Identification of male infertility-related long non-coding RNAs and their functions based on a competing endogenous RNA network.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33054493", "kind": "science-record", "revision": 8, "content_hash": "sha256:cbc54cc91990881015c553eccb63070fbd51c42e9726e939790b6fed3dec6120", "created_at": "2026-11-01T15:41:13Z", "updated_at": "2026-11-01T22:45:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of male infertility-related long non-coding RNAs and their functions based on a competing endogenous RNA network.", "doi": "10.1177/0300060520961277", "pmid": "33054493", "authors": ["Zuo Zhou", "Bing Wang"], "journal": "The Journal of international medical research", "year": 2020, "abstract": "OBJECTIVE: To identify male infertility-related long non-coding (lnc)RNAs and an lncRNA-related competing endogenous (ce)RNA network.\nMETHODS: Expression data including 13 normospermic and eight teratozoospermic samples from postmortem donors were downloaded from the GEO database (GSE6872). The limma R package was used to discriminate dysregulated lncRNA and micro (m)RNA profiles. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of differentially expressed (DE) mRNAs were performed using the clusterProfiler R package. The ceRNA network of dysregulated genes was visualized by Cytoscape.\nRESULTS: A total of 101 DE lncRNAs and 1722 mRNAs were identified as male infertility-specific RNAs with thresholds of |log2FoldChange| >2.0 and adjusted P-value <0.05. GO and KEGG pathways were analyzed for DE mRNAs. Gene set enrichment analysis revealed that DE genes were enriched in embryonic skeletal system development and cytokine-cytokine receptor interactions. A ceRNA network was constructed with 26 key lncRNAs, 33 microRNAs, and 133 mRNAs. DE lncRNAs in male sterility were mainly associated with transferring phosphorus-containing groups and complexes of histone methyltransferases, methyltransferases, PcG proteins, and serine/threonine protein kinases.\nCONCLUSION: This provides a novel perspective to study lncRNA-related ceRNA networks in male infertility and assist in identifying new potential biomarkers for diagnostic purposes.", "claims": [{"id": "claim-method", "statement": "We applied the R limma package to compute differentially expressed lncRNAs and mRNAs based on normalized mRNA and lncRNA expression data.18 Bayes test was used to select differentially expressed lncRNAs and mRNAs; a change ≥2 fold and a P value cutoff of 0.05 were defined as statistically significant.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33054493", "locator": "sections[3] \"Data sources and processing\" paragraph 2", "quote": "We applied the R limma package to compute differentially expressed lncRNAs and mRNAs based on normalized mRNA and lncRNA expression data.18 Bayes test was used to select differentially expressed lncRNAs and mRNAs; a change ≥2 fold and a P value cutoff of 0.05 were defined as statistically significant."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All datasets generated for this study are included in the manuscript.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33054493", "locator": "sections[12] \"Data availability\" paragraph 2", "quote": "All datasets generated for this study are included in the manuscript."