In the case of an uncultivable pathogen like P. carinii, analysis of gene expression during the infective process provides significant information about the metabolic processes used for basic growth functions as well as specialized processes that may permit it to adapt to the hostile environment of the host.
Metabolic processes that use ATP as an energy source convert it back into its precursors.
To analyze the relationship of DE genes with metabolic processes, we used the MapMan tool [ 25] to visualize the distribution of DE genes on known metabolic pathways.
For this analysis, phylogenetic footprinting results from all OXPHOS subunits as well as other randomly selected mitochondrial genes participating in various metabolic processes were used.
As CREB/CREM are involved in many physiological and metabolic processes, we used the KEGG pathway function of DAVID annotation (http://david.abcc.ncifcrf.gov/) to make a more comprehensive identification of potential CREB/CREM target genes in physiological functions (see Additional file 9, Table S5).
In the present study, we used stringent variant calling and filtering parameters and identified 10 somatic mutations mainly associated with DNA repair or the protein metabolic process by using whole-exome sequencing in combination with homozygosity mapping in a comparative analysis of BRC-responsive and BRC-resistant prolactinomas.
As an example for engineering a metabolic process, we use the tryptophan synthesis (entered search term is 'tryptophan') and compare this in the organisms E. coli and H. sapiens applying keyword as well as process searches.
When glucose metabolic process was used as the leading term, PGM1 (spot 7, up-regulated), LDHA (spot 12, up-regulated), PKM2 (spot 14, down-regulated), FBP2 (spot 17, up-regulated), GAPDH (spot 19, up-regulated) and PGK (spot 20, up-regulated) were found to be enriched.
Using a principal component-based analysis, called STASIS, in combination with pathway over enrichment analysis, conserved dynamics of metabolic processes were observed using publically available metabolic profiles for the investigated species.
