Biological processes, molecular functions, cellular components, and relevant pathways were identified using the DAVID algorithm (v6.7, [ 45- 47]).
To further explore the significance of the differentially expressed plasma membrane proteins, Ingenuity® Pathway Analysis (IPA; Ingenuity® Systems, www.ingenuity.com/) was used to search the relevant molecular functions, cellular processes and pathways of these identified proteins during the pathological changes of GC.
Random mutations are expected to occur more frequently in nucleotide positions that are not relevant for molecular functions and in genes not necessary to express a differentiated phenotype.
We plan to incorporate eGIFT (3) in the pipeline of eFIP for the detection of molecular functions, biological processes and subcellular localizations relevant to a phosphorylated protein.
The list of DE genes for each IT was uploaded into IPA (IPA; ver. 5.5, Ingenuity Systems, Redwood City, CA) to identify relevant categories of molecular functions, cellular components and biological processes.
According to the molecular functions and biological processes mentioned above, the most relevant gene network induced by TNFα was related to the immune response and immunological disease functions (additional file 7).
The molecular functions were searched against PANTHER[ 34], since PANTHER gave a more complete set of biologically-relevant results for our gene set than GO.
All concepts that are seen as relevant are represented by GO terms belonging to one of these three independent axis: molecular functions, biological processes and cellular components.
Protein GO enrichment based on molecular functions.
They may have related molecular functions.