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:33054493"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33054493", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1177/0300060520961277", "sha256": "sha256:458a109467f51fdd89d46dbbe572d2e1720cda06eb3ab0b9b3bdf9b038f4730d", "bytes": 21954, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1177/0300060520961277", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7580164", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:33054493:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0e9049216d9326edd9eacf951e2be351628034ee5698e00590efd0f1fda132bb", "bytes": 1601, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#table1-0300060520961277", "version": null, "note": "Differentially expressed lncRNAs involved in the ceRNA network.", "structure": {"pmcid": "PMC7580164", "section_index": 10, "section_title": "Construction of ceRNA network in male sterility", "row_count": 27, "column_count": 4}, "table": {"label": "Table 1.", "caption": "Differentially expressed lncRNAs involved in the ceRNA network.", "rows": [["lncRNA", "Expression change", "log2 fold change (case/normal)", "Adj. P-value"], ["C7orf69", "Upregulation", "2.54", "7.47E-08"], ["LINC00266-1", "Upregulation", "5.18", "3.25E-11"], ["LINC00467", "Downregulation", "–2.21", "6.49E-07"], ["ADARB2-AS1", "Upregulation", "2.67", "4.36E-10"], ["AP000525", "Upregulation", "2.27", "4.61E-06"], ["AC008088", "Downregulation", "–3.24", "8.41E-07"], ["HLA-F-AS1", "Downregulation", "–3.50", "1.34E-14"], ["COX10-AS1", "Upregulation", "2.31", "1.74E-08"], ["EPB41L4A-AS1", "Downregulation", "–4.07", "5.28E-11"], ["LINC00466", "Upregulation", "2.53", "7.29E-08"], ["PRICKLE2-AS3", "Upregulation", "3.50", "4.05E-09"], ["ST7-AS2", "Downregulation", "–2.03", "7.25E-05"], ["C12orf77", "Upregulation", "2.16", "4.08E-07"], ["AL022344", "Upregulation", "5.26", "7.26E-11"], ["LINC00276", "Upregulation", "2.15", "4.65E-05"], ["LINC00347", "Downregulation", "–2.67", "2.72E-05"], ["PARD6G-AS1", "Downregulation", "–2.80", "1.26E-05"], ["AC092620", "Upregulation", "2.94", "1.59E-05"], ["IGSF11-AS1", "Downregulation", "–2.65", "7.24E-07"], ["ZBTB20-AS1", "Downregulation", "–4.19", "8.07E-09"], ["ARHGEF26-AS1", "Upregulation", "2.56", "4.47E-05"], ["FAM13A-AS1", "Upregulation", "3.07", "5.31E-09"], ["SLIT2-IT1", "Downregulation", "–2.66", "2.44E-07"], ["MALAT1", "Downregulation", "–2.01", "3.18E-06"], ["LZTS1-AS1", "Upregulation", "2.58", "2.12E-06"], ["FAM181A-AS1", "Downregulation", "–2.38", "1.29E-06"]], "row_count": 27, "column_count": 4, "numeric_cells": 70, "header_rows": 1, "locator": "section[10]/table-wrap[1]#table1-0300060520961277"}}, {"id": "asset:table:pmid:33054493:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e3570dc5d9717c4e62ca9900739e426442eda13c9144adae475a4c981f476a1f", "bytes": 3443, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[2]#table2-0300060520961277", "version": null, "note": "miRNAs targeting male infertility-specific lncRNAs in the ceRNA network.", "structure": {"pmcid": "PMC7580164", "section_index": 10, "section_title": "Construction of ceRNA network in male sterility", "row_count": 27, "column_count": 2}, "table": {"label": "Table 2.", "caption": "miRNAs targeting male infertility-specific lncRNAs in the ceRNA