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Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases

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Published on: May 17, 2019

Benchmarking database performance for genomic data.

Matloob Khushi¹

¹Bioinformatics Unit, Children's Medical Research Institute, Westmead, NSW, Australia; Centre for Cancer Research, Westmead Millennium Institute; Sydney Medical School, Westmead, University of Sydney, Sydney, Australia.

Journal of Cellular Biochemistry

|January 7, 2015

Summary

This summary is machine-generated.

A new SQL-based algorithm, RegMap, efficiently identifies overlapping genomic regions. PostgreSQL databases outperform MySQL for these operations, revealing significant co-localization between HNF4G and STAG1.

Keywords:

DATABASE BENCHMARKING EPIGENETIC MODIFICATIONS MANAGING GENOMIC LOCATIONS DATA REGMAP TRANSCRIPTION FACTOR BINDING SITES

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Genomic operations like identifying overlapping regions are crucial for biological research.
Existing database systems lack comprehensive built-in algorithms for efficient genomic region analysis.

Purpose of the Study:

To develop a novel SQL-based algorithm (RegMap) for performing genomic operations.
To benchmark the performance of different database systems for genomic data management and analysis.

Main Methods:

Development of the region-mapping (RegMap) SQL-based algorithm.
Benchmarking PostgreSQL and MySQL for genomic region overlap detection, data insertion, and general searching.
Pair-wise analysis of over 1000 datasets of transcription factor binding sites and histone marks.

Main Results:

PostgreSQL demonstrated significantly faster extraction of overlapping genomic regions compared to MySQL.
PostgreSQL showed superior performance in data insertion and uploads.
General searching capabilities were comparable between PostgreSQL and MySQL.
Identified significant co-localization between HNF4G (Hepatocyte Nuclear Factor 4 Gamma) and cohesin subunit STAG1 (Stromal Antigen 1).

Conclusions:

The RegMap algorithm provides an efficient solution for genomic operations.
PostgreSQL is recommended over MySQL for tasks involving rapid identification of overlapping genomic regions.
The study identified a novel biological association between HNF4G and STAG1, warranting further investigation.