The idiosyncratic drug-induced gene expression changes in HepG2 cells.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28831409", "kind": "science-record", "revision": 6, "content_hash": "sha256:b343ac18c652efd819635efcdf7e072b404406960d775383ab8576a5631ee093", "created_at": "2026-11-01T15:40:27Z", "updated_at": "2026-11-01T21:21:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The idiosyncratic drug-induced gene expression changes in HepG2 cells.", "doi": "10.1016/j.dib.2017.07.074", "pmid": "28831409", "authors": ["J Jiang", "K Mathijs", "L Timmermans", "S M Claessen", "A Hecka", "J Weusten", "R Peters", "J H van Delft", "J C S Kleinjans", "D G J Jennen", "T M de Kok"], "journal": "Data in brief", "year": 2017, "abstract": "The inflammatory stress has been associated with an increase in susceptibility to idiosyncratic drug-induced liver injury (DILI). However, the molecular mechanisms of this inflammation-associated idiosyncratic drug hepatotoxicity remain unknown. We exposed HepG2 cells with high and low doses of three idiosyncratic (I) and three non-idiosyncratic (N) compounds, in the presence (I+ and N+) or absence (I- and N-) of a cytokine mix for 6, 12 and 24 h. To investigate the genome-wide expression patterns, microarray was performed using the Agilent 4×44K Whole Human Genome chips. The data presented in this DIB include the expression of genes participating in the ceramide metabolism, ER stress, apoptosis and cell survival pathways. The functions of these genes were illustrated in our associated article (Jiang et al., 2017) [1]. Raw and normalized gene expression data are available through NCBI GEO (accession number GSE102006).", "claims": [{"id": "claim-method", "statement": "A change was considered significant when the following criteria were fulfilled: (1) a false discovery rate-corrected p-value<0.05 and (2) a log2 fold change of ≤−0.58 or >0.58 (absolute fold change >1.5) for the average of the three replicates.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28831409", "locator": "sections[11] \"The selection of DEGs and the treatment-specific genes\" paragraph 2", "quote": "A change was considered significant when the following criteria were fulfilled: (1) a false discovery rate-corrected p-value<0.05 and (2) a log2 fold change of ≤−0.58 or >0.58 (absolute fold change >1.5) for the average of the three replicates."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Raw and normalized gene expression data are available through NCBI GEO (accession number GSE102006).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28831409", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Raw and normalized gene expression data are available through NCBI GEO (accession number GSE102006)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used Agilent 4×44K Whole Human Genome microarray analysis, and the raw and normalized gene-expression data are available through NCBI GEO under accession number GSE102006.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28831409", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "To investigate the genome‐wide expression patterns, microarray was performed using the Agilent 4×44K Whole Human Genome chips."}, {"asset": "source:pmid:28831409", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Raw and normalized gene expression data are available through NCBI GEO (accession number GSE102006)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used Agilent 4×44K Whole Human Genome microarray analysis, and the raw and normalized gene-expression data are available through NCBI GEO under accession number GSE102006.", "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:28831409"], "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:GSE102006"], "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:GSE102006"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28831409", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2017.07.074", "sha256": "sha256:f260debab1d4606dad286a7e1e1ab3aa603ec12c82ed5bfaa2d28e7362a0c59f", "bytes": 10620, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2017.07.074", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5554930", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE102006", "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=GSE102006", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE102006", "version": null, "note": "Raw and normalized gene expression data are available through NCBI GEO (accession number GSE102006).