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Related Experiment Videos

GO-Diff: mining functional differentiation between EST-based transcriptomes.

Zuozhou Chen1, Weilin Wang, Xuefeng Bruce Ling

  • 1College of Life Science, Zhejiang University, Hangzhou 310029, China. zzchen@genetics.ac.cn

BMC Bioinformatics
|February 17, 2006
PubMed
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GO-Diff is a new software for high-throughput comparative transcriptomics using Expressed Sequence Tags (ESTs). It enables functional profiling by analyzing gene expression differences between biological samples, aiding in discovery.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Millions of Expressed Sequence Tags (ESTs) represent diverse biological states.
  • EST data is valuable for comparative transcriptomics, but lacks high-throughput functional profiling methods.
  • Existing methods integrate gene expression with Gene Ontology (GO) databases, but not for ESTs.

Purpose of the Study:

  • To develop a novel, high-throughput functional profiling approach for EST-based comparative transcriptomics.
  • To enable the mining of functional differentiation between biological systems using EST data and GO knowledge.

Main Methods:

  • Developed GO-Diff software for EST-based gene expression analysis.
  • Converts EST frequencies into EST Coverage Ratios of GO Terms.

Related Experiment Videos

  • Tests ratios for statistical significance to identify differentially represented GO terms.

    • Main Results:

    • GO-Diff successfully identified differentially represented GO terms in intra-species, inter-species, and meta-analysis comparisons.
    • Findings were consistent with prior knowledge and suggested new research avenues.
    • High consistency levels were observed in human-human (61%), mouse-mouse (69%), and human-mouse (47%) tissue comparisons.

    Conclusions:

    • GO-Diff is the first software to integrate EST profiles with GO databases for functional differentiation analysis.
    • It serves as a valuable screening tool for comparative transcriptomics, especially with growing EST resources.