BOG (version 2.0)

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

Description

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

Details

Package:

BOG

Type:

Package

Version:

1.0

Date:

2015-2-23

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.