Down-regulated Solute Carrier Family 4 Member 4 Predicts Poor Progression in Colorectal Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32284764", "kind": "science-record", "revision": 8, "content_hash": "sha256:3961968b8ebe9fa77e5e32e52c1d9bc33a2bd7bb13dc0ab884660d73c9446b8d", "created_at": "2026-11-01T15:40:59Z", "updated_at": "2026-11-01T22:01:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Down-regulated Solute Carrier Family 4 Member 4 Predicts Poor Progression in Colorectal Cancer.", "doi": "10.7150/jca.36696", "pmid": "32284764", "authors": ["Hong Yang", "Yao Lu", "Weilan Lan", "Bin Huang", "Jiumao Lin"], "journal": "Journal of Cancer", "year": 2020, "abstract": "Aim: To identify potential key candidate genes, whose expression and clinical significance was further assessed in colorectal cancer (CRC). Methods: Three original microarray datasets (GSE41328, GSE22598, and GSE23878) from NCBI-GEO were used to analyze differentially expressed genes (DEGs) in CRC. Online database analyses through Oncomine and GEIPA were performed to evaluate SLC4A4 expression and explore the prognostic merit of SLC4A4 expression, which was further confirmed by analyses from QPCR based cDNA array and IHC based tissue microarray (TMA). STRING website was used to explore the interaction between SLC4A4 with other DEGs based on the protein-protein interaction (PPI) networks. Results: Analysis of three original microarray datasets from GEO identified 82 shared, differentially expressed genes (28 upregulated and 54 down-regulated) in CRC tissues. Online analyses from Oncomine and GEIPA revealed lower SLC4A4 mRNA expression in CRC tissues compared to adjacent normal tissues, which were further confirmed by QPCR based cDNA array and IHC based TMA analyses on both mRNA and protein levels. Survival analyses through GEIPA and from TMA demonstrated that low SLC4A4 expression is correlated with worse overall survival among patients with CRC. Survival analysis from Kaplan-meier plotter demonstrated that low SLC4A4 expression is significantly associated with poor progression (including relapse-free survival, overall survival, distant metastasis-free survival, post-progression survival) of patients with breast cancer, lung cancer, gastric cancer, and ovarian cancer. PPI analysis found that SLC4A4 is highly correlated with various genes, including SLC9A3, SLC26A6, ENSG00000214921, SLC26A4, SLC9A3R1, and SLC9A1. Conclusion: The mRNA and protein levels of SLC4A4 were decreased in CRC tissues, and low expression of SLC4A4 significantly correlated with shorter survival of CRC patients and poorer progression of patients with breast cancer, lung cancer, gastric cancer and ovarian cancer, suggesting potential role of SLC4A4 on tumor suppression and prognostic prediction in multiple malignancies including CRC.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes (DEGs) were identified using the classical t-test, and statistically significant DEGs were defined with P < 0.01 and [logFC] > 2 as the cutoff criteria.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32284764", "locator": "sections[3] \"Microarray data information and DEGs identification\" paragraph 3", "quote": "Differentially expressed genes (DEGs) were identified using the classical t-test, and statistically significant DEGs were defined with P < 0.01 and [logFC] > 2 as the cutoff criteria."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray data in GSE22598 included 17 pairs of cancer and non-cancerous tissues from CRC patients (Submission date: December 04, 2011) 13.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32284764", "locator": "sections[3] \"Microarray data information and DEGs identification\" paragraph 2", "quote": "The microarray data in GSE22598 included 17 pairs of cancer and non-cancerous tissues from CRC patients (Submission date: December 04, 2011) 13."}], "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:32284764"], "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": ["survival_km"], "assets": ["source:pmid:32284764", "data:geo:GSE22598", "asset:table:pmid:32284764:1", "asset:table:pmid:32284764:2", "asset:table:pmid:32284764:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE22598"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:19:19Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 27829, "completion_tokens": 2153, "cached_tokens": 9480}}, "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:32284764", "type": "paper", "label": "pmid:32284764"}, {"id": "source:pmid:32284764", "type": "manuscript", "label": "PMID 32284764 full text"}, {"id": "data:geo:GSE22598", "type": "dataset", "label": "GEO GSE22598"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32284764", "type": "paper", "label": "pmid:32284764"}, {"id": "source:pmid:32284764", "type": "manuscript", "label": "PMID 32284764 full text"}, {"id": "data:geo:GSE22598", "type": "dataset", "label": "GEO GSE22598"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32284764", "type": "extraction", "used": ["source:pmid:32284764"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE22598", "type": "accession_resolution", "used": ["data:geo:GSE22598"], "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:32284764", "parent_hash": "sha256:51496082c74c7d745ae2f3b72350340080995c4c91496111b3f5fd094b2324e0", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE22598 licence not read", "asset:data:geo:GSE22598 not downloaded", "asset:data:geo:GSE23878 licence not read", "asset:data:geo:GSE23878 not downloaded", "asset:data:geo:GSE41328 licence not read", "asset:data:geo:GSE41328 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": ["rectal cancer (CRC). Methods: Three original microarray datasets (GSE41328, GSE22598, and GSE23878)", "m QPCR based cDNA array and IHC based tissue microarray (TMA). STRING website was used to explore th", "etworks. Results: Analysis of three original microarray datasets from GEO identified 82 shared, diff"], "order_basis": "paper_text_order:215", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["which was further confirmed by analyses from QPCR based cDNA array and IHC based tissue microa", "mal tissues, which were further confirmed by QPCR based cDNA array and IHC based TMA analyses"], "order_basis": "paper_text_order:548", "id": "assay:2"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["d by analyses from QPCR based cDNA array and IHC based tissue microarray (TMA). 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