Risk-Related Genes and Associated Signaling Pathways of Gastrointestinal Stromal Tumors.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35431569", "kind": "science-record", "revision": 5, "content_hash": "sha256:335164213ddf569044620321af0acc98c1be4f45614ec888a6871123ecf7a6d2", "created_at": "2026-11-01T18:14:15Z", "updated_at": "2026-11-01T22:48:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Risk-Related Genes and Associated Signaling Pathways of Gastrointestinal Stromal Tumors.", "doi": "10.2147/IJGM.S357224", "pmid": "35431569", "authors": ["Fulai Gao", "Jiaqi Wang", "Changjuan Li", "Changshun Xie", "Miao Su", "Chunyan Zou", "Xiaoli Xie", "Dongqiang Zhao"], "journal": "International journal of general medicine", "year": 2022, "abstract": "Purpose: Knowledge on the potential association between differential gene expression and risk of gastrointestinal stromal tumors (GISTs) is currently limited. We used bioinformatics tools to identify differentially expressed genes in GIST samples and the related signaling pathways of these genes.\nPatients and Methods: The GSE136755 dataset was obtained from the GEO database and differentially expressed genes (CENPA, CDK1, TPX2, CCNB1, CCNA2, BUB1, AURKA, KIF11, NDC80) were screened using String and Cytoscape bioinformatics tools. Then, three groups of eight patients at high, intermediate and low risk of GIST were selected from patients diagnosed with GIST by immunohistochemistry in our hospital from October 2020 to March 2021. Differential expression of CDK1 and BUB1 was verified by comparing the amount of expressed p21-Activated kinase 4 (PAK4) protein in pathological sections.\nResults: SPSS26.0 analysis showed that the expression level of PAK4 in GISTs was significantly higher than in normal tissues and paratumoral tissues and there was significant difference among the three groups of patients (P < 0.01). PAK4 levels in paratumoral and normal tissues were negligible with no significant difference between the tissues.\nConclusion: CENPA, CDK1, TPX2, CCNB1, CCNA2, BUB1, AURKA, KIF11 and NDC80 gene expression can be used as biomarkers to assess the risk of gastrointestinal stromal tumors whereby expression increases gradually with the increased risk of GIST formation. The genes encode proteins that regulate the division, proliferation and apoptosis of gastrointestinal stromal tumors mainly through PI3K/AKT, MARK, P53, WNT and other signaling pathways.", "claims": [{"id": "claim-method", "statement": "We used the Limma package software of the R language to compare the gene expression profiles of selected genes within the three groups of patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35431569", "locator": "sections[4] \"Differential Gene Screening\" paragraph 2", "quote": "We used the Limma package software of the R language to compare the gene expression profiles of selected genes within the three groups of patients."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the data in the present study are available in the public database (https://www.ncbi.nlm.nih.gov).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35431569", "locator": "sections[14] \"Data Sharing Statement\" paragraph 2", "quote": "All the data in the present study are available in the public database (https://www.ncbi.nlm.nih.gov)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "PAK4 expression was significantly higher in GISTs than in normal and paratumoral tissues and differed significantly among the three risk groups (p<0.01).", "kind": "quantitative", "target": {"value": 0.01, "unit": "p-value", "tolerance": null, "source": "SPSS26.0 analysis showed that the expression level of PAK4 in GISTs was significantly higher than that in normal tissues and paratumoral tissues (Tables 1–4), there was significant difference among the three groups (p<0.01) and the expression of PAK4 in paratumoral tissues and normal tissues was negligible with no notable significant difference between the control samples (Figure 3)."}, "evidence": [{"asset": "source:pmid:35431569", "locator": "sections[9] \"Results\" paragraph 3", "quote": "SPSS26.0 analysis showed that the expression level of PAK4 in GISTs was significantly higher than that in normal tissues and paratumoral tissues (Tables 1–4), there was significant difference among the three groups (p<0.01) and the expression of PAK4 in paratumoral tissues and normal tissues was negligible with no notable significant difference between the control samples (Figure 3)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "PAK4 expression was significantly higher in GISTs than in normal and paratumoral tissues and differed significantly among the three risk groups (p<0.01).", "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:35431569"], "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:GSE136755"], "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:GSE136755"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35431569", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/IJGM.S357224", "sha256": "sha256:b5e6acce125d14383e79c323f77db25eeef8ecfdb58fdcea0763aa3367cb18ee", "bytes": 25183, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/IJGM.S357224", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9005359", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE136755", "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=GSE136755", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE136755", "version": null, "note": "All the data in the present study are available in the public database (https://www.ncbi.nlm.nih.gov).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the data in the present study are available in the public database (https://www.ncbi.nlm.nih.gov).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4057318", "GSM4057319", "GSM4057320", "GSM4057321", "GSM4057322", "GSM4057323", "GSM4057324", "GSM4057325", "GSM4057326", "GSM4057327", "GSM4057328", "GSM4057329", "GSM4057330", "GSM4057331", "GSM4057332", "GSM4057333", "GSM4057334", "GSM4057335", "GSM4057336", "GSM4057337", "GSM4057338", "GSM4057339", "GSM4057340", "GSM4057341", "GSM4057342", "GSM4057343", "GSM4057344", "GSM4057345", "GSM4057346", "GSM4057347", "GSM4057348", "GSM4057349", "GSM4057350", "GSM4057351", "GSM4057352", "GSM4057353", "GSM4057354", "GSM4057355", "GSM4057356", "GSM4057357", "GSM4057358", "GSM4057359", "GSM4057360", "GSM4057361", "GSM4057362", "GSM4057363", "GSM4057364", "GSM4057365", "GSM4057366", "GSM4057367", "GSM4057368", "GSM4057369", "GSM4057370", "GSM4057371", "GSM4057372", "GSM4057373", "GSM4057374", "GSM4057375", "GSM4057376", "GSM4057377", "GSM4057378", "GSM4057379", "GSM4057380", "GSM4057381", "GSM4057382"], "sample_count": 65, "group_sizes": null, "group_sizes_basis": null, "platform": "17077", "taxon": "Homo sapiens", "title": "Driver gene alterations and activated signaling pathways toward malignant progression of gastrointestinal stromal tumors", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE136755 not downloaded", "asset:data:geo:GSE136755 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We used the Limma package software of the R language to compare the gene expression profiles of selected genes within the three groups of patients."}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "differential_expression_fit", "expected_value": 0.01, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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