Celiac disease microarray analysis based on System Biology Approach.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30013745", "kind": "science-record", "revision": 8, "content_hash": "sha256:75f40a7af1d437ad33e604aff1ab5bece375201055945398bcddc46b09ed1a00", "created_at": "2026-11-01T15:40:35Z", "updated_at": "2026-11-01T21:59:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "partial", "title": "Celiac disease microarray analysis based on System Biology Approach.", "doi": null, "pmid": "30013745", "authors": ["Mostafa Rezaei Tavirani", "Davood Bashash", "Fatemeh Tajik Rostami", "Sina Rezaei Tavirani", "Abdolrahim Nikzamir", "Majid Rezaei Tavirani", "Mohammad Hossain Haidary"], "journal": "Gastroenterology and hepatology from bed to bench", "year": 2018, "abstract": "AIM: Aim of this study is screen of the large numbers of related genes of CD to find the key ones.\nBACKGROUND: Celiac disease (CD) is known as a gluten sensitive and immune system dependent disease. There are several high throughput investigations about CD but it is necessary to clarify new molecular aspects mechanism of celiac.\nMETHODS: Whole-genome profile (RNA) of the human peripheral blood mononuclear cells (PBMCs) as Gene expression profile GSE113469 was retrieved Gene Expression Omnibus (GEO) database. The significant genes were selected and analyzed via protein-protein interaction (PPI) network by Cytoscape software. The key genes were introduced and enriched via ClueGO to find the related biochemical pathways.\nRESULTS: Among 250 significant genes 47 genes with expressed change above 2 fold change (FC) were interacted and the constructed network were analyzed. The network characterized by poor connections so it was promoted by addition 50 related nodes and 18 crucial nodes were introduced. Two clusters of biochemical pathways were identified and discussed.\nCONCLUSION: There is an obvious conflict between microarray finding and the well-known related genes of CD. This problem can be solve by more attention to the interpretation of PPI ntwork analysis results.", "claims": [{"id": "claim-method", "statement": "Numbers of 250 top score genes were selected and differences between control and celiac samples were calculated using the Student’s t test statistical p-values less than 0.05 and adjusted p-values via GEO2R analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30013745", "locator": "sections[2] \"Methods\" paragraph 2", "quote": "Numbers of 250 top score genes were selected and differences between control and celiac samples were calculated using the Student’s t test statistical p-values less than 0.05 and adjusted p-values via GEO2R analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Gene expression profile GSE113469 was retrieved Gene Expression Omnibus (GEO) database. The profile was provided based on the GPL10558 Illumina HumanHT-12 V4.0 expression bead chip. Whole-genome profile (RNA) of the human peripheral blood mononuclear cells (PBMCs) of celiac patients on gluten free diet (GFD) vs. controls is investigated.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30013745", "locator": "sections[2] \"Methods\" paragraph 2", "quote": "Gene expression profile GSE113469 was retrieved Gene Expression Omnibus (GEO) database. The profile was provided based on the GPL10558 Illumina HumanHT-12 V4.0 expression bead chip. Whole-genome profile (RNA) of the human peripheral blood mononuclear cells (PBMCs) of celiac patients on gluten free diet (GFD) vs. controls is investigated."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using Student’s t test and GEO2R-adjusted p-values on GSE113469 RNA-expression data retrieved from GEO, the study identified 47 differentially expressed genes distinguishing gluten-free-diet celiac patients from controls at FC≥2.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:30013745", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Whole-genome profile (RNA) of the human peripheral blood mononuclear cells (PBMCs) as Gene expression profile GSE113469 was retrieved Gene Expression Omnibus (GEO) database."}, {"asset": "source:pmid:30013745", "locator": "sections[3] \"Results\" paragraph 2", "quote": "Among 250 top score genes 47 up and down-regulated genes based on statistic method (as described in methods) and considering FC≥2 were identified as the significant DEGs (see figure 2)."