The GOrilla functional enrichment test produces a list of significant individual gene ontology (GO) terms, whereas DAVID performs enrichment tests using a number of different functional terms, including GO terms, SwissProt keywords, and UniProt sequence features.
Using this uniform data basis we analyze their evolutionary history in terms of individual gene phylogenies and in terms of preservation of genomic nearness across species.
A major goal of systems biology is to integrate biological functions of individual genes in terms of their interactions.
Existing methods can identify significant association between individual genes and terms from the medical subject heading (MeSH) index and Gene ontology (GO) databases [ 11], manually curated biological lists [ 12], or disease-specific lists [ 13].
The term "individual gene" is used here to address each gene individually irrespective of its state, so that for a diploid individual there are always 2· l individual genes at l gene loci.
GO terms are used primarily for the annotation of individual gene products, whereas KEGG pathway terms are used for the annotation of classes of gene products, thus providing a more precise delineation of functionalities for a group of genes that act together to some extent.
By combining the probabilities about expression of individual genes, probabilistic GO term inference considers thus additional information which is discarded by a threshold-based enrichment analysis.
GO terms and individual gene analysis revealed that there was concordance in the main upregulated proinflammatory transcripts between SOD1-mutant hiPSC-astrocytes and the astrocyte-specific translational profile in SOD1-mutant ALS mice25 (Fig. 6c).
These techniques are reliable for assessing DNA methylation status at an individual gene scale, but have limitations in terms of assessing genome-wide methylation [34].
However, it remains unclear whether this inheritance can direct long-term memory of individual gene expression states (cis memory) or instead if local chromatin states are dictated by the concentrations of diffusible factors (trans memory).
To obtain a general overview of putative gene function within significant gene clusters, individual gene sets were analysed for enrichment of Gene Ontology (GO) terms using the Term Enrichment Tool at AmiGO [ 22].
