Screening of the prognostic targets for breast cancer based co-expression modules analysis.

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The microarray dataset GSE73383 was downloaded from the Gene Expression Omnibus (GEO) database, including 15 breast cancer samples with good prognosis and 9 breast cancer samples with poor prognosis. The differentially expressed genes (DEGs) were identified with the limma package. The Database for Annotation, Visualization and Integrated Discovery was used to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Furthermore, the co‑expression analysis of DEGs was conducted with weighted correlation analysis. The interaction associations were analyzed with the Human Protein Reference Database and BioGRID. The protein‑protein interactions (PPI) network was constructed and visualized by Cytoscape software. A total of 491 DEGs were identified in breast cancer samples with poor prognosis compared with those with good prognosis, and they were enriched in 85 GO terms and 4 KEGG pathways. 368 DEGs were co‑expressed with others, and they were clustered into 10 modules. Module 6 was the most relevant to the clinical features, and 21 genes and 273 interaction pairs were selected out. Abnormal expression levels of required for meiotic nuclear division 5 homolog A (RMND5A) and angiopoietin‑like protein 1 (ANGPTL1) were associated with a poor prognosis. It was indicated that SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily D, member 1, SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily D, member 1, dihydropyrimidinase‑like 2, RMND5A and ANGPTL1 were potential prognostic markers in breast cancer, and the cell cycle may be involved in the regulation of breast cancer.", "claims": [{"id": "claim-method", "statement": "Afterwards, the limma (11) package of R was used to identify the differentially expressed genes (DEGs) in the 9 samples with poor prognosis compared with the 15 samples with good prognosis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28731166", "locator": "sections[5] \"Data pre-processing and identification of differentially expressed genes\" paragraph 2", "quote": "Afterwards, the limma (11) package of R was used to identify the differentially expressed genes (DEGs) in the 9 samples with poor prognosis compared with the 15 samples with good prognosis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The expression microarray dataset GSE73383 was downloaded from the Gene Expression Omnibus (www.ncbi.nlm.nih.gov/geo) database. In this profile, there was a subset of 24 breast cancer samples comprising 15 samples that remained free of disease after surgery (good prognosis) and 9 samples that developed metastasis (poor prognosis).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28731166", "locator": "sections[4] \"Microarray data\" paragraph 2", "quote": "The expression microarray dataset GSE73383 was downloaded from the Gene Expression Omnibus (www.ncbi.nlm.nih.gov/geo) database. In this profile, there was a subset of 24 breast cancer samples comprising 15 samples that remained free of disease after surgery (good prognosis) and 9 samples that developed metastasis (poor prognosis)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using the limma package on microarray dataset GSE73383, the study identified 491 differentially expressed genes in breast cancer samples with poor prognosis compared with those with good prognosis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28731166", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The microarray dataset GSE73383 was downloaded from the Gene Expression Omnibus (GEO) database, including 15 breast cancer samples with good prognosis and 9 breast cancer samples with poor prognosis. The differentially expressed genes (DEGs) were identified with the limma package."}, {"asset": "source:pmid:28731166", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 491 DEGs were identified in breast cancer samples with poor prognosis compared with those with good prognosis, and they were enriched in 85 GO terms and 4 KEGG pathways."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using the limma package on microarray dataset GSE73383, the study identified 491 differentially expressed genes in breast cancer samples with poor prognosis compared with those with good prognosis.", "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:28731166"], "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. 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