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modMine specifications

Information


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

Maintainer


  • person_outline Gos Micklem

Publication for modMine

modMine citations

 (20)
library_books

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

2017
PMCID: 5677173
PMID: 28916647
DOI: 10.1534/g3.117.1133

[…] the distances between those genes. c.i.s were calculated as 2.5–97.5% quantiles from the corresponding random sample distribution., 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 […]

library_books

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

2017
PMCID: 5555470
PMID: 28624774
DOI: 10.1534/g3.117.043836

[…] 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 […]

library_books

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

2016
PMCID: 5295594
PMID: 27974438
DOI: 10.1534/g3.116.037333

[…] (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 […]

library_books

High throughput assessment of context dependent effects of chromatin proteins

2016
PMCID: 5069885
PMID: 27777628
DOI: 10.1186/s13072-016-0096-y

[…] 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 (http://intermine.modencode.org v33 28jul2014)., this work was supported by erc advanced grant 293662, nih u54 grant 1u54dk107965-01 and by an nwo-alw grant to wa and m. van […]

library_books

CBP binding outside of promoters and enhancers in Drosophila melanogaster

2015
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 (http://intermine.modencode.org/). two additional proteins, trx and m1bp (geo entries gsm604729, gsm1208162), that were not used in the classification, were included in the heatmap […]

library_books

Ethosuximide ameliorates neurodegenerative disease phenotypes by modulating DAF 16/FOXO target gene expression

2015
Mol Neurodegener
PMCID: 4587861
PMID: 26419537
DOI: 10.1186/s13024-015-0046-3

[…] shared by at least 3 treated strains was used to subdivide the ethosuximide-responsive transcripts into groups based on gene ontology (go) identifiers (additional file : figure s4). both david and modmine go analyses yielded a significant enrichment for go terms related to “lipid glycosylation”, “lipid modification”, “oxidation reduction”, “determination of adult lifespan” and “chromatin […]


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

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