine []. We used a Holm-Bonferroni cutoff of p adj < 0.05 for GO analysis and all tests were based on the background of expressed genes in any of our samples rather than all genes. We used the phea […]

library_books

RNA seq analysis of Drosophila clock and non clock neurons reveals neuron specific cycling and novel candidate neuropeptides

2017
PLoS Genet
PMCID: 5325595
PMID: 28182648
DOI: 10.1371/journal.pgen.1006613

[…] hly expressed in each group of circadian neurons relative to the whole brain (data for brains from []. The peptide sequence of all genes with higher expression in circadian neurons was obtained using FlyMine [] and submitted to NeuroPID [] http://neuropid.cs.huji.ac.il. NeuroPID was used to identify putative neuropeptide precursors that contained candidate signal peptides and were identified as hi […]

library_books

Transcriptional responses to hyperplastic MRL signalling in Drosophila

2017
Open Biol
PMCID: 5356444
PMID: 28148822
DOI: 10.1098/rsob.160306

[…] scs belonging to five main categories (a), with translation and chromosome organization being the most significant (p = 3.6 × 10−3 and p = 8.4 × 10−3, respectively). Drosophila-specific searches with FlyMine also revealed enrichment of ribosome pathways (p = 2.7 × 10−6, Holm–Bonferroni). We used STRING [] to help visualize overexpressed protein networks, which revealed 6 key network hubs genes ove […]

Citations

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FlyMine institution(s)
Cambridge Systems Biology Centre, University of Cambridge, Tennis Court Road, Cambridge, UK; Department of Genetics, University of Cambridge, UK; Laboratory of Molecular Biology, Hills Road, Cambridge, UK
FlyMine funding source(s)
FlyBase grant (National Human Genome Research Institute at the US NIH P41 HG000739 to FlyBase); EPSRC MPhil studentship; Medical Research Council and; Royal Society University Research Fellowship.

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