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Raw and normalized gene expression data are available through NCBI GEO (accession number GSE102006).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2720393", "GSM2720394", "GSM2720395", "GSM2720396", "GSM2720397", "GSM2720398", "GSM2720399", "GSM2720400", "GSM2720401", "GSM2720402", "GSM2720403", "GSM2720404", "GSM2720405", "GSM2720406", "GSM2720407", "GSM2720408", "GSM2720409", "GSM2720410", "GSM2720411", "GSM2720412", "GSM2720413", "GSM2720414", "GSM2720415", "GSM2720416", "GSM2720417", "GSM2720418", "GSM2720419", "GSM2720420", "GSM2720421", "GSM2720422", "GSM2720423", "GSM2720424", "GSM2720425", "GSM2720426", "GSM2720427", "GSM2720428", "GSM2720429", "GSM2720430", "GSM2720431", "GSM2720432", "GSM2720433", "GSM2720434", "GSM2720435", "GSM2720436", "GSM2720437", "GSM2720438", "GSM2720439", "GSM2720440", "GSM2720441", "GSM2720442", "GSM2720443", "GSM2720444", "GSM2720445", "GSM2720446", "GSM2720447", "GSM2720448", "GSM2720449", "GSM2720450", "GSM2720451", "GSM2720452", "GSM2720453", "GSM2720454", "GSM2720455", "GSM2720456", "GSM2720457", "GSM2720458", "GSM2720459", "GSM2720460", "GSM2720461", "GSM2720462", "GSM2720463", "GSM2720464", "GSM2720465", "GSM2720466", "GSM2720467", "GSM2720468", "GSM2720469", "GSM2720470", "GSM2720471", "GSM2720472", "GSM2720473", "GSM2720474", "GSM2720475", "GSM2720476", "GSM2720477", "GSM2720478", "GSM2720479", "GSM2720480", "GSM2720481", "GSM2720482", "GSM2720483", "GSM2720484", "GSM2720485", "GSM2720486", "GSM2720487", "GSM2720488", "GSM2720489", "GSM2720490", "GSM2720491", "GSM2720492", "GSM2720493", "GSM2720494", "GSM2720495", "GSM2720496", "GSM2720497", "GSM2720498", "GSM2720499", "GSM2720500", "GSM2720501", "GSM2720502", "GSM2720503", "GSM2720504", "GSM2720505", "GSM2720506", "GSM2720507", "GSM2720508", "GSM2720509", "GSM2720510", "GSM2720511", "GSM2720512", "GSM2720513", "GSM2720514", "GSM2720515", "GSM2720516", "GSM2720517", "GSM2720518", "GSM2720519", "GSM2720520", "GSM2720521", "GSM2720522", "GSM2720523", "GSM2720524", "GSM2720525", "GSM2720526", "GSM2720527", "GSM2720528", "GSM2720529", "GSM2720530", "GSM2720531", "GSM2720532", "GSM2720533", "GSM2720534", "GSM2720535", "GSM2720536", "GSM2720537", "GSM2720538", "GSM2720539", "GSM2720540", "GSM2720541", "GSM2720542", "GSM2720543", "GSM2720544", "GSM2720545", "GSM2720546", "GSM2720547", "GSM2720548", "GSM2720549", "GSM2720550", "GSM2720551", "GSM2720552", "GSM2720553", "GSM2720554", "GSM2720555", "GSM2720556", "GSM2720557", "GSM2720558", "GSM2720559", "GSM2720560", "GSM2720561", "GSM2720562", "GSM2720563", "GSM2720564", "GSM2720565", "GSM2720566", "GSM2720567", "GSM2720568", "GSM2720569", "GSM2720570", "GSM2720571", "GSM2720572", "GSM2720573", "GSM2720574", "GSM2720575", "GSM2720576", "GSM2720577", "GSM2720578", "GSM2720579", "GSM2720580", "GSM2720581", "GSM2720582", "GSM2720583", "GSM2720584", "GSM2720585", "GSM2720586", "GSM2720587", "GSM2720588", "GSM2720589", "GSM2720590", "GSM2720591", "GSM2720592", "GSM2720593", "GSM2720594", "GSM2720595", "GSM2720596", "GSM2720597", "GSM2720598", "GSM2720599", "GSM2720600", "GSM2720601", "GSM2720602", "GSM2720603", "GSM2720604", "GSM2720605", "GSM2720606", "GSM2720607", "GSM2720608", "GSM2720609", "GSM2720610", "GSM2720611", "GSM2720612", "GSM2720613", "GSM2720614", "GSM2720615", "GSM2720616", "GSM2720617", "GSM2720618", "GSM2720619", "GSM2720620", "GSM2720621", "GSM2720622", "GSM2720623", "GSM2720624", "GSM2720625", "GSM2720626", "GSM2720627", "GSM2720628", "GSM2720629", "GSM2720630", "GSM2720631", "GSM2720632", "GSM2720633", "GSM2720634", "GSM2720635", "GSM2720636", "GSM2720637", "GSM2720638", "GSM2720639", "GSM2720640", "GSM2720641", "GSM2720642", "GSM2720643", "GSM2720644"], "sample_count": 