Barrett's esophagus network analysis revealed that arginine, alanine, aspartate, glutamate, valine, leucine and isoleucine can be biomarkers.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30774814", "kind": "science-record", "revision": 8, "content_hash": "sha256:b58c6c85cad8b538d1248fae9475b26e90b58ec46653561af707052f95edca60", "created_at": "2026-11-01T15:40:42Z", "updated_at": "2026-11-01T22:00:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "partial", "title": "Barrett's esophagus network analysis revealed that arginine, alanine, aspartate, glutamate, valine, leucine and isoleucine can be biomarkers.", "doi": null, "pmid": "30774814", "authors": ["Mohammad Reza Zali", "Mohammad-Mehdi Zadeh-Esmaeel", "Majid Rezaei Tavirani", "Sina Rezaei Tavirani", "Mohsen Norouzinia", "Mostafa Rezaei-Tavirani"], "journal": "Gastroenterology and hepatology from bed to bench", "year": 2018, "abstract": "AIM: Identification of crucial genes and possible biomarkers which are involved in Barrett's esophagus (BE) disease was aim of this study.\nBACKGROUND: BE is diagnosed by endoscopy and biopsy and is characterized by esophageal columnar metaplastic epithelium. BE can convert into dysplasia that finally results cancer condition.\nMETHODS: Gene expression profiles of BE and normal gastric cardia which are characterized by GSE34619 and GPL6244 platform (1) were retrieved from gene expression omnibus (GEO). The significant differentially expressed genes (DEGs) were analyzed via protein-protein interaction network (PPI) analysis. The nodes of network were enriched via gene ontology (GO) to find biological terms. Action map of network elements was provided.\nRESULTS: Among 250 top DEGs, 100 ones were included in PPI network and KIT, CFTR, IMPDH2, MYB, FLT1, ATP4A, and CPS1 were recognized as prominent genes related to BE. Seven amino acids including arginine, alanine, aspartate, glutamate, valine, leucine and isoleucine which are related to BE were highlighted.\nCONCLUSION: In conclusion five central DEGs; KIT, CFTR, IMPDH2, MYB, and FLT1 were proposed as possible biomarkers for BE. However, validation and more experimental information is require to finalize the findings.", "claims": [{"id": "claim-method", "statement": "The gene expression profiles were analyzed by GEO2R and the top 250 significant DEGs were selected.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30774814", "locator": "sections[2] \"Methods\" paragraph 2", "quote": "The gene expression profiles were analyzed by GEO2R and the top 250 significant DEGs were selected."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Gene expression data series GSE34619, GPL6244 platform (14) were obtain from GEO database. 10 differential gene expression profiles of BE (GSM851983-92) and 10 normal gastric cardia (1) samples (GSM852001-10) were matched via boxplot analysis. The gene expression profiles were analyzed by GEO2R and the top 250 significant DEGs were selected.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30774814", "locator": "sections[2] \"Methods\" paragraph 2", "quote": "Gene expression data series GSE34619, GPL6244 platform (14) were obtain from GEO database. 10 differential gene expression profiles of BE (GSM851983-92) and 10 normal gastric cardia (1) samples (GSM852001-10) were matched via boxplot analysis. The gene expression profiles were analyzed by GEO2R and the top 250 significant DEGs were selected."}], "state": "complete"}], "gaps": ["doi"]}, "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:30774814"], "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:GSE34619"], "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:GSE34619"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30774814", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": null, "sha256": "sha256:a189c0edfc569d091a7943c79df8dcf745348a47089ac8d08ebba945818dd138", "bytes": 18256, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "30774814", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6347987", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE34619", "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=GSE34619", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE34619", "version": null, "note": "Gene expression data series GSE34619, GPL6244 platform (14) were obtain from GEO database. 10 differential gene expression profiles of BE (GSM851983-92) and 10 normal gastric cardia (1) samples (GSM852001-10) were matched via boxplot analysis. The gene expression profiles were analyzed by GEO2R and the top 250 significant DEGs were selected.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Gene expression data series GSE34619, GPL6244 platform (14) were obtain from GEO database. 10 differential gene expression profiles of BE (GSM851983-92) and 10 normal gastric cardia (1) samples (GSM852001-10) were matched via boxplot analysis. The gene expression profiles were analyzed by GEO2R and the top 250 significant DEGs were selected.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM851983", "GSM851984", "GSM851985", "GSM851986", "GSM851987", "GSM851988", "GSM851989", "GSM851990", "GSM851991", "GSM851992", "GSM851993", "GSM851994", "GSM851995", "GSM851996", "GSM851997", "GSM851998", "GSM851999", "GSM852000", "GSM852001", "GSM852002", "GSM852003", "GSM852004", "GSM852005", "GSM852006", "GSM852007", "GSM852008", "GSM852009", "GSM852010"], "sample_count": 28, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Gene expression profile in Barrett's esopahgus", "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:30774814:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a4b9f08f857dd9f67f8d94ec8112dd95819c66919c80524fcae6996667bc4a67", "bytes": 1491, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#T1", "version": null, "note": "Central nodes of Main connected component of PPI network of BE relative to gastric cardia,. BC and CC refer to betweenness centrality and closeness centrality, respectively. The common genes between top nodes based on Degree, BC, and CC are shown in red