Bioinformatics combined with quantitative proteomics analyses and identification of potential biomarkers in cholangiocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32336950", "kind": "science-record", "revision": 8, "content_hash": "sha256:0ed1beceff789ed9c070240e19cb1664bc9ea941a6b47e8bc3958c7bfb4dbd8a", "created_at": "2026-11-01T15:41:00Z", "updated_at": "2026-11-01T22:44:47Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics combined with quantitative proteomics analyses and identification of potential biomarkers in cholangiocarcinoma.", "doi": "10.1186/s12935-020-01212-z", "pmid": "32336950", "authors": ["Zijian Da", "Long Gao", "Gang Su", "Jia Yao", "Wenkang Fu", "Jinduo Zhang", "Xu Zhang", "Zhaoji Pei", "Ping Yue", "Bing Bai", "Yanyan Lin", "Wenbo Meng", "Xun Li"], "journal": "Cancer cell international", "year": 2020, "abstract": "BACKGROUND: Cholangiocarcinoma (CCA) is an invasive malignancy arising from biliary epithelial cells; it is the most common primary tumour of the bile tract and has a poor prognosis. The aim of this study was to screen prognostic biomarkers for CCA by integrated multiomics analysis.\nMETHODS: The GSE32225 dataset was derived from the Gene Expression Omnibus (GEO) database and comprehensively analysed by using R software and The Cancer Genome Atlas (TCGA) database to obtain the differentially expressed RNAs (DERNAs) associated with CCA prognosis. Quantitative isobaric tags for relative and absolute quantification (iTRAQ) proteomics was used to screen differentially expressed proteins (DEPs) between CCA and nontumour tissues. Through integrated analysis of DERNA and DEP data, we obtained candidate proteins APOF, ITGAV and CASK, and immunohistochemistry was used to detect the expression of these proteins in CCA. The relationship between CASK expression and CCA prognosis was further analysed.\nRESULTS: Through bioinformatics analysis, 875 DERNAs were identified, of which 10 were associated with the prognosis of the CCA patients. A total of 487 DEPs were obtained by using the iTRAQ technique. Comprehensive analysis of multiomics data showed that CASK, ITGAV and APOF expression at both the mRNA and protein levels were different in CCA compared with nontumour tissues. CASK was found to be expressed in the cytoplasm and nucleus of CCA cells in 38 (45%) of 84 patients with CCA. Our results suggested that patients with positive CASK expression had significantly better overall survival (OS) and recurrence-free survival (RFS) than those with negative CASK expression. Univariate and multivariate analyses demonstrated that negative expression of CASK was a significantly independent risk factor for OS and RFS in CCA patients.\nCONCLUSIONS: CASK may be a tumour suppressor; its low expression is an independent risk factor for a poor prognosis in CCA patients, and so it could be used as a clinically valuable prognostic marker.", "claims": [{"id": "claim-method", "statement": "Matrix files from the GSE32225 dataset were obtained from the GEO (https://www.ncbi.nlm.nih.gov/geo/) database. We used the “limma” package to identify DERNAs between CCA tissues and nontumour tissues [16].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32336950", "locator": "sections[3] \"Data obtaining and preprocessing\" paragraph 2", "quote": "Matrix files from the GSE32225 dataset were obtained from the GEO (https://www.ncbi.nlm.nih.gov/geo/) database."}, {"asset": "source:pmid:32336950", "locator": "sections[4] \"Identification of differentially expressed RNAs\" paragraph 2", "quote": "We used the “limma” package to identify DERNAs between CCA tissues and nontumour tissues [16]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to sustain the results of this work are included in the article and its supplementary information files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32336950", "locator": "sections[36] \"notes\" paragraph 1", "quote": "The data used to sustain the results of this work are included in the article and its supplementary information files."