252, "group_sizes": null, "group_sizes_basis": null, "platform": "6480", "taxon": "Homo sapiens", "title": "Omics-based identification of the combined effects of idiosyncratic drugs and inflammatory cytokines on the development of drug-induced liver injury", "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:28831409:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9f7932580cd18f3dedce86b2b663bda4049864907328bd5879026f765f7c4b3b", "bytes": 1949, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#t0005", "version": null, "note": "The high-dose treatment-induced fold changes of genes involved in TNF signaling, apoptosis pathways and ceramide metabolism (6 h).", "structure": {"pmcid": "PMC5554930", "section_index": 5, "section_title": "Data", "row_count": 41, "column_count": 5}, "table": {"label": "Table 1", "caption": "The high-dose treatment-induced fold changes of genes involved in TNF signaling, apoptosis pathways and ceramide metabolism (6 h).", "rows": [["Gene symbol", "High-dose induced fold change 6 h"], ["I+", "I−", "N+", "N−"], ["TNF and apoptosis pathway"], ["ATF6", "1.34", "−1.02", "−1.04", "1.12"], ["BAD", "−1.38", "−1.37", "−1.19", "−1.11"], ["BAX", "−1.62", "−1.39", "−1.19", "−1.15"], ["BCL2", "1.06", "1.16", "−1.28", "1.04"], ["BCL2L11", "1.11", "1.08", "1.76", "1.05"], ["CASP3", "1.39", "1.19", "1.04", "−1.06"], ["CASP4", "1.23", "−1.30", "1.09", "1.05"], ["CYCS", "−1.34", "−1.56", "1.07", "−1.05"], ["CHOP/DDIT3", "3.49", "1.99", "−1.04", "1.10"], ["ERN1", "1.59", "1.82", "1.32", "1.14"], ["FAS", "−1.05", "1.04", "1.10", "1.02"], ["MAP2K4", "1.24", "1.28", "1.06", "1.08"], ["MAP3K1", "1.32", "1.16", "−1.08", "−1.07"], ["MAP3K14", "1.07", "1.32", "1.26", "1.25"], ["MAPK8", "1.30", "1.66", "1.04", "1.02"], ["NFKB1", "1.38", "1.41", "1.24", "1.21"], ["NFKB2", "−1.14", "1.22", "1.09", "1.02"], ["TNF", "5.14", "2.60", "1.28", "1.07"], ["TNFRSF1A", "1.29", "1.47", "1.11", "1.10"], ["TNFSF13B", "1.32", "1.41", "1.32", "1.09"], ["TRAF2", "1.09", "−1.10", "−1.02", "−1.10"], ["TRAF6", "1.82", "2.34", "1.14", "1.09"], [""], ["Ceramide metabolism"], ["ASAH1", "1.05", "−1.09", "1.03", "1.02"], ["ASAH2", "1.20", "1.35", "1.07", "−1.13"], ["ASAHL/NAAA", "1.29", "−1.10", "1.03", "−1.05"], ["CERS6", "−1.13", "−1.09", "1.05", "1.06"], ["SGMS1", "−1.13", "−1.31", "1.05", "1.06"], ["SGMS2", "4.43", "4.82", "1.28", "1.58"], ["SGPP1", "1.62", "1.06", "−1.02", "1.12"], ["SMPD1", "−1.03", "−1.17", "1.05", "−1.24"], ["SMPD2", "−1.61", "−1.28", "−1.06", "1.02"], ["SMPD3", "−1.15", "−1.30", "−1.22", "1.00"], ["SPHK1", "−1.37", "−1.24", "−1.03", "−1.12"], ["SPHK2", "1.39", "−1.19", "1.19", "−1.04"], ["SPTLC1", "−1.07", "1.19", "1.14", "1.23"], ["SPTLC2", "1.40", "1.23", "−1.07", "1.02"]], "row_count": 41, "column_count": 5, "numeric_cells": 148, "header_rows": 2, "locator": "section[5]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:28831409:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e59540b5d15213d2880e824151453dc83c32c7760e3270d86eb1db969908c05f", "bytes": 1991, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[2]#t0010", "version": null, "note": "The high-dose treatment-induced fold changes of genes involved in TNF signaling, apoptosis pathways and ceramide metabolism (12 h).", "structure": {"pmcid": "PMC5554930", "section_index": 5, "section_title": "Data", "row_count": 41, "column_count": 5}, "table": {"label": "Table 2", "caption": "The high-dose treatment-induced fold changes of genes involved in TNF signaling, apoptosis pathways and ceramide metabolism (12 