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Protocols

TargetMine specifications

Information


Unique identifier OMICS_11351
Name TargetMine
Restrictions to use None
Data access Browse, Application programming interface
Maintained Yes

Maintainer


  • person_outline Kenji Mizuguchi

Publications for TargetMine

TargetMine citations

 (5)
library_books

Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates

2017
Sci Rep
PMCID: 5431224
PMID: 28469246
DOI: 10.1038/s41598-017-01500-1

[…] PPARα and Wnt/Ca2+ signalling pathways.Figure 3 In this way, the new functions of Toxygates were used to identify gene sets of interest visually, characterise them, as well as further analyse them in TargetMine, to support an interactive toxicological investigation process. A hypothesis can be formulated and gradually refined, validated or invalidated, as multiple analysis functions reinforce each […]

library_books

Principal Components Analysis Based Unsupervised Feature Extraction Applied to Gene Expression Analysis of Blood from Dengue Haemorrhagic Fever Patients

2017
Sci Rep
PMCID: 5343617
PMID: 28276456
DOI: 10.1038/srep44016

[…] confirmed the robustness of our results, we next investigated the biological reliability of the 46 selected genes. We uploaded the 46 genes to three enrichment analysis servers, DAVID, g:pfofiler and TargetMine (see in for the full list of enriched biological terms and pathways), to compensate for the bias introduced by each individual enrichment server. g:Profiler reported the enhancement of th […]

call_split

Hypothalamic transcriptomic alterations in male and female California mice (Peromyscus californicus) developmentally exposed to bisphenol A or ethinyl estradiol

2017
PMCID: 5309579
PMID: 28196854
DOI: 10.14814/phy2.13133
call_split See protocol

[…] e heatmap was done using the ComplexHeatmap (Gu et al. ) package. Functional assessments of sets of differentially expressed genes such as pathway analyses and enrichment analyses were done using the TargetMine website (Chen et al. ). Before doing functional analyses, de novo‐assembled transcripts were mapped to human proteins based on extended amino acid similarity. […]

library_books

Identification of miRNAs Potentially Involved in Bronchiolitis Obliterans Syndrome: A Computational Study

2016
PLoS One
PMCID: 5001701
PMID: 27564214
DOI: 10.1371/journal.pone.0161771

[…] G Markup Language (KGML) description of a pathway and systematically integrate TF information for each described gene (see ). TF information is retrieved by connecting to the RESTful APIs provided by TargetMine []. For a given gene, the “Upstream Transcription Factors Template Query” (Targetmine) enables the retrieval of all upstream regulatory genes (TFs) from the AMADEUS [][] and ORegAnno [] lib […]

library_books

Comparison of Gene Coexpression Profiles and Construction of Conserved Gene Networks to Find Functional Modules

2015
PLoS One
PMCID: 4493118
PMID: 26147120
DOI: 10.1371/journal.pone.0132039

[…] ction algorithm implemented in networkx [] to find the functional modules, according to Palla et al. []. To characterize the functional roles of the modules, enrichment analyses were performed, using TargetMine [] and based on Fisher’s exact test. We defined the representative GO term as the GO term with the smallest p-value in a module.Since some gene modules had overlaps or similar annotations, […]

Citations

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TargetMine institution(s)
National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
TargetMine funding source(s)
This work was in part supported by Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (25430186 and 25293079) and from Japan Agency for Medical Research and Development (The adjuvant database project).

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