Integrated transcriptome analysis identifies APPL1/RPS6KB2/GALK1 as immune-related metastasis factors in breast cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37273920", "kind": "science-record", "revision": 2, "content_hash": "sha256:79ffdeb0f740e60f710cc2e8e659f75a67d5509fcfe1f15b8370a7e1839d70f6", "created_at": "2026-11-01T19:01:59Z", "updated_at": "2026-11-01T21:30:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated transcriptome analysis identifies APPL1/RPS6KB2/GALK1 as immune-related metastasis factors in breast cancer.", "doi": "10.1515/med-2023-0732", "pmid": "37273920", "authors": ["Gang Chen", "Kun Zhang", "Zhi Liang", "Song Zhang", "Yuanping Dai", "Yizi Cong", "Guangdong Qiao"], "journal": "Open medicine (Warsaw, Poland)", "year": 2023, "abstract": "The aim of this study is to investigate the prognostic immune-related factors in breast cancer (BC) metastasis. The gene expression chip GSE159956 was downloaded from the gene expression omnibus database. Differentially expressed genes (DEGs) were selected using GEO2R online tools based on lymph node and metastasis status. The intersected survival-associated DEGs were screened from the Kaplan-Meier curve. Gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) annotation analyses were performed to determine the survival-associated DEGs. Immune-related prognostic factors were screened based on immune infiltration. The screened prognostic factors were verified by the Cancer Genome Atlas (TCGA) database and single-sample gene set enrichment analysis (ssGSEA). As a result, twenty-eight upregulated and three downregulated genes were generated by the survival analysis. The enriched GO and KEGG pathways were mostly correlated with \"regulation of cellular amino acid metabolic process,\" \"proteasome complex,\" \"endopeptidase activity,\" and \"proteasome.\" Six of 19 (17 upregulated and 2 downregulated) immune-related prognostic factors were verified by the TCGA database. Four immune-related factors were obtained after ssGSEA, and three significant immune-related factors were selected after univariate and multivariate analyses. Based on the risk score receiver operating characteristic, the three immune-related prognosis factors could be potential biomarkers of BC metastasis. In conclusion, APPL1, RPS6KB2, and GALK1 may play a pivotal role as potential biomarkers for prediction of BC metastasis.", "claims": [{"id": "claim-method", "statement": "LASSO regression was carried out, and four prognosis factors were selected (Figure 7a and b).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37273920", "locator": "sections[16] \"Three immune-associated prognostic features were recognized by the ssGSEA\" paragraph 2", "quote": "LASSO regression was carried out, and four prognosis factors were selected (Figure 7a and b)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data availability statement: The data used to support the findings of this study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37273920", "locator": "sections[19] \"fn-group\" paragraph 1", "quote": "Data availability statement: The data used to support the findings of this study are available from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "APPL1, RPS6KB2, and GALK1 may play a pivotal role as potential biomarkers for prediction of BC metastasis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37273920", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In conclusion, APPL1, RPS6KB2, and GALK1 may play a pivotal role as potential biomarkers for prediction of BC metastasis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "APPL1, RPS6KB2, and GALK1 may play a pivotal role as potential biomarkers for prediction of BC metastasis.", "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:37273920"], "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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