Identification of IMPA2 as the hub gene associated with colorectal cancer and liver metastasis by integrated bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35483170", "kind": "science-record", "revision": 4, "content_hash": "sha256:20044a3d421da92254bd86f3080aeda06666e85178f423bac3c6c92afc25f1cf", "created_at": "2026-11-01T18:14:21Z", "updated_at": "2026-11-01T22:06:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of IMPA2 as the hub gene associated with colorectal cancer and liver metastasis by integrated bioinformatics analysis.", "doi": "10.1016/j.tranon.2022.101435", "pmid": "35483170", "authors": ["Liuli Wang", "Deming Liu", "Shuo Liu", "Tianyi Liao", "Yajun Jiao", "Xianglai Jiang", "Yongfeng Wang", "Yaqiong Chen", "Haizhong Ma", "Hui Cai"], "journal": "Translational oncology", "year": 2022, "abstract": "BACKGROUND AND OBJECTIVES: Colorectal cancer (CRC) is one of the most common malignant tumors worldwide with high incidence and mortality rate, while colorectal liver metastasis (CRLM) is one of the major causes of cancer-related deaths. Therefore, the present study aims to identify the hub gene associated with CRC carcinogenesis and liver metastasis, and then explore its diagnostic and prognostic value as well as the potential regulation mechanism.\nMETHODS: The overlapping differential co-expression genes among CRC, CRLM, and normal tissues were explored on the GSE49355 and GSE81582 datasets from the Gene Expression Omnibus (GEO) database by integrated bioinformatics analysis. Then, the hub prognostic genes were selected from the overlapping genes by univariate Cox proportional hazard analysis and online database Gene Expression Profiling Interactive Analysis 2 (GEPIA2). Subsequently, the clinical value of the hub genes was evaluated in the TCGA and GSE39582 cohorts. Finally, the underlying mechanisms of the hub gene regulating CRC carcinogenesis and metastasis were explored by Gene function annotation and DNA methylation analysis.\nRESULTS: Inositol mono-phosphatase 2 (IMPA2) was identified as the hub gene associated with CRC carcinogenesis and liver metastasis. IMPA2 had an excellent diagnostic efficiency, and its expression was significantly decreased in CRC and liver metastasis samples, being positively correlated with poor prognosis. Moreover, its low expression was associated with AJCC stage III+IV, T4, N1+2, and M1. In addition, our results revealed that the potential mechanisms used by IMPA2 to mediate CRC carcinogenesis and metastasis could be associated with lipid metabolism and epithelial mesenchymal transition (EMT). Finally, IMPA2 expression could be regulated by DNA methylation.\nCONCLUSIONS: IMPA2 was identified and reported for the first time as a hub gene biomarker in the diagnosis and prognosis of CRC, which could regulate CRC carcinogenesis and liver metastasis through the regulation of lipid metabolism, EMT, and DNA methylation.", "claims": [{"id": "claim-data-access", "statement": "Gene expression raw microarray profiles of CRC were evaluated in five independent datasets (accession nos. GSE49355 [15], GSE81582 [16], GSE39582 [17], GSE41258 [18], and GSE17536 [19]) from the GEO database (www.ncbi.nlm.nih.gov/geo). GSE49355 included 57 samples (19 CRLM, 20 primary CRC and 18 normal tissues);", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35483170", "locator": "sections[3] \"GEO data set and data processing\" paragraph 2", "quote": "Gene expression raw microarray profiles of CRC were evaluated in five independent datasets (accession nos. GSE49355 [15], GSE81582 [16], GSE39582 [17], GSE41258 [18], and GSE17536 [19]) from the GEO database (www.ncbi.nlm.nih.gov/geo). GSE49355 included 57 samples (19 CRLM, 20 primary CRC and 18 normal tissues);"}], "state": "complete"}, {"id": "claim-target-result", "statement": "The overlapping differential co-expression genes among CRC, CRLM, and normal tissues were explored on the GSE49355 and GSE81582 datasets from the Gene Expression Omnibus (GEO) database by integrated bioinformatics analysis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35483170", "locator": "sections[0] \"Abstract\" paragraph 6", "quote": "The overlapping differential co-expression genes among CRC, CRLM, and normal tissues were explored on the GSE49355 and GSE81582 datasets from the Gene Expression Omnibus (GEO) database by integrated bioinformatics analysis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The overlapping differential co-expression genes among CRC, CRLM, and normal tissues were explored on the GSE49355 and GSE81582 datasets from the Gene Expression Omnibus (GEO) database by integrated bioinformatics analysis.", "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:35483170"], "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:GSE17536"], "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:GSE17536"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35483170", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.tranon.2022.101435", "sha256": "sha256:ddd339879c73cde0cfaf9e6e61061b9c5bfcf23cd33b6f2710667d6dcc69587e", "bytes": 35467, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.tranon.2022.101435", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9136607", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE17536", "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=GSE17536", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE17536", "version": null, "note": "Gene expression raw microarray profiles of CRC were evaluated in five independent datasets (accession nos. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE49355", "GSE81582", "GSE39582", "GSE41258", "GSE17536"], "resolved_accessions": ["GSE49355", "GSE81582", "GSE39582", "GSE41258", "GSE17536"], "statements": ["Gene expression raw microarray profiles of CRC were evaluated in five independent datasets (accession nos. GSE49355 [15], GSE81582 [16], GSE39582 [17], GSE41258 [18], and GSE17536 [19]) from the GEO database (www.ncbi.nlm.nih.gov/geo). GSE49355 included 57 samples (19 CRLM, 20 primary CRC and 18 normal tissues);"], "basis": "The paper names GSE49355, GSE81582, GSE39582, GSE41258, GSE17536 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:35483170", "data:geo:GSE17536"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE17536"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:43:56Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": null}, "calls": 5, "usage": {"prompt_tokens": 9951, "completion_tokens": 1540, "cached_tokens": 128}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:35483170", "type": "paper", "label": "pmid:35483170"}, {"id": "source:pmid:35483170", "type": "manuscript", "label": "PMID 35483170 full text"}, {"id": "data:geo:GSE17536", "type": "dataset", "label": "GEO GSE17536"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35483170", "type": "paper", "label": "pmid:35483170"}, {"id": "source:pmid:35483170", "type": "manuscript", "label": "PMID 35483170 full text"}, {"id": "data:geo:GSE17536", "type": "dataset", "label": "GEO GSE17536"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35483170", "type": "extraction", "used": ["source:pmid:35483170"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE17536", "type": "accession_resolution", "used": ["data:geo:GSE17536"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:35483170", "parent_hash": "sha256:e4ef94e2cede4c78ca7aa656add01eea0ef0af0d43eca155cfd4d26367fd9466", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE17536 licence not read", "asset:data:geo:GSE17536 not downloaded", "asset:data:geo:GSE39582 licence not read", "asset:data:geo:GSE39582 not downloaded", "asset:data:geo:GSE41258 licence not read", "asset:data:geo:GSE41258 not downloaded", "asset:data:geo:GSE49355 licence not read", "asset:data:geo:GSE49355 not downloaded", "asset:data:geo:GSE81582 licence not read", "asset:data:geo:GSE81582 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["set and data processing Gene expression raw microarray profiles of CRC were evaluated in five indep", "” package [20] and the normalization for the microarray data was completed using the “limma” package"], "order_basis": "paper_text_order:2249", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["limma"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}