}, {"asset": "source:pmid:30013745", "locator": "sections[3] \"Results\" paragraph 2", "quote": "Therefor 47 DEGs differentiate the GFD patients from control samples."}], "state": "complete"}], "gaps": ["doi"]}, "experiment": {"state": "complete", "objective": "Using Student’s t test and GEO2R-adjusted p-values on GSE113469 RNA-expression data retrieved from GEO, the study identified 47 differentially expressed genes distinguishing gluten-free-diet celiac patients from controls at FC≥2.", "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:30013745"], "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:GSE113469"], "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:GSE113469"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30013745", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": null, "sha256": "sha256:22dd9930710738f0ee0590912a6134bfb595893f258f04ba6967dd7a6449d54b", "bytes": 15283, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "30013745", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6040039", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE113469", "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=GSE113469", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE113469", "version": null, "note": "Gene expression profile GSE113469 was retrieved Gene Expression Omnibus (GEO) database. The profile was provided based on the GPL10558 Illumina HumanHT-12 V4.0 expression bead chip. Whole-genome profile (RNA) of the human peripheral blood mononuclear cells (PBMCs) of celiac patients on gluten free diet (GFD) vs. controls is investigated.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Gene expression profile GSE113469 was retrieved Gene Expression Omnibus (GEO) database. The profile was provided based on the GPL10558 Illumina HumanHT-12 V4.0 expression bead chip. Whole-genome profile (RNA) of the human peripheral blood mononuclear cells (PBMCs) of celiac patients on gluten free diet (GFD) vs. controls is investigated.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM3106457", "GSM3106458", "GSM3106459", "GSM3106460", "GSM3106461", "GSM3106462", "GSM3106463", "GSM3106464", "GSM3106465", "GSM3106466", "GSM3106467", "GSM3106468", "GSM3106469", "GSM3106470", "GSM3106471", "GSM3106472", "GSM3106473", "GSM3106474", "GSM3106475", "GSM3106476", "GSM3106477", "GSM3106478", "GSM3106479", "GSM3106480", "GSM3106481", "GSM3106482", "GSM3106483", "GSM3106484", "GSM3106485", "GSM3106486", "GSM3106487", "GSM3106488", "GSM3106489", "GSM3106490", "GSM3106491", "GSM3106492", "GSM3106493"], "sample_count": 37, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Identification of peculiar gene expression profile in peripheral blood mononuclear cells (PBMC) of celiac patients on gluten free diet", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30013745:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4dc010f6635747cf6fe3d6a367eb9ef5c4514c3f456afbf8a7120ed16b8ca489", "bytes": 1693, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[2]/table-wrap[1]#T1", "version": null, "note": "Rows 1-10 are the hub-nodes and The 1, 3, and 11-18 rows are bottleneck genes of celiac network. The rend color refers to hub-bottleneck nodes and green color is corresponded to bottleneck genes. The query genes are presented as yellow highlighted nodes. The normalized betweenness centrality (NBC) is shown in the last column of table.", "structure": {"pmcid": "PMC6040039", "section_index": 2, "section_title": "Methods", "row_count": 19, "column_count": 5}, "table": {"label": "Table 1", "caption": "Rows 1-10 are the hub-nodes and The 1, 3, and 11-18 rows are bottleneck genes of celiac network. The rend color refers to hub-bottleneck nodes and green color is corresponded to bottleneck genes. The query genes are presented as yellow highlighted nodes. The normalized betweenness centrality (NBC) is shown in the last column of table.", "rows": [["R", "Gene name", "description", "Degree", "N BC"], ["1", "GAPDH", "glyceraldehyde-3-phosphate dehydrogenase", "60", "0.625"], ["2", "AKT1", "v-akt murine thymoma viral oncogene homolog 1", "56", "0.375"], ["3", "TP53", "tumor protein p53", "54", "0.813"], ["4", "PRDM10", "PR domain containing 10", "54", "0.313"], ["5", "SRC", "v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian)", "53", "0.188"], ["6", "NFKB1", "nuclear factor of kappa light polypeptide gene enhancer in B-cells 1", "53", "0.156"], ["7", "IL6", "interleukin 