h).", "rows": [["Gene symbol", "High-dose induced fold change 12 h"], ["I+", "I−", "N+", "N−"], ["TNF and apoptosis pathway"], ["ATF6", "1.42", "1.10", "1.14", "1.10"], ["BAD", "−1.43", "−1.30", "−1.04", "1.04"], ["BAX", "−1.87", "−1.52", "1.04", "1.04"], ["BCL2", "1.49", "1.29", "1.30", "1.23"], ["BCL2L11", "−1.05", "−1.33", "−1.03", "−1.23"], ["CASP3", "1.34", "1.27", "−1.05", "−1.09"], ["CASP4", "1.32", "1.35", "1.33", "1.03"], ["CYCS", "−1.33", "−1.45", "−1.11", "−1.03"], ["CHOP/DDIT3", "3.58", "1.52", "1.15", "1.05"], ["ERN1", "2.23", "2.19", "−1.08", "1.01"], ["FAS", "−1.05", "−1.03", "−1.04", "−1.10"], ["MAP2K4", "1.46", "1.49", "1.10", "1.07"], ["MAP3K1", "−1.02", "1.13", "−1.12", "−1.04"], ["MAP3K14", "1.23", "1.16", "1.16", "1.10"], ["MAPK8", "1.64", "1.47", "1.10", "−1.05"], ["NFKB1", "1.85", "1.33", "1.26", "−1.02"], ["NFKB2", "1.77", "1.46", "1.47", "1.04"], ["TNF", "12.23", "1.26", "1.83", "−1.21"], ["TNFRSF1A", "1.44", "1.76", "1.13", "1.19"], ["TNFSF13B", "1.39", "1.41", "1.01", "−1.10"], ["TRAF2", "1.31", "−1.04", "1.16", "−1.04"], ["TRAF6", "1.91", "2.11", "1.04", "1.01"], [""], ["Ceramide metabolism"], ["ASAH1", "−1.42", "−1.17", "−1.03", "−1.03"], ["ASAH2", "1.12", "1.50", "−1.25", "1.19"], ["ASAHL/NAAA", "−1.59", "−1.38", "−1.02", "−1.05"], ["CERS6", "−1.28", "−1.38", "1.04", "−1.08"], ["SGMS1", "−1.24", "−1.13", "−1.04", "−1.01"], ["SGMS2", "3.48", "2.51", "1.13", "−1.02"], ["SGPP1", "1.58", "1.42", "1.13", "1.04"], ["SMPD1", "−1.46", "−1.27", "−1.23", "1.05"], ["SMPD2", "−1.61", "−1.02", "1.13", "1.19"], ["SMPD3", "−1.81", "−1.77", "−1.04", "−1.15"], ["SPHK1", "−1.19", "1.02", "−1.01", "−1.01"], ["SPHK2", "1.01", "−1.05", "−1.08", "1.04"], ["SPTLC1", "1.05", "1.25", "−1.20", "1.06"], ["SPTLC2", "1.20", "1.29", "−1.06", "−1.12"]], "row_count": 41, "column_count": 5, "numeric_cells": 148, "header_rows": 2, "locator": "section[5]/table-wrap[2]#t0010"}}, {"id": "asset:table:pmid:28831409:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:887cfdcf32c468ec5bbfbb013ae7b8aff2c98c6066fb330c2b223677ac86940e", "bytes": 1978, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[3]#t0015", "version": null, "note": "The high-dose treatment-induced fold changes of genes involved in TNF signaling, apoptosis pathways and ceramide metabolism (24 h).", "structure": {"pmcid": "PMC5554930", "section_index": 5, "section_title": "Data", "row_count": 41, "column_count": 5}, "table": {"label": "Table 3", "caption": "The high-dose treatment-induced fold changes of genes involved in TNF signaling, apoptosis pathways and ceramide metabolism (24 h).", "rows": [["Gene symbol", "High-dose induced fold change 24 h"], ["I+", "I−", "N+", "N−"], ["TNF and apoptosis pathway"], ["ATF6", "1.33", "1.05", "−1.04", "1.03"], ["BAD", "−1.04", "−1.34", "1.10", "−1.06"], ["BAX", "−1.62", "−1.21", "1.33", "−1.05"], ["BCL2", "1.19", "1.29", "1.24", "1.47"], ["BCL2L11", "2.38", "1.08", "1.44", "−1.02"], ["CASP3", "1.37", "1.15", "−1.04", "−1.15"], ["CASP4", "1.22", "1.14", "−1.03", "1.13"], ["CYCS", "−1.21", "−1.16", "−1.16", "−1.07"], ["CHOP/DDIT3", "3.80", "2.55", "1.04", "−1.07"], ["ERN1", "3.07", "3.31", "−1.01", "1.17"], ["FAS", "1.58", "1.19", "−1.01", "1.06"], ["MAP2K4", "1.38", "1.29", "1.02", "−1.12"], ["MAP3K1", "1.30", "1.19", "−1.07", "1.10"], ["MAP3K14", "1.68", "1.02", "−1.02", "−1.03"], ["MAPK8", "1.52", "1.40", "−1.02", "−1.04"], ["NFKB1", "1.33", "1.11", "−1.15", "1.06"], ["NFKB2", "1.31", "1.21", "−1.11", "1.29"], ["TNF", "4.29", "1.84", "−1.04", "1.22"], ["TNFRSF1A", "1.56", "1.81", "−1.08", "−1.02"], ["TNFSF13B", "1.89", "1.68", "1.06", "1.02"], ["TRAF2", "1.22", "−1.20", "1.05", "−1.08"], ["TRAF6", "1.73", "1.82", "1.04", "1.01"], [""], ["Ceramide