1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Comprehensive RNA, protein interaction and SNP analysis of CAX1 in the Arabidopsis thaliana: integrated systems biology approach
Paper ID : 1471-ICB10
Authors:
Kianoush Sanei Ataabadi1, Fatemeh Ahmadi2, Behrooz Salehi-Eskandari *3, Zohre nasirian2
1آموزشگاه زیست فناوری نوین
2آموزشگاه فنی و حرفه ای زیست فناوری نوین
31 Department of Biology, Payame Noor University (PNU), P.O. Box 19395-4697, Tehran, Iran
Abstract:
Calcium exchanger 1 (CAX1) is the encoder of vacuolar Ca2+/3H+ antiporter. This protein involves regulating Ca2+ levels in the Arabidopsis thaliana. In this study, we performed a protein-protein network analysis to demonstrate the possible regulatory gene network of the transporter Ca2+/3H+ in the Arabidopsis Thaliana. After literature mining, we indicated the protein-protein interaction network of the CAX1 gene in the Arabidopsis by STRING online software. The miRNA-mRNA interactions analysis of the selected genes was performed by the miRWalk 2.0 online database. The analysis of single nucleotide polymorphism (SNP) was performed by miRNASNP-v3. Based on this network analysis, the CAX1 has significant protein interactions with CAX3, TPC1, CAX11, ACA11, CXIP4, SOS2, SSE1, NHX1, T22C5.23, and ECA. There is no possible Arabidopsis microRNA interaction with the selected genes. However, there is a significant microRNA interaction with hsa-miR-6894-3p and SOS2 in the 3UTR position (Score: 1.00). Among mentioned genes, TPC1 is a key regulatory network in the conductance of sodium and calcium ions and the intravascular pH. ACA11 is a ATPase in the mature vacuole membrane expressed in transgenic plants and visualized in root cells. Based on miRNA SNP, rs1314179105 is an innovative and significant SNP on the 3UTR region of the SOS2 gene (14 gains and 15 losses). The expression level and RNA interactions of the mentioned genes are highly recommended to be evaluated in the Arabidopsis thaliana, bioinformatically and experimentally.
Keywords:
Arabidopsis Thaliana, protein interaction, gene network, SNP, CAX1
Status : Paper Accepted (Poster Presentation)