Additional File 4 summarizes the GO results (Biological Processes) for both SAM signatures ordered by FDR, defined as the median number of false positive genes divided by the number of significant genes.
In order to retrieve biological processes affected by zinc we performed GO enrichment analysis [ 26].
Given that many of the non-redundant sequences derive from common genes, we turned to annotating the clustered sequences in order to gain a more accurate view of the range of biological processes represented by the expressed sequences.
GO has three independently structured, controlled vocabularies: molecular functions – activities, such as catalysis or binding, at the molecular level; biological processes – events accomplished by one or more ordered assemblies of molecular functions; and cellular components – components that are part of some larger objects, such as an anatomical structure or gene product group [ 2].
In order to identify key biological processes affected by diet in liver, skeletal muscle and WAT, we performed integrated analysis using three biological networks to capture different levels of information.
The aim of this study was to determine the in vivo genome-wide transcriptional response to local administration of butyrate in the distal colon in healthy volunteers in order to identify the biological processes mediated by butyrate, providing new leads for clinical and mechanistic studies.
This biological process is regulated by ordered patterns of gene expression, where specific combinations of transcription factors or chromatin remodelling complexes result to be responsible for the genetic program of each hematopoietic precursor [ 28- 30].
In order to identify sets of biological processes regulated by MYCN, Gene Ontology (GO) analysis [20], [21] was performed using the subset of 265 sites common to all NB cell lines.
Each cluster was examined for overrepresentation of GO terms in order to identify biological processes predominantly controlled by the genes in the respective cluster.
Biological processes represented by only one transcript were discarded from the analysis in order to minimize the occurrence of false positives.
