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modMine specifications


Unique identifier OMICS_03817
Name modMine
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Gos Micklem

Publication for modMine

modMine citations


The Effect of Common Inversion Polymorphisms In(2L)t and In(3R)Mo on Patterns of Transcriptional Variation in Drosophila melanogaster

PMCID: 5677173
PMID: 28916647
DOI: 10.1534/g3.117.1133

[…] TFs and TGs were defined by Drosophila Interaction Database modMine () (v2015_12). Genes in this analysis were those that are present in Affymetrix Drosophila2 genome array annotation (Release 35), the DroID TF-TG database v2015_12, and FlyBase v5.49 annotatio […]


Sex and Genetic Background Influence Superoxide Dismutase (cSOD) Related Phenotypic Variation in Drosophila melanogaster

PMCID: 5555470
PMID: 28624774
DOI: 10.1534/g3.117.043836

[…] nzyme genotype in which males are more sensitive to differences in NADP(H) enzyme genotypes than females (). Interestingly, examination of gene expression data for cSOD, MEN, IDH, and G6PD, using the modMine function of ModENCODE, showed no indication of sex-specific expression at the whole organism level () in the lines available through FlyBase (data not shown). Overall, the biochemical phenotyp […]


Transcriptome Analysis of Drosophila melanogaster Third Instar Larval Ring Glands Points to Novel Functions and Uncovers a Cytochrome p450 Required for Development

PMCID: 5295594
PMID: 27974438
DOI: 10.1534/g3.116.037333

[…] em (Australian Genome Research Facility, AGRF). In addition to the reads obtained from the six RG samples, duplicate RNA-seq reads for the Oregon-R wandering third instar CNS were downloaded from the modMINE database (accession: SRX029398) (). These reads were downloaded in SRA (short read archive) format, and converted to paired end fastq format using the fastq-dump utility included in the NCBI S […]


High throughput assessment of context dependent effects of chromatin proteins

PMCID: 5069885
PMID: 27777628
DOI: 10.1186/s13072-016-0096-y

[…] loaded from GEO (GSE22069). Annotation according to the nine-state model (accession # modENCODE_21955), ChIP-seq peak data for H3K36me3 (modENCODE_302) and JIL-1 (modENCODE_3037) were downloaded from modMine ( v33 28JUL2014). […]


DANIO CODE: Toward an Encyclopedia of DNA Elements in Zebrafish

PMCID: 4742988
PMID: 26671609
DOI: 10.1089/zeb.2015.1179

[…] 000 gene expression patterns, 82,000 phenotypes, and 7,000 registered researchers, ZFIN links to major genome annotation databases and also features the data mining tool ZebrafishMine, similar to the modMINE resource of the modENCODE initiative. Monte Westerfield (University of Oregon, USA) gave an update on ZFIN's resources and how they can integrate into the DANIO-CODE initiative, explaining for […]


CBP binding outside of promoters and enhancers in Drosophila melanogaster

PMCID: 4657240
PMID: 26604986
DOI: 10.1186/s13072-015-0042-4

[…] Figure S1, 27 histone modifications, DNAse hypersensitivity and expression data produced in Drosophila S2 cells as well as H3K27ac and expression in different developmental stages) was obtained from modMine ( Two additional proteins, Trx and M1BP (GEO entries GSM604729, GSM1208162), that were not used in the classification, were included in the heatmap (Additional […]

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modMine institution(s)
Department of Genetics, University of Cambridge, Downing Street, Cambridge, UK

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