Construction of a ceRNA-based lncRNA–mRNA network to identify functional lncRNAs in premature ovarian insufficiency

Abstract

Premature ovarian insufficiency, characterized by ovarian infertility and low fertility, has become a significant problem in developed countries due to its propensity for late delivery. It has been described that the vital role of lncRNA in the development and progression of POI. The aim of this work was to create a POI-based lncRNA–mRNA network (POILMN) to recognize key lncRNAs. Overall, differently expressed mRNAs (DEGs) and differently expressed lncRNAs (DELs) were achieved by using the AnnoProbe and limma R packages. POI-based lncRNA–mRNA network (POILMN) construction was carried out using the tinyarray R package and hypergeometric distribution. To identify key lncRNAs, we used CentiScaPe plug-in Cytoscape as a screening tool. In total, 244 differentially expressed lncRNAs (DELs) and 288 differentially expressed mRNAs (DEGs) were obtained in this study. Also, 177 lncRNA/mRNA pairs (including 39 lncRNAs and 86 mRNAs) were selected using the hypergeometric test. Finally, we identified four lncRNA (HCP5, NUTM2A-AS1, GABPB1-IT1, and SMIM25) intersections by topological analysis between two centralities (degree and betweenness), and we explored their subnetwork GO and KEGG pathway enrichment analysis. Here, we have provided strong evidence for a relationship with apoptosis, DNA repair damage, and energy metabolism terms and pathways in the key lncRNAs in our POI-based lncRNA–mRNA network. In addition, we evaluated the localization information of genes related to POI and found that genes were more distributed on chromosomes 15, 16, 17, and 19. However, more experiments are needed to confirm the functional significance of such predicted lncRNA/mRNA. In conclusion, our study identified four long non-coding RNA molecules that may be relevant to the progress of premature ovarian insufficiency.

Coordinating single‐cell and bulk RNA‐seq in deciphering the intratumoral immune landscape and prognostic stratification of prostate cancer patients

“…To uncover prognostic genes in prostate cancer, we performed univariate COX analysis on DEGs using the tinyarray R package in the GSE46602 cohort. Least absolute shrinkage and selection operator (LASSO) regression analysis was conducted by glmnet R package 18 . Prognostic genes were screened and carried for construct a risk score model.…”

“…Least absolute shrinkage and selection operator (LASSO) regression analysis was conducted by glmnet R package. 18 Prognostic genes were screened and carried for construct a risk score model. The risk score was calculated as follows: risk score = Σ (βi  Expi) (β: coefficients, Exp: mRNA expression level).…”

LncRNA‐associated competing endogenous RNA network analysis uncovered key lncRNAs involved in temozolomide resistance and tumor recurrence of glioblastoma

“…After obtaining significantly positively correlated lncRNA‐mRNA pairs, we adopted a comprehensive computational approach to identify significant ceRNA candidates 31 . Several methods have been used to predict the ceRNA network, such as the hypergeometric test, which predicts the ceRNAs based on the number of common miRNAs binding to mRNA or lncRNA 32–34 . These studies considered only a single parameter.…”

“…31 Several methods have been used to predict the ceRNA network, such as the hypergeometric test, which predicts the ceRNAs based on the number of common miRNAs binding to mRNA or lncRNA. [32][33][34] These studies considered only a single parameter. We used several attributes, such as expression levels of F I G U R E 1 Workflow of the study to obtain long non-coding RNA (lncRNA)-associated competing endogenous RNAs (ceRNAs) possibly involved in temozolomide (TMZ) resistance and tumor recurrence.…”

LncRNA HOTAIR regulates autophagy and proliferation mechanisms in premature ovarian insufficiency through the miR-148b-3p/ATG14 axis

“…Prior investigations have implicated lncRNAs in the pathogenesis of diverse conditions, including cancer [ 9 ], immune dysfunction [ 10 ] and embryogenesis [ 11 ]. Our previous research also identified aberrantly expressed lncRNAs in POI [ 12 ]. Consequently, we are intrigued by the exploration of lncRNAs’ roles in POI.…”