GO Analysis of BEAF & DREF targets

Eldon Emberly & Olivier Cuvier

Symbol Definitions:

    BEAF/DREF = 7045 predictions which consist of single BEAF elements and BEAF elements that contain a DREF site
    BEAF = 5064 predictions which only contain BEAF sites
    DREF = 2661 elements which contain a DREF binding site (680 lone DREF elements and 1981 BEAF+DREF elements)

Analysis of Promoters:

   Analyzed the occurence of selected elements within +/- 500 bp of all genes in D.mel genome (Release 3)

	BEAF/DREF	BEAF	DREF
Number of genes	2352	1295	1311

Computed the p-value for over-representation of given GO terms for the above 3 groups of genes

GO terms for BEAF/DREF genes               GO terms for BEAF genes               GO terms for DREF genes

Compared the GO classes of BEAF vs DREF genes to highlight significant differences. This was done by calculating the log-odds ratio
a given GO term between the BEAF the DREF classes.

Enriched BEAF GO terms                   Enriched DREF GO terms

Summary:
    1) BEAF is associated chromatin processess, cell cycle
    2) DREF is associated with biosynthesis, apoptosis, ...

Analysis of Gene Expression:

    Analyzed the correlation coefficient (r) of all genes to the expression patterns of BEAF and DREF.

    BEAF correlation:

	BEAF/DREF	BEAF
Number of genes with r > 0.5	599	308

   Analyzed the GO terms for this subset of BEAF target genes.

    GO terms for BEAF/DREF +ve correlated genes                   GO terms for BEAF +ve correlated genes

    Analyzed which of the above GO terms of the +ve correlated genes are enriched compared to the entire set of BEAF target genes.

     Enriched BEAF/DREF +ve GO terms                            Enriched BEAF +ve GO terms

    Summary:
        1) +ve correlated BEAF genes are more enriched for cell cycle, M phase and chromatin segregation

    DREF correlation:

	DREF
Number of genes with r > 0.7	147
Number of genes with r < -0.65	96

    Analyzed the GO terms for these subsets of DREF genes.

    GO terms for DREF +ve correlated genes                   GO terms for DREF -ve correlated genes

    Analyzed which of the above GO terms of the +ve and -ve correlated genes are enriched compared to the DREF target genes

    Enriched DREF +ve GO terms                      Enriched DREF -ve GO terms

    Summary:
       1) +ve correlated DREF genes are associated with the regulation of metabolism, regulation of RNA processing
       2) -ve correlated DREF genes are associated with mitochondrial processes