metabolism"], ["ASAH1", "−1.54", "1.01", "−1.01", "−1.07"], ["ASAH2", "1.48", "1.29", "1.03", "−1.05"], ["ASAHL/NAAA", "−1.45", "−1.15", "1.08", "−1.09"], ["CERS6", "1.31", "1.03", "−1.10", "1.11"], ["SGMS1", "1.28", "1.17", "−1.09", "−1.11"], ["SGMS2", "3.34", "2.89", "−1.26", "1.01"], ["SGPP1", "2.00", "1.50", "1.07", "1.23"], ["SMPD1", "−1.02", "−1.46", "−1.01", "−1.09"], ["SMPD2", "1.14", "1.03", "1.08", "−1.06"], ["SMPD3", "−1.27", "−2.39", "−1.19", "−1.19"], ["SPHK1", "−1.07", "−1.23", "−1.12", "−1.09"], ["SPHK2", "−1.48", "−1.03", "1.08", "1.02"], ["SPTLC1", "2.25", "2.21", "1.07", "−1.01"], ["SPTLC2", "1.30", "1.18", "−1.04", "1.08"]], "row_count": 41, "column_count": 5, "numeric_cells": 148, "header_rows": 2, "locator": "section[5]/table-wrap[3]#t0015"}}], "gaps": ["asset:data:geo:GSE102006 not downloaded", "asset:data:geo:GSE102006 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "False discovery rate-corrected significance testing with log2 fold-change filtering", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "A change was considered significant when the following criteria were fulfilled: (1) a false discovery rate-corrected p-value<0.05 and (2) a log2 fold change of ≤−0.58 or >0.58 (absolute fold change >1.5) for the average of the three replicates."}}], "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (False discovery rate-corrected significance testing with log2 fold-change filtering), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE102006"], "resolved_accessions": ["GSE102006"], "statements": ["Raw and normalized gene expression data are available through NCBI GEO (accession number GSE102006)."], "basis": "The paper names GSE102006 in NCBI GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:28831409", "data:geo:GSE102006", "asset:table:pmid:28831409:1", "asset:table:pmid:28831409:2", "asset:table:pmid:28831409:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE102006"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:31:52Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 25647, "completion_tokens": 3125, "cached_tokens": 2112}}, "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:28831409", "type": "paper", "label": "pmid:28831409"}, {"id": "source:pmid:28831409", "type": "manuscript", "label": "PMID 28831409 full text"}, {"id": "data:geo:GSE102006", "type": "dataset", "label": "GEO GSE102006"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28831409", "type": "paper", "label": "pmid:28831409"}, {"id": "source:pmid:28831409", "type": "manuscript", "label": "PMID 28831409 full text"}, {"id": "data:geo:GSE102006", "type": "dataset", "label": "GEO GSE102006"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28831409", "type": "extraction", "used": ["source:pmid:28831409"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE102006", "type": "accession_resolution", "used": ["data:geo:GSE102006"], "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:28831409", "parent_hash": "sha256:fc4d3d5fca62a67d15f211d8efe300b2d54ef62595d7513b7fc1abfed8f971c9", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE102006 licence not read", "asset:data:geo:GSE102006 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["atic drug-induced gene expression changes in HepG2 cells.", "ug hepatotoxicity remain unknown. We exposed HepG2 cells with high and low doses of three idios", "Cell culture and treatment HepG2 cells were cultured in T25 flasks in the presence of minimal essent", "rials and methods Cell culture and treatment HepG2 cells were cultured in T25 flasks in the pre"], "order_basis": "paper_text_order:13", "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": ["stigate the genome-wide expression patterns, microarray was performed using the Agilent 4×44K Whole"], "order_basis": "paper_text_order:530", "id": "assay:2"}, {"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": ["ating in the ceramide metabolism, ER stress, apoptosis and cell survival pathways. The functions of", "lved in the significant pathways related to ‘apoptosis and survival’ are available in Table 1, Tabl"], "order_basis": "paper_text_order:721", "id": "assay:3"}]}