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:32336950"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32336950", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12935-020-01212-z", "sha256": "sha256:19f30492b3d1285ab1fa8cd11287bc1337a2781a660a9cef8edf0112e7ebfa37", "bytes": 43018, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12935-020-01212-z", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7178764", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:32336950:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f8ffdafecd4d494b54a77e05a825aebe8b703a5566c193d6987c02625ac65cd6", "bytes": 659, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#Tab1", "version": null, "note": "Summary of clinic parameters of CCA patients collected for iTRAQ", "structure": {"pmcid": "PMC7178764", "section_index": 7, "section_title": "Selection of patients and collection of clinical samples", "row_count": 7, "column_count": 6}, "table": {"label": "Table 1", "caption": "Summary of clinic parameters of CCA patients collected for iTRAQ", "rows": [["Code", "Pathology diagnosis", "Age", "Gender", "Grade", "Lymph node metastasis"], ["1", "Cholangiocarcinoma", "51", "Female", "Well", "Positive"], ["2", "Cholangiocarcinoma", "55", "Female", "Poorly", "Negative"], ["3", "Cholangiocarcinoma", "51", "Male", "Poorly", "Positive"], ["4", "Cholangiocarcinoma", "58", "Male", "Moderately", "Positive"], ["5", "Cholangiocarcinoma", "72", "Male", "Moderately", "Negative"], ["6", "Cholangiocarcinoma", "75", "Male", "Moderately", "Negative"]], "row_count": 7, "column_count": 6, "numeric_cells": 12, "header_rows": 1, "locator": "section[7]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:32336950:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:533f898afb5cbd3360d0e805982939f688407fd182d0d216aedc1107d2d8e65f", "bytes": 719, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[2]#Tab2", "version": null, "note": "Summary of clinical characteristic of CCA patients collected for TMAs", "structure": {"pmcid": "PMC7178764", "section_index": 7, "section_title": "Selection of patients and collection of clinical samples", "row_count": 25, "column_count": 2}, "table": {"label": "Table 2", "caption": "Summary of clinical characteristic of CCA patients collected for TMAs", "rows": [["Characteristic", "No. patients (%)"], ["Age"], ["< 55", "34 (39.5)"], ["≥ 55", "52 (60.5)"], ["Gender"], ["Female", "43 (50.0)"], ["Male", "43 (50.0)"], ["Histologic grade"], ["Poorly", "17 (19.8)"], ["Moderate", "64 (74.4)"], ["Well", "5 (5.8)"], ["T classification"], ["T1", "6 (7.0)"], ["T2", "59 (68.6)"], ["T3", "18 (20.9)"], ["T4", "3 (3.5)"], ["N classification"], ["N0", "58 (67.4)"], ["N1", "28 (32.6)"], ["Vascular invasion"], ["No", "57 (66.3)"], ["Yes", "29 (33.7)"], ["Recurrence"], ["No", "31 (36.0)"], ["Yes", "55 (64.0)"]], "row_count": 25, "column_count": 2, "numeric_cells": 19, "header_rows": 1, "locator": "section[7]/table-wrap[2]#Tab2"}}, {"id": "asset:table:pmid:32336950:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:df1108a2ee693463b0a30e01e3f3bab32d8bcc2d953d4bb63ccc1a2b700f2bbf", "bytes": 417, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[1]#Tab3", "version": null, "note": "The Basic Properties of candidate protein", "structure": {"pmcid": "PMC7178764", "section_index": 20, "section_title": "Differentially expressed proteins (DEPs) and integrated analysis", "row_count": 4, "column_count": 5}, "table": {"label": "Table 3", "caption": "The Basic Properties of candidate protein", "rows": [["Accession no.", "Gene symbol", "Sequence coverage (%)", "Peptides", "Gene