Analyzing large scale gene expression data in colorectal cancer reveals important clues; CLCA1 and SELENBP1 downregulated in CRC not in normal and not in adenoma.

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Since molecular biomarkers can help us diagnose colorectal cancer early, we need to identify novel gene for predicting the early stages of tumorigenesis. Here, we integrated five independent CRC gene expression datasets derived from expression profiling by array comparing CRC with normal samples in: GSE21510, GSE4107, GSE25071, GSE15781 dataset, and GSE8671 dataset, including 64 samples from 32 patients comparing 32 colonic normal mucosa with 32 colorectal adenoma. To detect genes that expressed differentially in experimental circumstances of these datasets, we used web tool of GEO2R to compare groups of samples in the GEO data series. Furthermore, we constructed the protein-protein interactions network by STRING database for mostly downregulated genes and the expression of their members in PPI network were studied into five datasets separately. Also, the level of expression of selected biomarker genes in different stages of CRC compared to normal was studied. Our data revealed 17 common downregulated genes (average fold change (FC) in five tests ≥6) in CRC in comparison with normal (Test 1 to Test 4) and in adenoma compared with normal (Test 5). Studying of gene expression of PPI network members of these downregulated genes led to identifying of CLCA1, SELENBP1, CWC25, ACOT11, GUCY2C and ALDH1A1 as suppressor genes and PTGS2, PROCR, MOCS3 and NFS1 as oncogenes which respectively downregulated and upregulated in CRC. Since decreasing of gene expression was seen in CRC comparing with normal and due to no different expression seen for these 10 genes in adenoma, they, especially CLCA1 and SELENBP1, could be considered as biomarkers for early detection of CRC. Before using these signature genes in the clinic; however, further validations are required.", "claims": [{"id": "claim-method", "statement": "To detect genes that expressed differentially in experimental circumstances of these datasets, we used web tool of GEO2R to compare groups of samples in the GEO data series.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35141024", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "To detect genes that expressed differentially in experimental circumstances of these datasets, we used web tool of GEO2R to compare groups of samples in the GEO data series."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Here, we integrated five independent CRC gene expression datasets derived from expression profiling by array comparing CRC with normal samples in: GSE21510, GSE4107, GSE25071, GSE15781 dataset, and GSE8671 dataset, including 64 samples from 32 patients comparing 32 colonic normal mucosa with 32 colorectal adenoma.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35141024", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here, we integrated five independent CRC gene expression datasets derived from expression profiling by array comparing CRC with normal samples in: GSE21510, GSE4107, GSE25071, GSE15781 dataset, and GSE8671 dataset, including 64 samples from 32 patients comparing 32 colonic normal mucosa with 32 colorectal adenoma."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used GEO2R to compare groups of samples from five independent CRC gene-expression datasets and revealed 17 common downregulated genes, with average fold change (FC) in five tests ≥6.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35141024", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "To detect genes that expressed differentially in experimental circumstances of these datasets, we used web tool of GEO2R to compare groups of samples in the GEO data series."}, {"asset": "source:pmid:35141024", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Our data revealed 17 common downregulated genes (average fold change (FC) in five tests ≥6) in CRC in comparison with normal (Test 1 to Test 4) and in adenoma compared with normal (Test 5)."}], "state": "complete"}], "gaps": ["doi"]}, "experiment": {"state": "complete", "objective": "The study used GEO2R to compare groups of samples from five independent CRC gene-expression datasets and revealed 17 common downregulated genes, with average fold change (FC) in five tests ≥6.", "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:35141024"], "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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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:35141024", "data:geo:GSE15781"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE15781"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:33:43Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 2033, "completion_tokens": 1792, "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:35141024", "type": "paper", "label": "pmid:35141024"}, {"id": "source:pmid:35141024", "type": "manuscript", "label": "PMID 35141024 full text"}, {"id": "data:geo:GSE15781", "type": "dataset", "label": "GEO GSE15781"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35141024", "type": "paper", "label": "pmid:35141024"}, {"id": "source:pmid:35141024", "type": "manuscript", "label": "PMID 35141024 full text"}, {"id": "data:geo:GSE15781", "type": "dataset", "label": "GEO GSE15781"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35141024", "type": "extraction", "used": ["source:pmid:35141024"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE15781", "type": "accession_resolution", "used": ["data:geo:GSE15781"], "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:35141024", "parent_hash": "sha256:9d37a48f38a974c2b2693be6ccf371017ceeeef9d6b82c0d56875ecc5fdbf3ee", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE15781 licence not read", "asset:data:geo:GSE15781 not downloaded", "asset:data:geo:GSE21510 licence not read", "asset:data:geo:GSE21510 not downloaded", "asset:data:geo:GSE25071 licence not read", "asset:data:geo:GSE25071 not downloaded", "asset:data:geo:GSE4107 licence not read", "asset:data:geo:GSE4107 not downloaded", "asset:data:geo:GSE8671 licence not read", "asset:data:geo:GSE8671 not downloaded", "doi", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["PPI"], "order_basis": "analysis_only", "id": "assay:1"}]}