Ingenuity pathway analysis of differentially expressed genes involved in signaling pathways and molecular networks in RhoE gene‑edited cardiomyocytes

Abstract

RhoE/Rnd3 is an atypical member of the Rho superfamily of proteins, However, the global biological function profile of this protein remains unsolved. In the present study, a RhoE-knockout H9C2 cardiomyocyte cell line was established using cRISPR/Cas9 technology, following which differentially expressed genes (DEGs) between the knockout and wild-type cell lines were screened using whole genome expression gene chips. A total of 829 DEGs, including 417 upregulated and 412 downregulated, were identified using the threshold of fold changes ≥1.2 and P<0.05. Using the ingenuity pathways analysis system with a threshold of-Log (P-value)>2, 67 canonical pathways were found to be enriched. Many of the detected signaling pathways, including that of oncostatin M signaling, were found to be associated with the inflammatory response. Subsequent disease and function analysis indicated that apart from cardiovascular disease and development function, RhoE may also be involved in other diseases and function, including organismal survival, cancer, organismal injury and abnormalities, cell-to-cell signaling and interaction, and molecular transport. In addition, 885 upstream regulators were enriched, including 59 molecules that were predicated to be strongly activated (Z-score >2) and 60 molecules that were predicated to be significantly inhibited (Z-scores <-2). In particular, 33 regulatory effects and 25 networks were revealed to be associated with the DEGs. Among them, the most significant regulatory effects were 'adhesion of endothelial cells' and 'recruitment of myeloid cells' and the top network was 'neurological disease', 'hereditary disorder, organismal injury and abnormalities'. In conclusion, the present study successfully edited the RhoE gene in H9c2 cells using cRISPR/cas9 technology and subsequently analyzed the enriched DEGs along with their associated canonical signaling pathways, diseases and functions classification, upstream regulatory molecules, regulatory effects and interaction networks. The results of the present study should facilitate the discovery of the global biological and functional properties of RhoE and provide new insights into role of RhoE in human diseases, especially those in the cardiovascular system.

In-Silico Evaluation of Genetic Alterations in Ovarian Carcinoma and Therapeutic Efficacy of NSC777201, as a Novel Multi-Target Agent for TTK, NEK2, and CDK1

“…The network of interaction between molecules, including genes, proteins chemicals, and drugs can be visualized in the experimental system. IPA uncovers the interaction and functional roles of the DEGs associated with the signaling pathways and their related disease and functions [ 33 ]. The disease and function classification given in Figure 3 C indicated that the DEGs are associated with the activation of cellular movement, immune cell trafficking, cell death and survival, cell cycle, cellular development, cellular growth and proliferation, cell to cell signaling, tissue development, connective tissue development, and hematological system development and function.…”

“…The IPA system is a QIAGEN’s bioinformatics pathway analytical tool ( (Accessed on 30 November 2021)) that uses a network generation algorithm to segment the network map of molecules into multiple networks and assign scores to each network [ 33 ]. For the canonical pathway, disease, and function analyses, a threshold of the Z-score of ≥2 was defined as significant activation, and a Z-score of ≤−2 was defined as significant inhibition [ 33 ]. Algorithms to calculate the overlap of Z-scores and p values were described previously [ 31 ].…”

The Effects of Melatonin Administration on Intestinal Injury Caused by Abdominal Irradiation from Mice

“…IPA is a robust and expertly curated database that can help to understand the characters of various molecules such as gene, protein, chemical substance, and drug and interaction network among the molecules [ 11 ]. The data from Mel.Rad mice were further analyzed by IPA to group the identified genes and locate the canonical pathways that the genes were involved in.…”

RNA-Seq Analysis Reveals Dendrobium officinale Polysaccharides Inhibit Precancerous Lesions of Gastric Cancer through PER3 and AQP4

“…Enrichment of the focus genes in networks in IPA was assessed via Fisher's exact test. Furthermore, the software identifies top functions associated with each network via enrichment scores ( z -score), highlighting the predicted biological significance of the results [ 18 , 19 ].…”