ID"], ["sp|O14936|CSKP_HUMAN", "CASK", "9.5", "5", "8573"], ["sp|Q13790|APOF_HUMAN", "APOF", "24.7", "16", "319"], ["sp|P06756|ITAV_HUMAN", "ITGAV", "4.3", "1", "3685"]], "row_count": 4, "column_count": 5, "numeric_cells": 12, "header_rows": 1, "locator": "section[20]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:32336950:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:43e66d0ba4298f79cee8f3b33b33ebb1cd490501173a90b6fcecfc6a5878cc90", "bytes": 1133, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[23]/table-wrap[1]#Tab4", "version": null, "note": "The summary of relationship between CASK expression and clinicopathological features of CCA patients", "structure": {"pmcid": "PMC7178764", "section_index": 23, "section_title": "Relationship between CASK expression and clinicopathological features of CCA patients", "row_count": 31, "column_count": 4}, "table": {"label": "Table 4", "caption": "The summary of relationship between CASK expression and clinicopathological features of CCA patients", "rows": [["Category", "No. patients (%)", "CASK", "P value"], ["Negative", "Positive", ""], ["Age", "0.974"], ["< 55", "33 (39.3)", "18", "15"], ["≥ 55", "51 (60.7)", "28", "23"], ["Gender", "0.130"], ["Female", "43 (51.2)", "27", "16"], ["Male", "41 (48.8)", "19", "22"], ["Histologic grade", "0.300"], ["Poorly", "17 (20.2)", "12", "5"], ["Moderate", "62 (73.8)", "32", "30"], ["Well", "5 (6.0)", "2", "3"], ["Stage", "0.491"], ["I", "8 (9.5)", "3", "5"], ["II", "38 (45.2)", "19", "19"], ["III", "25 (29.8)", "16", "9"], ["IV", "13 (15.5)", "8", "5"], ["T classification", "0.017"], ["T1", "6 (7.1)", "2", "4"], ["T2", "58 (69.0)", "30", "28"], ["T3", "17 (20.2)", "14", "3"], ["T4", "3 (3.7)", "0", "3"], ["N classification", "0.757"], ["N0", "56 (66.7)", "30", "26"], ["N1", "28 (33.3)", "16", "12"], ["Vascular invasion", "0.009"], ["No", "56 (66.7)", "25", "31"], ["Yes", "28 (33.3)", "21", "7"], ["Recurrence", "0.117"], ["No", "30 (35.7)", "13", "17"], ["Yes", "54 (64.3)", "33", "21"]], "row_count": 31, "column_count": 4, "numeric_cells": 73, "header_rows": 2, "locator": "section[23]/table-wrap[1]#Tab4"}}, {"id": "asset:table:pmid:32336950:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6964e2b60d34f2ba76dbce3695b630b6a14b76703211d03cc34bd288beeb77d3", "bytes": 903, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[24]/table-wrap[1]#Tab5", "version": null, "note": "Univariate analysis and multivariate analysis of the relationship of CASK expression with OS among CCA patients", "structure": {"pmcid": "PMC7178764", "section_index": 24, "section_title": "Relationship between positive CASK expression and overall survival rate", "row_count": 10, "column_count": 7}, "table": {"label": "Table 5", "caption": "Univariate analysis and multivariate analysis of the relationship of CASK expression with OS among CCA patients", "rows": [["Parameter", "Univariate analysis", "Multivariate analysis"], ["HR", "95% CI", "P", "HR", "95% CI", "P"], ["Age", "1.018", "0.560–1.854", "0.952", "", "", ""], ["Gender", "0.746", "0.422–1.318", "0.313", "", "", ""], ["Histologic grade", "2.050", "1.126–3.732", "0.019", "1.795", "0.939–3.430", "0.077"], ["Stage", "1.681", "1.208–2.340", "0.002", "1.528", "0.944–2.474", "0.085"], ["T classification", "1.262", "0.852–1.869", "0.246", "", "", ""], ["N classification", "1.659", "0.930–2.960", "0.087", "", "", ""], ["Vascular invasion", "2.644", "1.501–4.656", "0.001", "1.236", "0.523–2.918", "0.629"], ["CASK", "2.155", "1.188–3.909", "0.012", "2.031", "1.083–3.809", "0.027"]], "row_count": 10, "column_count": 7, "numeric_cells": 38, "header_rows": 2, "locator": "section[24]/table-wrap[1]#Tab5"}}, {"id": "asset:table:pmid:32336950:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e926fe009cdf15dc5d598334615b0af3f1b1705b67de72471b4d23b27b46cf1c", "bytes": 904, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[25]/table-wrap[1]#Tab6", "version": null, "note": "Univariate