Prognostic biomarkers related to breast cancer recurrence identified based on Logit model analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32977823", "kind": "science-record", "revision": 6, "content_hash": "sha256:1032f10a377fd5e5bdfd58bbfe3dfd9c4493c4c2284956d4519f41c0975b67d8", "created_at": "2026-11-01T15:41:11Z", "updated_at": "2026-11-01T21:23:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognostic biomarkers related to breast cancer recurrence identified based on Logit model analysis.", "doi": "10.1186/s12957-020-02026-z", "pmid": "32977823", "authors": ["Xiaoying Zhou", "Chuanguang Xiao", "Tong Han", "Shusheng Qiu", "Meng Wang", "Jun Chu", "Weike Sun", "Liang Li", "Lili Lin"], "journal": "World journal of surgical oncology", "year": 2020, "abstract": "BACKGROUND: This study intended to determine important genes related to the prognosis and recurrence of breast cancer.\nMETHODS: Gene expression data of breast cancer patients were downloaded from TCGA database. Breast cancer samples with recurrence and death were defined as poor disease-free survival (DFS) group, while samples without recurrence and survival beyond 5 years were defined as better DFS group. Another gene expression profile dataset (GSE45725) of breast cancer was downloaded as the validation data. Differentially expressed genes (DEGs) were screened between better and poor DFS groups, which were then performed function enrichment analysis. The DEGs that were enriched in the GO function and KEGG signaling pathway were selected for cox regression analysis and Logit regression (LR) model analysis. Finally, correlation analysis between LR model classification and survival prognosis was analyzed.\nRESULTS: Based on the breast cancer gene expression profile data in TCGA, 540 DEGs were screened between better DFS and poor DFS groups, including 177 downregulated and 363 upregulated DEGs. A total of 283 DEGs were involved in all GO functions and KEGG signaling pathways. Through LR model screening, 10 important feature DEGs were identified and validated, among which, ABCA3, CCL22, FOXJ1, IL1RN, KCNIP3, MAP2K6, and MRPL13, were significantly expressed in both groups in the two data sets. ABCA3, CCL22, FOXJ1, IL1RN, and MAP2K6 were good prognostic factors, while KCNIP3 and MRPL13 were poor prognostic factors.\nCONCLUSION: ABCA3, CCL22, FOXJ1, IL1RN, and MAP2K6 may serve as good prognostic factors, while KCNIP3 and MRPL13 may be poor prognostic factors for the prognosis of breast cancer.", "claims": [{"id": "claim-method", "statement": "The DEGs that were enriched in the GO function and KEGG signaling pathway were selected for cox regression analysis and Logit regression (LR) model analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32977823", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The DEGs that were enriched in the GO function and KEGG signaling pathway were selected for cox regression analysis and Logit regression (LR) model analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and analyzed in the current study are available from the corresponding author in response to reasonable requests.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32977823", "locator": "sections[24] \"Availability of data and materials\" paragraph 2", "quote": "The datasets used and analyzed in the current study are available from the corresponding author in response to reasonable requests."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "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:32977823"], "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:GSE45725"], "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:GSE45725"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32977823", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12957-020-02026-z", "sha256": "sha256:73ab61d88b71f2adb2843f47b5a9fac467b5d4100e61929a6b28c9744dcccbe0", "bytes": 36327, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12957-020-02026-z", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7519567", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE45725", "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=GSE45725", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE45725", "version": null, "note": "The datasets used and analyzed in the current study are available from the corresponding author in response to reasonable requests.", 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