What is KOBAS 3.0?

KOBAS 3.0 is a web server for gene/protein functional annotation (Annotate module) and functional gene set enrichment(Enrichment module). For Annotate module, it accepts gene list as input, including IDs or sequences, and generates annotations for each gene based on multiple databases about pathways, diseases, and Gene Ontology. For Enrichment module, it can accept either gene list or gene expression data as input, and generates enriched gene sets, corresponding name, p-value or a probability of enrichment and enrichment score based on results of multiple methods.

What is new in KOBAS 3.0?

We integrated gene expression data format for functional sets enrichment analysis. We support both microarray data and RNA-Seq data.

We also integrated 9 gene set enrichment(GSE) methods which performed well based on our GSE evaluation test. The 9 methods are including set-based methods (GSEA, GSA, PADOG, PLAGE, GAGE, GLOBALTEST) and net-based methods (GANPA, GGEA, CEPA).

Most importantly, we developed KOBAS 3.0, a function to integrate the results of the 9 methods, it gives gene set enrichment score and probability of being enriched sets based on the results of 9 gene set enrichment methods.

KOBAS 3.0.0, which is a standalone platform, can be downloaded now.

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How to cite KOBAS?

  1. Ai, C., Kong, L. CGPS: A machine learning-based approach integrating multiple gene set analysis tools for better prioritization of biologically relevant pathways.
  2. Xie, C. et al. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Research 39, W316–W322 (2011).
  3. Wu, J., Mao, X., Cai, T., Luo, J., Wei, L. KOBAS server: a web-based platform for automated annotation and pathway identification. Nucleic Acids Res 34, W720–W724 (2006).