network.", "rows": [["lncRNA", "miRNAs"], ["C7orf69", "miR-1297"], ["LINC00266-1", "miR-140-5p, miR-876-3p, miR-1244, miR-217, miR-24-3p, miR-363-3p, miR-1297, miR-27a-3p"], ["LINC00467", "miR-27a-3p, miR-107"], ["ADARB2-AS1", "miR-216b-5p, miR-24-3p, miR-27a-3p, miR-107, miR-125a-5p, miR-125b-5p, miR-455-5p"], ["AP000525", "miR-139-5p, miR-140-5p, miR-876-3p, miR-1244, miR-142-3p, miR-17-5p, miR-20b-5p, miR-761, miR-3619-5p, miR-216b-5p, miR-1297, miR-425-5p, miR-125a-5p, miR-125b-5p, miR-129-5p, miR-490-3p"], ["AC008088", "miR-507, miR-193a-3p, miR-129-5p"], ["HLA-F-AS1", "miR-507, miR-137, miR-17-5p, miR-20b-5p, miR-193a-3p, miR-761, miR-3619-5p, miR-217, miR-22-3p, miR-23b-3p, miR-24-3p, miR-363-3p, miR-27a-3p, miR-107, miR-425-5p, miR-455-5p, miR-129-5p"], ["COX10-AS1", "miR-140-5p, miR-876-3p, miR-1244, miR-142-3p, miR-17-5p, miR-20b-5p, miR-206, miR-761, miR-3619-5p, miR-22-3p, miR-363-3p, miR-10a-5p"], ["EPB41L4A-AS1", "miR-139-5p, miR-17-5p, miR-20b-5p, miR-429, miR-761, miR-3619-5p, miR-217, miR-22-3p, miR-23b-3p, miR-425-5p, miR-129-5p"], ["LINC00466", "miR-507, miR-137, miR-206, miR-429, miR-761, miR-3619-5p, miR-216b-5p, miR-22-3p, miR-23b-3p, miR-24-3p, miR-363-3p, miR-27a-3p, miR-33a-3p, miR-129-5p, miR-490-3p"], ["PRICKLE2-AS3", "miR-137, miR-140-5p, miR-876-3p, miR-1244, miR-206, miR-761, miR-3619-5p, miR-23b-3p, miR-24-3p, miR-363-3p, miR-125a-5p, miR-125b-5p, miR-490-3p"], ["ST7-AS2", "miR-137, miR-139-5p, miR-206, miR-429, miR-216b-5p, miR-22-3p, miR-23b-3p, miR-27a-3p, miR-425-5p, miR-125a-5p, miR-125b-5p, miR-129-5p"], ["C12orf77", "miR-507, miR-137, miR-17-5p, miR-20b-5p, miR-193a-3p, miR-206, miR-761, miR-3619-5p, miR-216b-5p, miR-24-3p, miR-1297"], ["AL022344", "miR-137, miR-1297"], ["LINC00276", "miR-137, miR-206, miR-429, miR-761, miR-3619-5p, miR-216b-5p, miR-23b-3p, miR-363-3p, miR-27a-3p, miR-425-5p, miR-129-5p, miR-490-3p"], ["LINC00347", "miR-139-5p, miR-206, miR-22-3p, miR-363-3p, miR-425-5p"], ["PRMT5-AS1", "miR-139-5p, miR-217, miR-24-3p, miR-107, miR-125a-5p, miR-125b-5p, miR-129-5p"], ["AC092620", "miR-193a-3p, miR-107, miR-455-5p"], ["IGSF11-AS1", "miR-206, miR-429, miR-217, miR-27a-3p, miR-129-5p, miR-490-3p"], ["ZBTB20-AS1", "miR-301b-3p, miR-212-3p, miR-206, miR-761, miR-3619-5p, miR-217, miR-24-3p, miR-1297, miR-27a-3p, miR-129-5p"], ["ARHGEF26-AS1", "miR-139-5p, miR-17-5p, miR-20b-5p, miR-761, miR-3619-5p, miR-217, miR-23b-3p, miR-363-3p, miR-27a-3p, miR-107, miR-425-5p, miR-125a-5p, miR-125b-5p, miR-10a-5p, miR-455-5p, miR-490-3p"], ["FAM13A-AS1", "miR-507, miR-137, miR-139-5p, miR-142-3p, miR-17-5p, miR-20b-5p, miR-217, miR-22-3p, miR-23b-3p, miR-24-3p, miR-363-3p, miR-107, miR-125a-5p, miR-125b-5p, miR-455-5p, miR-129-5p"], ["SLIT2-IT1", "miR-139-5p, miR-33a-3p"], ["MALAT1", "miR-507, miR-140-5p, miR-876-3p, miR-1244, miR-142-3p, miR-17-5p, miR-20b-5p, miR-193a-3p, miR-206, miR-429, miR-761, miR-3619-5p, miR-216b-5p, miR-217, miR-22-3p, miR-23b-3p, miR-24-3p, miR-363-3p, miR-1297, miR-425-5p, miR-125a-5p, miR-125b-5p, miR-455-5p, miR-129-5p, miR-490-3p"], ["LZTS1-AS1", "miR-212-3p, miR-22-3p, miR-24-3p, miR-33a-3p, miR-129-5p"], ["FAM181A-AS1", "miR-507, miR-193a-3p, miR-206, miR-761, miR-3619-5p, miR-216b-5p, miR-23b-3p, miR-1297, miR-33a-3p, miR-455-5p, miR-129-5p"]], "row_count": 27, "column_count": 2, "numeric_cells": 44, "header_rows": 1, "locator": "section[10]/table-wrap[2]#table2-0300060520961277"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", 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