Analysis Of Expression Patterns Of Differential LncRNAs-DEGs In Ovarian Cancer Based On Bioinformatics

Objectives:Analysis of long non-coding RNA(lncRNA)in ovarian cancer based on bioinformatics,and screening key lncRNAs and differentially expressed genes(DEGs)to explore the biological expression pattern of differentially expressed LncRNAs-DEGs in ovarian cancer.Methods:The microarray data of GSE74448 was downloaded from the High Throughput Gene Expression Omnibus database,including 29 ovarian cancer samples and 11 normal ovarian tissue samples.The differential expression probes in this data set were screened by R and Bioconductor software,and the differentially expressed probes were annotated using SangerBox to screen for differentially expressed long noncoding RNAs(IncRNAs)and differentially expressed genes(DEGs).The selected differentially expressed genes were subjected to functional enrichment analysis by R and Bioconductor software.A protein-protein interaction(PPI)network was constructed for DEGs based on the STRING database and visualized in Cytoscape software.Co-expression analysis identified co-expressed lncRNA-DEG pairs,screened for key lncRNAs and DEGs associated with ovarian cancer.The GEPIA(Gene Expression Profiling Interactive Analysis)database was used to analyze the expression of DEGs associated with IncRNAs in ovarian cancer and its relationship with ovarian cancer prognosis.Results:1.From the chip GSE74448,183 differentially expressed LncRNAs were screened(63 up-regulated and 120 down-regulated),and 1433 differentially expressed genes(708up-regulated and 725 down-regulated).2.Functional enrichment analysis of differentially expressed genes in ovarian cancer was performed by R and Bioconductor software.The GO function annotation found that the up-regulated differentially expressed genes are mainly involved in biological processes including nuclear chromosome segregation,mitotic nuclear division,sister chromatid separation,and mitotic sister chromatid separation;The participating cellular components are mainly spindles,concentrated chromosomes,microtubules,condensed nuclear chromosomes,cell-cell junctions,etc.;The molecular functions involved are actin binding,locomotor activity,purine-nucleotide exchange factor activity,microtubule binding,nucleotide exchange factor activity,etc.;Pathway analysis revealed that up-regulated differentially expressed genes are mainly involved in cell cycle,signaling,mitosis,and resolution of sister chromatid cohesion.Down-regulated differentially expressed genes are mainly involved in biological processes such as renal phylogeny,development of the genitourinary system,and development of smooth muscle tissue;The main cellular components involved are extracellular matrix,proteinaceous extracellular matrix,contractile fiber fraction,interstitial matrix,cell-substrate junction,etc.;The molecular functions involved include steroid hormone receptor activity,RNA polymerase II transcription factor activity,transcription factor activity,glycosaminoglycan binding,and Guanosine triphosphate(GTP)enzyme activity;Pathway analysis of the down-regulated differentially expressed genes revealed that these down-regulated differentially expressed genes are mainly involved in the nuclear receptor transcription pathway.3.The interaction network of the proteins encoded by the differentially expressed genes was analyzed by STRING database and Cytoscape software.It was found that the key proteins in the up-regulated differentially expressed genes were CDK1,TOP2A,BUB1,CCNA2 and CCNB2,and the key proteins in the down-regulated differentially expressed genes were GNG7,GNG4,GNB5,RPL9 and RPL31.4.By analyzing the co-expressed IncRNA-DEG pair,it was found that the top 5 most up-regulated differentially expressed lncRNAs were RNF157-AS1,AC108860.2,AP000251.1,AL583810.1 and C1RL-AS1,respectively,and the top 5 most down-regulated differentially expressed lncRNAs were LINC01197,LINC00909,AC008669.1,AC 1 17489.1,and ZEB1-AS 1,respectively.5.Through the GEPIA database,we founded that high expression of up-regulated genes ELF3,CLDN4,SCNN1A,KLHL14,KRT7,GRB7,TMC4,and MSLN is associated with poor survival in ovarian cancer patients,and low expression of down-regulated genes TMA7,ALG13,NDUFB6,and TCEAL9 It is associated with better survival in patients with ovarian cancer.The expression levels of 9 genes were significantly different between Ovarian cancer(OC)tissues and normal tissues.ELF3,CLDN4,SCNN1A,KLHL14,KRT7,GRB7,TMC4 and MSLN were highly expressed in OC tissues,while TCEAL9 was significant low expression.Conclusions:1.Successfully screened 183 differentially expressed IncRNAs and 1433 differentially expressed genes in ovarian cancer,and performed biological function annotation and pathway analysis on differentially expressed genes,which provided a theoretical basis for the study of the disease.2.Successfully constructed a protein interaction network map of differentially expressed genes in ovarian cancer,and screened out key proteins,which is helpful to further study the interaction relationship between differentially expressed genes and provide direction for the diagnosis and treatment of OC.3.The co-expressed IncRNA-DEG pair was successfully constructed.It was found that ZEB1-AS1 was co-expressed with ELF3,CLDN4 and KRT7 in ovarian cancer,HOXA-AS 3 and MEF2C-AS1 were co-expressed with GRB 7,and LINC00909 was co-expressed with MSLN.The selected key lncRNAs and differentially expressed genes provide research directions for early diagnosis and targeted therapy of the disease.4.The GEPIA database confirmed that the gene expression levels of ELF3,CLDN4,KRT7,GRB7 and MSLN in OC were up-regulated,and their high expression was associated with a poor prognosis in patients with ovarian cancer.The key differentially expressed genes screened provide a new research direction for predicting the prognosis of the disease.