color", "structure": {"pmcid": "PMC6347987", "section_index": 3, "section_title": "Results", "row_count": 12, "column_count": 6}, "table": {"label": "Table 1", "caption": "Central nodes of Main connected component of PPI network of BE relative to gastric cardia,. BC and CC refer to betweenness centrality and closeness centrality, respectively. The common genes between top nodes based on Degree, BC, and CC are shown in red color", "rows": [["R", "display name", "description", "BC", "CC", "Degree"], ["1", "KIT", "v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog", "0.12969", "0.34375", "12"], ["2", "CFTR", "cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)", "0.332112", "0.385214", "11"], ["3", "IMPDH2", "IMP (inosine 5'-monophosphate) dehydrogenase 2", "0.269152", "0.366667", "11"], ["4", "MYB", "v-myb myeloblastosis viral oncogene homolog (avian)", "0.250107", "0.346154", "11"], ["5", "FLT1", "fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)", "0.076052", "0.326733", "9"], ["6", "GLUL", "glutamate-ammonia ligase", "0.070194", "0.313291", "9"], ["7", "ADHFE1", "alcohol dehydrogenase, iron containing, 1", "0.046399", "0.303681", "8"], ["8", "ATP4A", "ATPase, H+/K+ exchanging, alpha polypeptide", "0.172493", "0.339041", "8"], ["9", "CCKBR", "cholecystokinin B receptor", "0.065433", "0.280453", "8"], ["10", "CPS1", "carbamoyl-phosphate synthase 1, mitochondrial", "0.083989", "0.321429", "8"], ["11", "HDC", "histidine decarboxylase", "0.074607", "0.304615", "8"]], "row_count": 12, "column_count": 6, "numeric_cells": 50, "header_rows": 1, "locator": "section[3]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:30774814:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:849fdfa1c10403b4f2afbfad77a88c6b8736c3f9977b57dd80a1d3b8d5d78c72", "bytes": 1258, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[2]#T2", "version": null, "note": "Biochemical pathways and their associated genes among 100 nodes of main connected component. The pathways are retrieved from KEGG_20.11.2017. * Corrected with Bonferroni step down, %G/T; percentage of genes per term, and G/T; genes per term", "structure": {"pmcid": "PMC6347987", "section_index": 3, "section_title": "Results", "row_count": 10, "column_count": 7}, "table": {"label": "Table 2", "caption": "Biochemical pathways and their associated genes among 100 nodes of main connected component. The pathways are retrieved from KEGG_20.11.2017. * Corrected with Bonferroni step down, %G/T; percentage of genes per term, and G/T; genes per term", "rows": [["R", "GOTerm", "P Value", "Group", "% G/T", "G/T", "Associated Genes Found"], ["1", "Arginine and proline metabolism", "0.04", "1", "6.00", "3", "[AGMAT, CKB, CKMT2]"], ["2", "Mitophagy", "0.03", "2", "4.62", "3", "[BNIP3, GABARAPL1, MITF]"], ["3", "Gastric acid secretion", "0.00", "3", "13.33", "10", "[ATP4A, ATP4B, CCKBR, CFTR, HRH2, KCNE2, KCNJ16, KCNQ1, SLC26A7, SLC4A2]"], ["4", "Arginine biosynthesis", "0.04", "4", "14.29", "3", "[CPS1, GLUL, GPT2]"], ["5", "Alanine, aspartate and glutamate metabolism", "0.04", "4", "8.57", "3", "[CPS1, GLUL, GPT2]"], ["6", "Valine, leucine and isoleucine degradation", "0.00", "5", "10.42", "5", "[ACAT1, ALDH6A1, BCKDHB, DBT, OXCT1]"], ["7", "Propanoate metabolism", "0.00", "5", "12.50", "4", "[ACAT1, ALDH6A1, BCKDHB, DBT]"], ["8", "Pancreatic secretion", "0.03", "6", "4.17", "4", "[CCKAR, CFTR, KCNQ1, SLC4A2]"], ["9", "Bile secretion", "0.03", "6", "4.23", "3", "[AQP4, CFTR, SLC4A2]"]], "row_count": 10, "column_count": 7, "numeric_cells": 46, "header_rows": 1, "locator": "section[3]/table-wrap[2]#T2"}}], "gaps": ["asset:data:geo:GSE34619 not downloaded", "asset:data:geo:GSE34619 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": null, "specific": null, "label": "GEO2R", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The gene expression profiles were analyzed by GEO2R and the top 250 significant DEGs were selected."}}], "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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE34619"], "resolved_accessions": ["GSE34619"], "statements": ["Gene expression data series GSE34619, GPL6244 platform (14) were obtain from GEO database. 10 differential gene expression profiles of BE (GSM851983-92) and 10 normal gastric cardia (1) samples (GSM852001-10) were matched via boxplot analysis. The gene expression profiles were analyzed by GEO2R and the top 250 significant DEGs were selected."], "basis": "The paper names GSE34619 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": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:30774814", "data:geo:GSE34619", "asset:table:pmid:30774814:1", "asset:table:pmid:30774814:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE34619"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:14:04Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 15535, "completion_tokens": 1036, "cached_tokens": 784}}, "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:30774814", "type": "paper", "label": "pmid:30774814"}, {"id": "source:pmid:30774814", "type": "manuscript", "label": "PMID 30774814 full text"}, {"id": "data:geo:GSE34619", "type": "dataset", "label": "GEO GSE34619"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30774814", "type": "paper", "label": "pmid:30774814"}, {"id": "source:pmid:30774814", "type": "manuscript", "label": "PMID 30774814 full text"}, {"id": "data:geo:GSE34619", "type": "dataset", "label": "GEO GSE34619"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30774814", "type": "extraction", "used": ["source:pmid:30774814"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE34619", "type": "accession_resolution", "used": ["data:geo:GSE34619"], "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:30774814", "parent_hash": "sha256:af9ed3d3e74a1c1e6325f04654513c5854affee3c697fd977d8aca3d08e057f7", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE34619 licence not read", "asset:data:geo:GSE34619 not downloaded", "doi", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "analysis_only", "id": "assay:1"}]}