Mouse liver regeneration data used in the previous section to investigate co-annotation include five time points up to the partial recovery of liver at 36 h post PH. Thus, here we consider only the dataset of DE genes after PH in rat24 consisting of a selection of 767 DE genes whose expression was measured over 10 different time points up to 7 days post injury, when the regrowth process can be considered complete.
Further investigation on the role of these DE genes in disease-related pathways, allows us to observe that most of them are membrane proteins or mitochondria-related genes.
The analysis of the pathways yields six pathways associated to seven genes: “Alzheimer disease-presenilin”, “CCKR signaling map2, “Heterotrimeric G-protein signaling pathway-rod outer segment phototransduction”, “Nicotinic acetylcholine receptor signaling”, “Ornithine degradation”, and “TGF-β signaling”.
We analyzed 2436 murine and 767 rat DE genes during liver regeneration after PH.24,25 Among the murine DE genes reported by Pibiri and coworkers,25 1901 genes have a correspondence in the Swissprot database.
We also consider human and zebrafish genes involved in the “Adherens Junction” pathway, since a deregulation of this pathway is related to EMT. Using the same strategy described above, we selected 89 Swissprot-annotated genes from this pathway and found a large core of representative genes strictly conserved in the considered organisms and DE during all the regeneration processes.
Number of genes related to EMT and involved in adherens junction detected in H. magnipapillata, S. mediterranea, and A. japonicus transcriptomes and differentially expressed during regeneration process.
Histogram shows the comparison between fraction of total DE genes and EMT-annotated genes that result in deregulated during regeneration process for the three organisms.