A role of TTI1 in the colorectal cancer by promoting proliferation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35116463", "kind": "science-record", "revision": 5, "content_hash": "sha256:8eb478d9f6ccf4daa39718a0f363c2b635aa2cbe017106a58f027d6707f85908", "created_at": "2026-11-01T17:36:50Z", "updated_at": "2026-11-01T22:48:21Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A role of TTI1 in the colorectal cancer by promoting proliferation.", "doi": "10.21037/tcr-20-3322", "pmid": "35116463", "authors": ["Peng Xu", "Guangsheng Du", "Haidi Guan", "Weidong Xiao", "Lihua Sun", "Hua Yang"], "journal": "Translational cancer research", "year": 2021, "abstract": "BACKGROUND: Colorectal cancer (CRC) is one of the most malignant cancer worldwide, which leads to a high incidence and mortality. The molecular mechanism in CRC is still limited. The aim of this study was to identify hub genes and its related function in CRC.\nMETHODS: The expression dataset (GSE44076) was downloaded from Gene Expression Omnibus (GEO) and differentially expressed genes (DEGs) analysis was done using R 'limma' packages. Weighted gene co-expression network analysis (WGCNA) was done and tumor-specific modules were picked up for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The hub gene was selected with higher inter-connectivity. Expression levels of TTI1 were verified by in clinical CRC tissues. The cell counting kit-8 (CCK-8) assay was to measure the proliferative ability of TTI1.\nRESULTS: Eight hundred and eight up-regulated and 929 down-regulated DEGs were screened out. Up-regulated genes enriched in cell proliferation and down-regulated genes enriched in oxidation-reduction process. After WGCNA, the yellow module was found to be the most significant tumor-specific module. Function analysis showed genes in the yellow module enriched in oxidation-reduction, cell proliferation and extracellular matrix (ECM)-receptor interaction. TTI1 was demonstrated as the hub gene. Real-time quantitative reverse transcription((qRT-PCR) results showed TTI1 significantly expressed higher in CRC tissues than adjacent normal tissues. TTI1 dramatically correlated with proliferation in CRC.\nCONCLUSIONS: These findings regarded TTI1 as a vital promoting factor in CRC development and provided a potential biomarker for CRC treatment.", "claims": [{"id": "claim-method", "statement": "DEGs were obtained through R language software 3.6.1 using ‘limma’ packages.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35116463", "locator": "sections[4] \"Microarray data source and analysis\" paragraph 2", "quote": "DEGs were obtained through R language software 3.6.1 using ‘limma’ packages."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression dataset (GSE44076) was downloaded from GEO. Gene expression profiles of paired normal adjacent mucosa and tumor samples from 98 individuals and 50 healthy colon mucosae were obtained through Affymetrix Human Genome U219 Arrays.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35116463", "locator": "sections[4] \"Microarray data source and analysis\" paragraph 2", "quote": "The gene expression dataset (GSE44076) was downloaded from GEO. Gene expression profiles of paired normal adjacent mucosa and tumor samples from 98 individuals and 50 healthy colon mucosae were obtained through Affymetrix Human Genome U219 Arrays."}], "state": "complete"}, {"id": "claim-target-result", "statement": "TTI1 was identified as a CRC-associated hub gene that promotes colorectal cancer cell proliferation.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35116463", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "These findings regarded TTI1 as a vital promoting factor in CRC development and provided a potential biomarker for CRC treatment."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "TTI1 was identified as a CRC-associated hub gene that promotes colorectal cancer cell proliferation.", "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:35116463"], "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:GSE21510"], "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:GSE21510"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35116463", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tcr-20-3322", "sha256": "sha256:589f9fd2ca434a546501a8b9658aa7694eac7078a7c85341cc6b2ca7763faebc", "bytes": 34380, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tcr-20-3322", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8798799", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE21510", "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=GSE21510", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE21510", "version": null, "note": "The gene expression dataset (GSE44076) was downloaded from GEO. 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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": ["GSE44076", "GSE32323", "GSE21510"], "resolved_accessions": ["GSE44076", "GSE32323", "GSE21510"], "statements": ["The gene expression dataset (GSE44076) was downloaded from GEO. Gene expression profiles of paired normal adjacent mucosa and tumor samples from 98 individuals and 50 healthy colon mucosae were obtained through Affymetrix Human Genome U219 Arrays."], "basis": "The paper names GSE44076, GSE32323, GSE21510 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:35116463", "data:geo:GSE21510"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE21510"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:31:49Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 10474, "completion_tokens": 1054, "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:35116463", "type": "paper", "label": "pmid:35116463"}, {"id": "source:pmid:35116463", "type": "manuscript", "label": "PMID 35116463 full text"}, {"id": "data:geo:GSE21510", "type": "dataset", "label": "GEO GSE21510"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35116463", "type": "paper", "label": "pmid:35116463"}, {"id": "source:pmid:35116463", "type": "manuscript", "label": "PMID 35116463 full text"}, {"id": "data:geo:GSE21510", "type": "dataset", "label": "GEO GSE21510"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35116463", "type": "extraction", "used": ["source:pmid:35116463"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE21510", "type": "accession_resolution", "used": ["data:geo:GSE21510"], "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:35116463", "parent_hash": "sha256:951165ca00c3121c1d13cddca2bbe5e2d8f5f9e7f1982e3c32d36480ee86dd9e", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE21510 licence not read", "asset:data:geo:GSE21510 not downloaded", "asset:data:geo:GSE32323 licence not read", "asset:data:geo:GSE32323 not downloaded", "asset:data:geo:GSE44076 licence not read", "asset:data:geo:GSE44076 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["inical CRC tissues. The cell counting kit-8 (CCK-8) assay was to measure the proliferative abil"], "order_basis": "paper_text_order:801", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Methods Cell culture and transfection Human CRC cancer cell lines (CaCO2, HT29) we", ") was used coupled with LipofectamineTM 2000 Transfection Reagent (Invitrogen, USA). siRNA duplexes ta", "of cells reached 30–50% and then cells were transfected with the siRNA targeting TTI1 and negative c", "Con) through the use of LipofectamineTM 2000 Transfection Reagent (Invitrogen, USA). After a 6-hour tr"], "order_basis": "paper_text_order:1755", "id": "assay:2"}, {"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": 1.0, "evidence": ["DEGs were obtained through R language software 3.6.1 using ‘limma’ packages."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}