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Related Experiment Videos

KOBAS server: a web-based platform for automated annotation and pathway identification.

Jianmin Wu1, Xizeng Mao, Tao Cai

  • 1Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, PR China.

Nucleic Acids Research
|July 18, 2006
PubMed
Summary

The KOBAS server automatically annotates genes and proteins with KEGG Orthology (KO) terms and identifies enriched pathways. This tool aids in understanding biological pathways from various experimental data, including Alzheimer's Disease research.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Automated gene and protein annotation is crucial for interpreting high-throughput biological data.
  • KEGG Orthology (KO) provides an effective controlled vocabulary for functional annotation.
  • Previous development of the standalone KO-Based Annotation System (KOBAS) demonstrated its utility.

Purpose of the Study:

  • To report the development and functionalities of the KOBAS server, a web-based platform for gene/protein annotation and pathway enrichment analysis.
  • To enhance KOBAS with a user-friendly interface and expanded capabilities for broader accessibility.
  • To facilitate the identification of statistically enriched biological pathways from diverse datasets.

Main Methods:

  • The KOBAS server accepts nucleotide/amino acid sequences or identifiers for annotation via BLAST or direct ID mapping.

Related Experiment Videos

  • It annotates input data with KO terms and maps them to KEGG pathways.
  • Statistical enrichment analysis is performed using four statistical tests with multiple testing correction options.

    • Main Results:

    • The KOBAS server offers a web interface for sequence-based or ID-based annotation.
    • It identifies both frequent and statistically enriched pathways.
    • Demonstrated usability by identifying enriched pathways in Alzheimer's Disease upregulated genes.

    Conclusions:

    • The KOBAS server provides a powerful and accessible tool for automated gene/protein annotation and pathway enrichment analysis.
    • Its enhanced functionalities and user-friendly interface support diverse research needs in genomics and proteomics.
    • The tool aids in discovering biologically relevant pathways from experimental data, as exemplified by AD research.