6 (interferon, beta 2)", "52", "0.281"], ["8", "PIK3CG", "phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma", "51", "0.063"], ["9", "INS", "Insulin", "50", "0.313"], ["10", "TNF", "tumor necrosis factor", "50", "0.000"], ["11", "IL1B", "interleukin 1, beta", "44", "1.000"], ["12", "NOTCH1", "notch 1", "44", "0.719"], ["13", "HSPA5", "heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa)", "42", "0.563"], ["14", "PTPRC", "protein tyrosine phosphatase, receptor type, C", "38", "0.594"], ["15", "UBC", "ubiquitin C", "34", "0.469"], ["16", "TOP2A", "topoisomerase (DNA) II alpha 170kDa", "32", "0.531"], ["17", "ACLY", "ATP citrate lyase", "29", "0.844"], ["18", "PELI1", "pellino E3 ubiquitin protein ligase 1", "3", "0.500"]], "row_count": 19, "column_count": 5, "numeric_cells": 69, "header_rows": 1, "locator": "section[2]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:30013745:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:51bd9be6605eeef120b9e4ab4ab2dd33068c61896834d1e6c9e76a0dba075ff9", "bytes": 1844, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[2]/table-wrap[2]#T2", "version": null, "note": "The enriched pathways from KEGG related to the 18 central nodes of celiac disease network are shown. The 22 terms are grouped in 2 clusters (blue and green color terms) which the names of groups are highlighted with yellow color. At least presence of 4 genes in a term and 2%genes/term were considered for term determination. P-value for all identified terms was less than 0.01. The repeated termsare marked by (-1).", "structure": {"pmcid": "PMC6040039", "section_index": 2, "section_title": "Methods", "row_count": 30, "column_count": 4}, "table": {"label": "Table 2", "caption": "The enriched pathways from KEGG related to the 18 central nodes of celiac disease network are shown. The 22 terms are grouped in 2 clusters (blue and green color terms) which the names of groups are highlighted with yellow color. At least presence of 4 genes in a term and 2%genes/term were considered for term determination. P-value for all identified terms was less than 0.01. The repeated termsare marked by (-1).", "rows": [["R", "Term", "%Genes/Term", "No. of Genes"], ["1", "Sphingolipid signaling pathway", "3.4", "4"], ["2", "Apoptosis", "2.9", "4"], ["3", "Longevity regulating pathway", "4.5", "4"], ["4", "Cellular senescence", "2.5", "4"], ["5", "Prolactin signaling pathway", "5.7", "4"], ["6", "Hepatitis C", "3.1", "4"], ["7", "Measles", "3.0", "4"], ["8", "Prostate cancer", "4.2", "4"], ["9", "HIF-1signaling pathway", "5.0", "5"], ["10", "Sphingolipid signaling pathway-1", "3.4", "4"], ["11", "Apoptosis-1", "2.9", "4"], ["12", "Longevity regulating pathway-1", "4.5", "4"], ["13", "Cellular senescence-1", "2.5", "4"], ["14", "Toll-like receptor signaling pathway", "3.8", "4"], ["15", "TNF signaling pathway", "3.6", "4"], ["16", "Insulin resistance", "4.7", "5"], ["17", "Non-alcoholic fatty liver diseases (NAFLD)", "3.3", "5"], ["18", "AGE-RAGE signaling pathway in diabetic complications", "4.1", "4"], ["19", "Chagas disease (American trypanosomiasis", "3.8", "4"], ["20", "Toxoplasmosis", "3.5", "4"], ["21", "Tuberculosis", "2.7", "5"], ["22", "Hepatitis C-1", "3.1", "4"], ["23", "Hepatitis B", "4.2", "6"], ["24", "Measles-1", "3.0", "4"], ["25", "Influenza A", "2.3", "4"], ["26", "Kaposis sarcoma-associated herpesvirus infection", "3.3", "6"], ["27", "Herpes simplex infection", "2.1", "4"], ["28", "Prostate cancer-1", "4.2", "4"], ["29", "Fluid shear stress and atherosclerosis", "3.6", "5"]], "row_count": 30, "column_count": 4, "numeric_cells": 95, "header_rows": 1, "locator": "section[2]/table-wrap[2]#T2"}}], "gaps": ["asset:data:geo:GSE113469 not downloaded", "asset:data:geo:GSE113469 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-2", "family": "network_analysis", "specific": "centrality", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "centrality"}}, {"id": "method-3", "family": null, "specific": null, "label": "Student’s t test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Numbers of 250 top score genes were selected and differences between control and celiac samples were calculated using the Student’s t test statistical p-values less than 0.05 and adjusted p-values via GEO2R analysis."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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