Therefore, in PANTHER database classification we found four significant functional biological processes in our 238 down-regulated genes list.
Recent catalogs of lncRNAs in humans reveal a wide diversity of functional biological processes in which these RNAs participate [ 2, 3].
The latter genes were analysed further using DAVID tools (Functional Annotation Bioinformatics Microarray Analysis) (http://david.abcc.ncifcrf.gov) (Huang da et al, 2009a; Huang da et al, 2009b), to identify enrichment in Gene Ontology biological processes and in functional pathways (Supporting Information Table S2).
We ranked biological processes in terms of significance for all functional enrichment tests and calculated the numbers of processes in common for increasing length of ranked lists for results based on sequence motif versus ChIP/chip results from naive, BaP-treated, TCDD-treated, and negative control c35 cells.
This provides a global view of the functional structure of biological processes in yeast, including the degree of data-driven associations between processes, the experimental cohesiveness of gene behavior within each process, and the coverage of individual biological processes by currently available data.
Although we observe the percentage of shared edges between the E. coli GRN to TRN is larger compared to the E. coli GRN to PPN the GPEA analysis shows a larger functional variety of biological processes in the GRN to PPN comparison as observed for S. cerevisiae.
The functional profiles were represented by the biological processes in the GO database (Gene Ontology Consortium 2006).
Emerging reports have suggested that lncRNAs play important functional roles in disease, development and various biological processes in eukaryotes.
Finally, GO functional enrichment analysis was performed to determine enriched biological processes in each community.
