BOG (version 1.0)

BOG-package: BOG is a package for identifying differentially regulated genes in the light of gene functions.

Description

It is designed to identify COG (Cluster of Orthologous Groups) that are either over or under-represented among genes that show differential expression under two different conditions using statistical analysis and graphical representations. Particular statistical analysis includes the hypergeometric test, Mann-Whitney test, and Gene set enrichment analysis (GSEA) test. The results are then organized and presented graphically for easy visualization and understanding.

Details

ll{ Package: BOG Type: Package Version: 1.0 Date: 2013-3-1 License: GPL-3 }

References

Carlson, P. et al. (2009) Transcriptional Profiling of Bacillus anthracis Sterne (34F2) during Iron Starvation. PLOS ONE 4(9): e6988. Doi:10.1371/journal.pone.0006988.

Khalili, A. et al. (2009) A robust unified approach to analyzing methylation and gene expression data. Comput. Stat. Data Anal., 53, 1701-1710.

Subramian, A. et al.(2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. PNAS vol.102 no.43, 15545-15550.

Taslim, C. et al. (2010) DIME: R-package for Identifying Differential ChIP-seq Based on an Ensemble of Mixture Models. Bioinformatics, 27, 1569-1570.