analysis and multivariate analysis of the relationship of CASK expression with RFS among CCA patients", "structure": {"pmcid": "PMC7178764", "section_index": 25, "section_title": "Relationship between positive CASK expression and recurrence-free survival rate", "row_count": 10, "column_count": 7}, "table": {"label": "Table 6", "caption": "Univariate analysis and multivariate analysis of the relationship of CASK expression with RFS among CCA patients", "rows": [["Parameter", "Univariate analysis", "Multivariate analysis"], ["HR", "95% CI", "P", "HR", "95% CI", "P"], ["Age", "1.157", "0.655–2.045", "0.616", "", "", ""], ["Gender", "0.835", "0.485–1.437", "0.515", "", "", ""], ["Histologic grade", "1.983", "1.130–3.481", "0.017", "1.918", "1.044–3.526", "0.036"], ["Stage", "1.750", "1.273–2.408", "0.001", "1.612", "1.034–2.514", "0.035"], ["T classification", "1.377", "0.946–2.004", "0.095", "", "", ""], ["N classification", "1.591", "0.910–2.780", "0.103", "", "", ""], ["Vascular invasion", "2.797", "1.625–4.816", "0.000", "1.325", "0.616–2.851", "0.472"], ["CASK", "2.229", "1.259–3.947", "0.006", "2.114", "1.163–3.844", "0.014"]], "row_count": 10, "column_count": 7, "numeric_cells": 38, "header_rows": 2, "locator": "section[25]/table-wrap[1]#Tab6"}}], "gaps": []}, "analysis": {"state": "partial", "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": "reordered", "quote": "Matrix files from the GSE32225 dataset were obtained from the GEO (https://www.ncbi.nlm.nih.gov/geo/) database. We used the “limma” package to identify DERNAs between CCA tissues and nontumour tissues [16]."}}, {"id": "method-2", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["The data used to sustain the results of this work are included in the article and its supplementary information files."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:32336950", "asset:table:pmid:32336950:1", "asset:table:pmid:32336950:2", "asset:table:pmid:32336950:3", "asset:table:pmid:32336950:4", "asset:table:pmid:32336950:5", "asset:table:pmid:32336950:6"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:00:55Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 32328, "completion_tokens": 1436, "cached_tokens": 793}}, "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:32336950", "type": "paper", "label": "pmid:32336950"}, {"id": "source:pmid:32336950", "type": "manuscript", "label": "PMID 32336950 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32336950", "type": "paper", "label": "pmid:32336950"}, {"id": "source:pmid:32336950", "type": "manuscript", "label": "PMID 32336950 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32336950", "type": "extraction", "used": ["source:pmid:32336950"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:32336950", "parent_hash": "sha256:b82d0e2851a7f89189430b2ff111fcb67bf8066dbd140a1cc5ee3eb0b17e5904", "fork_of": null, "generation": 7}, "gaps": ["execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"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": ["candidate proteins APOF, ITGAV and CASK, and immunohistochemistry was used to detect the expression of these p", "versity from 2011 to 2016, and were used for immunohistochemical detection and tissue microarray (TMA) constr"], "order_basis": "paper_text_order:924", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["for immunohistochemical detection and tissue microarray (TMA) construction, respectively. This exper"], "order_basis": "paper_text_order:3344", "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": ["Matrix files from the GSE32225 dataset were obtained from the GEO (https://www.ncbi.nlm.nih.gov/geo/) database. We used the “limma” package to identify DERNAs between CCA tissues and nontumour tissues [16]."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}