A prognostic fibroblast-related risk signature in colorectal cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34735373", "kind": "science-record", "revision": 5, "content_hash": "sha256:712607155059b82ba07ffad1c4e9f4551a56fd7649f84d48e4ee0fc4cece5fd9", "created_at": "2026-11-01T17:36:25Z", "updated_at": "2026-11-01T22:47:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A prognostic fibroblast-related risk signature in colorectal cancer.", "doi": "10.18632/aging.203677", "pmid": "34735373", "authors": ["Hao Xu", "Yisheng Pan"], "journal": "Aging", "year": 2021, "abstract": "Colorectal cancer (CRC) is the third most common cancer in the world. The accessibility of the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus data allows the prognostic evaluation of CRC. Fibroblasts play a key role in the development and progression of tumors while fibroblast-related risk signature in CRC patients has rarely been mentioned. In this study, TCGA data was classified into high-fibroblast and low-fibroblast groups according to the median of fibroblast content. Among 3845 differentially expressed genes between two groups, 14 prognostic genes commonly expressed in GSE39582 and TCGA were identified by LASSO-COX analysis. Then we established a fibroblast-related risk signature in TCGA training group and validated in the GSE39582 testing group. The risk score was significantly associated with the overall survival (OS), and the poor prognosis of patients in high-risk group might relate to the immune cell infiltration in the tumor microenvironment, epithelial-mesenchymal transition, and extracellular matrix related processes. Overall, we proved that the fibroblast-related signature could predict the prognosis of patients which might shed light on the treatment of CRC.", "claims": [{"id": "claim-method", "statement": "Univariate Cox was used to obtain 222 prognostic genes in training set through traversing all DEGs in fibroblast high/low condition, and LASSO-penalized Cox regression was used to construct optimal prognostic risk signatures in training group. R package survival and survminer were applied to investigate the difference of prognosis between two groups by log-rank test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34735373", "locator": "sections[7] \"Development and validation of the prognostic signature\" paragraph 2", "quote": "Univariate Cox was used to obtain 222 prognostic genes in training set through traversing all DEGs in fibroblast high/low condition, and LASSO-penalized Cox regression was used to construct optimal prognostic risk signatures in training group."}, {"asset": "source:pmid:34735373", "locator": "sections[8] \"Survival analysis\" paragraph 2", "quote": "R package survival and survminer were applied to investigate the difference of prognosis between two groups by log-rank test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data for this study are available from the corresponding public database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34735373", "locator": "sections[12] \"Data availability statement\" paragraph 2", "quote": "All data for this study are available from the corresponding public database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study established a 14-gene fibroblast-related risk signature whose risk score was significantly associated with overall survival in the TCGA training cohort and the GSE39582 testing cohort.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34735373", "locator": "sections[15] \"Development of a fibroblast-related risk signature\" paragraph 2", "quote": "Then 14 genes identified by LASSO-COX analysis were used to establish a fibroblast-related risk signature of CRC in TCGA."}, {"asset": "source:pmid:34735373", "locator": "sections[15] \"Development of a fibroblast-related risk signature\" paragraph 2", "quote": "The results confirmed that the fibroblast-related risk signature was significantly associated with the OS of CRC patients in the testing group (Figure 2E)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study established a 14-gene fibroblast-related risk signature whose risk score was significantly associated with overall survival in the TCGA training cohort and the GSE39582 testing cohort.", "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:34735373"], "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:GSE39582"], "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:GSE39582"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34735373", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/aging.203677", "sha256": 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