Regulation of regeneration in Arabidopsis thaliana  

作　　者：Md Khairul Islam Sai Teja Mummadi Sanzhen Liu Hairong Wei 

机构地区：[1]Computational Science and Engineering Program,Michigan Technological University,Houghton,MI 49931,USA [2]Computer Science,Michigan Technological University,Houghton,MI 49931,USA [3]Department of Plant Pathology,Kansas State University,Manhattan,KS 66506,USA [4]College of Forest Resources and Environmental Science,Michigan Technological University,Houghton,MI 49931,USA

出　　处：《aBIOTECH》2023年第4期332-351,共20页生物技术通报（英文版）

基　　金：supported by the National Science Foundation Plant Genome Research Program[1703007 to S.L.and H.W]。

摘　　要：We employed several algorithms with high efficacy to analyze the public transcriptomic data,aiming to identify key transcription factors(TFs)that regulate regeneration in Arabidopsis thaliana.Initially,we utilized CollaborativeNet,also known as TF-Cluster,to construct a collaborative network of all TFs,which was subsequently decomposed into many subnetworks using the Triple-Link and Compound Spring Embedder(CoSE)algorithms.Functional analysis of these subnetworks led to the identification of nine subnetworks closely associated with regeneration.We further applied principal component analysis and gene ontology(GO)enrichment analysis to reduce the subnetworks from nine to three,namely subnetworks 1,12,and 17.Searching for TF-binding sites in the promoters of the co-expressed and co-regulated(CCGs)genes of all TFs in these three subnetworks and Triple-Gene Mutual Interaction analysis of TFs in these three subnetworks with the CCGs involved in regeneration enabled us to rank the TFs in each subnetwork.Finally,six potential candidate TFs-WOx9A,LEC2,PGA37,WIP5,PEI1,and AIL1 from subnetwork 1-were identified,and their roles in somatic embryogenesis(GO:0010262)and regeneration(GO:0031099)were discussed,so were the TFs in Subnetwork 12 and 17 associated with regeneration.The TFs identified were also assessed using the CIS-BP database and Expression Atlas.Our analyses suggest some novel TFs that may have regulatory roles in regeneration and embryogenesis and provide valuable data and insights into the regulatory mechanisms related to regeneration.The tools and the procedures used here are instrumental for analyzing high-throughput transcriptomic data and advancing our understanding of the regulation of various biological processes of interest.

关 键 词：REGENERATION PLURIPOTENCY Transcription factor Collaborative network 

分 类 号：Q94[生物学—植物学]