mRNA-miRNA bipartite networks reconstruction in different tissues of bladder cancer based on gene co-expression network analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35393513", "kind": "science-record", "revision": 3, "content_hash": "sha256:7986463fb67aee984f740cd9e38735e58b94d28ee38e38cdccd872dbfce2b15e", "created_at": "2026-11-01T18:14:12Z", "updated_at": "2026-11-01T21:27:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "mRNA-miRNA bipartite networks reconstruction in different tissues of bladder cancer based on gene co-expression network analysis.", "doi": "10.1038/s41598-022-09920-4", "pmid": "35393513", "authors": ["Zahra Abedi", "Habib MotieGhader", "Sahar Sadat Hosseini", "Mohammad Ali Sheikh Beig Goharrizi", "Ali Masoudi-Nejad"], "journal": "Scientific reports", "year": 2022, "abstract": "Bladder cancer (BC) is one of the most important cancers worldwide, and if it is diagnosed early, its progression in humans can be prevented and long-term survival will be achieved accordingly. This study aimed to identify novel micro-RNA (miRNA) and gene-based biomarkers for diagnosing BC. The microarray dataset of BC tissues (GSE13507) listed in the GEO database was analyzed for this purpose. The gene expression data from three BC tissues including 165 primary bladder cancer (PBC), 58 normal looking-bladder mucosae surrounding cancer (NBMSC), and 23 recurrent non-muscle invasive tumor tissues (RNIT) were used to reconstruct gene co-expression networks. After preprocessing and normalization, deferentially expressed genes (DEGs) were obtained and used to construct the weighted gene co-expression network (WGCNA). Gene co-expression modules and low-preserved modules were extracted among BC tissues using network clustering. Next, the experimentally validated mRNA-miRNA interaction information were used to reconstruct three mRNA-miRNA bipartite networks. Reactome pathway database and Gene ontology (GO) was subsequently performed for the extracted genes of three bipartite networks and miRNAs, respectively. To further analyze the data, ten hub miRNAs (miRNAs with the highest degree) were selected in each bipartite network to reconstruct three bipartite subnetworks. Finally, the obtained biomarkers were comprehensively investigated and discussed in authentic studies. The obtained results from our study indicated a group of genes including PPARD, CST4, CSNK1E, PTPN14, ETV6, and ADRM1 as well as novel miRNAs (e.g., miR-16-5p, miR-335-5p, miR-124-3p, and let-7b-5p) which might be potentially associated with BC and could be a potential biomarker. Afterward, three drug-gene interaction networks were reconstructed to explore candidate drugs for the treatment of BC. The hub miRNAs in the mRNA-miRNA bipartite network played a fundamental role in BC progression; however, these findings need further investigation.", "claims": [{"id": "claim-data-access", "statement": "The corresponding author can provide the datasets utilized in this study on a reasonable request. The raw dataset is available on Information Gene expression Omnibus (GEO) with GSE13507 accession number (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse13507). (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse13507).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35393513", "locator": "sections[21] \"Data availability\" paragraph 2", "quote": "The corresponding author can provide the datasets utilized in this study on a reasonable request. The raw dataset is available on Information Gene expression Omnibus (GEO) with GSE13507 accession number (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse13507). (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse13507)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The obtained results from our study indicated a group of genes including PPARD, CST4, CSNK1E, PTPN14, ETV6, and ADRM1 as well as novel miRNAs (e.g., miR-16-5p, miR-335-5p, miR-124-3p, and let-7b-5p) which might be potentially associated with BC and could be a potential biomarker.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35393513", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The obtained results from our study indicated a group of genes including PPARD, CST4, CSNK1E, PTPN14, ETV6, and ADRM1 as well as novel miRNAs (e.g., miR-16-5p, miR-335-5p, miR-124-3p, and let-7b-5p) which might be potentially associated with BC and could be a potential biomarker."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The obtained results from our study indicated a group of genes including PPARD, CST4, CSNK1E, PTPN14, ETV6, and ADRM1 as well as novel miRNAs (e.g., miR-16-5p, miR-335-5p, miR-124-3p, and let-7b-5p) which might be potentially associated with BC and could be a potential biomarker.", "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:35393513"], "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": "complete", "blocked_on": null, "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": ["data:geo:GSE13507"], "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": ["data:geo:GSE13507"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35393513", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-022-09920-4", "sha256": "sha256:0d734f3be6dbd83f4807c05eda1d6540af85b0d55c4342405c9ea675a39095cd", "bytes": 75503, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-022-09920-4", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8991185", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13507", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13507", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13507", "version": null, "note": "The corresponding author can provide the datasets utilized in this study on a reasonable request. The raw dataset is available on Information Gene expression Omnibus (GEO) with GSE13507 accession number (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse13507). (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse13507).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The corresponding author can provide the datasets utilized in this study on a reasonable request. The raw dataset is available on Information Gene expression Omnibus (GEO) with GSE13507 accession number (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse13507). 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The microarray dataset of BC tissues (GSE13507) listed in t"], "order_basis": "paper_text_order:381", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["ication, hormone-mediated signaling pathway, apoptosis, and cell death. Additionally, other signifi"], "order_basis": "paper_text_order:10691", "id": "assay:2"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["GO enrichment"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}