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Mining Spatial Transcriptomics Datasets using DeepSpaceDB

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The TargetMine Data Warehouse: Enhancement and Updates.

Yi-An Chen¹, Lokesh P Tripathi¹, Takeshi Fujiwara¹

¹Laboratory of Bioinformatics, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.

Frontiers in Genetics

|October 26, 2019

Summary

TargetMine now integrates more biological data types and offers enhanced analysis tools for disease biology and drug discovery. This updated platform aids researchers in uncovering gene-disease associations and interpreting genotype-phenotype relationships.

Keywords:

data mining data warehouse drug discovery gene prioritisation integrative data analysis knowledge discovery multi-omics data analysis

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

High-throughput 'omics' data generation necessitates advanced tools for biological data analysis.
Integrative platforms are crucial for combining diverse biological datasets to extract meaningful knowledge.
TargetMine was previously developed as an integrative platform for target prioritization and knowledge discovery.

Purpose of the Study:

To describe newly modeled biological data types in TargetMine.
To highlight enhanced visual and analytical features of the TargetMine platform.
To demonstrate the utility of TargetMine for trans-omics data analysis and gene-disease association extraction.

Main Methods:

Integration of enhanced gene-gene relations and small molecule metabolite to pathway mappings.
Implementation of an improved literature survey feature.
Inclusion of in silico prediction for gene functional associations (e.g., protein-protein interactions, gene co-expression).

Main Results:

TargetMine now covers a broader range of biological data types and relationships.
Enhanced features facilitate the analysis of trans-omics data.
The platform effectively aids in extracting gene-disease associations using MeSH descriptors.
Demonstrated improved interpretation of genotype-phenotype relations.

Conclusions:

The enhanced TargetMine platform provides expanded biological data coverage and analytical capabilities.
TargetMine facilitates deeper insights into disease biology and drug discovery through integrative data analysis.
The updated platform assists researchers in interpreting complex biological data and uncovering genotype-phenotype correlations.