Meta-analysis of gene expression in relapsed childhood B-acute lymphoblastic leukemia.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28183295", "kind": "science-record", "revision": 7, "content_hash": "sha256:6a6c41cf6eed6520071ac445d6ed3bb471e953b0503992728f4964206a6c29eb", "created_at": "2026-11-01T15:40:22Z", "updated_at": "2026-11-01T21:59:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Meta-analysis of gene expression in relapsed childhood B-acute lymphoblastic leukemia.", "doi": "10.1186/s12885-017-3103-1", "pmid": "28183295", "authors": ["Yock-Ping Chow", "Hamidah Alias", "Rahman Jamal"], "journal": "BMC cancer", "year": 2017, "abstract": "BACKGROUND: Relapsed pediatric B-acute lymphoblastic leukemia (B-ALL) remains as the leading cause of cancer death among children. Other than stem cell transplantation and intensified chemotherapy, no other improved treatment strategies have been approved clinically. Gene expression profiling represents a powerful approach to identify potential biomarkers and new therapeutic targets for various diseases including leukemias. However, inadequate sample size in many individual experiments has failed to provide adequate study power to yield translatable findings. With the hope of getting new insights into the biological mechanisms underpinning relapsed ALL and identifying more promising biomarkers or therapeutic targets, we conducted a meta-analysis of gene expression studies involving ALL from 3 separate studies.\nMETHOD: By using the keywords \"acute lymphoblastic leukemia\", and \"microarray\", a total of 280 and 275 microarray datasets were found listed in Gene Expression Omnibus database GEO and ArrayExpress database respectively. Further manual inspection found that only three studies (GSE18497, GSE28460, GSE3910) were focused on gene expression profiling of paired diagnosis-relapsed pediatric B-ALL. These three datasets which comprised of a total of 108 matched diagnosis-relapsed pediatric B-ALL samples were then included for this meta-analysis using RankProd approach.\nRESULTS: Our analysis identified a total of 1795 upregulated probes which corresponded to 1527 genes (pfp < 0.01; FC > 1), and 1493 downregulated probes which corresponded to 1214 genes (pfp < 0.01; FC < 1) respectively. S100A8 appeared as the top most overexpressed gene (pfp < 0.01, FC = 1.8) and is a potential target for further validation. Based on gene ontology biological process annotation, the upregulated genes were most enriched in cell cycle processes (enrichment score = 15.3), whilst the downregulated genes were clustered in transcription regulation (enrichment score = 12.6). Elevated expression of cell cycle regulators (e.g kinesins, AURKA, CDKs) was the key genetic defect implicated in relapsed ALL, and serve as attractive targets for therapeutic intervention.\nCONCLUSION: We identified S100A8 as the most overexpressed gene, and the cell cycle pathway as the most promising biomarker and therapeutic target for relapsed childhood B-ALL. The validity of the results warrants further investigation.", "claims": [{"id": "claim-method", "statement": "Meta-analysis was performed on the three datasets using the RankProd package [14] to identify the upregulated and downregulated genes between relapsed ALL and matched samples at diagnosis. The microarray datasets used in this study are publicly available in Gene Expression Omnibus database GEO and ArrayExpress databases.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28183295", "locator": "sections[5] \"Meta-analysis of multiple microarray datasets\" paragraph 2", "quote": "Meta-analysis was performed on the three datasets using the RankProd package [14] to identify the upregulated and downregulated genes between relapsed ALL and matched samples at diagnosis."}, {"asset": "source:pmid:28183295", "locator": "sections[15] \"Availability of data and materials\" paragraph 2", "quote": "The microarray datasets used in this study are publicly available in Gene Expression Omnibus database GEO and ArrayExpress databases."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All relevant data are within the paper. The microarray datasets used in this study are publicly available in Gene Expression Omnibus database GEO and ArrayExpress databases.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28183295", "locator": "sections[15] \"Availability of data and materials\" paragraph 2", "quote": "All relevant data are within the paper. The microarray datasets used in this study are publicly available in Gene Expression Omnibus database GEO and ArrayExpress databases."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used RankProd meta-analysis to combine three paired diagnosis–relapsed pediatric B-ALL microarray datasets obtained from GEO and ArrayExpress.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28183295", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "By using the keywords “acute lymphoblastic leukemia”, and “microarray”, a total of 280 and 275 microarray datasets were found listed in Gene Expression Omnibus database GEO and ArrayExpress database respectively."}, {"asset": "source:pmid:28183295", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "These three datasets which comprised of a total of 108 matched diagnosis-relapsed pediatric B-ALL samples were then included for this meta-analysis using RankProd approach."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used RankProd meta-analysis to combine three paired diagnosis–relapsed pediatric B-ALL microarray datasets obtained from GEO and ArrayExpress.", "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:28183295"], "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:GSE18497"], "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:GSE18497"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28183295", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12885-017-3103-1", "sha256": "sha256:4bc8f6477a518b876ff1550dc3770b399efc906a0fc2932a1ce67ec55e40435c", "bytes": 51723, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12885-017-3103-1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5301337", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE18497", "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=GSE18497", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE18497", "version": null, "note": "All relevant data are within the paper. The microarray datasets used in this study are publicly available in Gene Expression Omnibus database GEO and ArrayExpress databases.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All relevant data are within the paper. The microarray datasets used in this study are publicly available in Gene Expression Omnibus database GEO and ArrayExpress databases.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM461011", "GSM461012", "GSM461013", "GSM461014", "GSM461015", "GSM461016", "GSM461017", "GSM461018", "GSM461019", "GSM461020", "GSM461021", "GSM461022", "GSM461023", "GSM461024", "GSM461025", "GSM461026", "GSM461027", "GSM461028", "GSM461029", "GSM461030", "GSM461031", "GSM461032", "GSM461033", "GSM461034", "GSM461035", "GSM461036", "GSM461037", "GSM461038", "GSM461039", "GSM461040", "GSM461041", "GSM461042", "GSM461043", "GSM461044", "GSM461045", "GSM461046", "GSM461047", "GSM461048", "GSM461049", "GSM461050", "GSM461051", "GSM461052", "GSM461053", "GSM461054", "GSM461055", "GSM461056", "GSM461057", "GSM461058", "GSM461059", "GSM461060", "GSM461061", "GSM461062", "GSM461063", "GSM461064", "GSM461065", "GSM461066", "GSM461067", "GSM461068", "GSM461069", "GSM461070", "GSM461071", "GSM461072", "GSM461073", "GSM461074", "GSM461075", "GSM461076", "GSM461077", "GSM461078", "GSM461079", "GSM461080", "GSM461081", "GSM461082", "GSM461083", "GSM461084", "GSM461085", "GSM461086", "GSM461087", "GSM461088", "GSM461089", "GSM461090", "GSM461091", "GSM461092"], "sample_count": 82, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Diagnosis-relapse in ALL", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE28460", "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=GSE28460", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28460", "version": null, "note": "All relevant data are within the paper. The microarray datasets used in this study are publicly available in Gene Expression Omnibus database GEO and ArrayExpress databases.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All relevant data are within the paper. The microarray datasets used in this study are publicly available in Gene Expression Omnibus database GEO and ArrayExpress databases.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM703544", "GSM703545", "GSM703546", "GSM703547", "GSM703548", "GSM703549", "GSM703550", "GSM703551", "GSM703552", "GSM703553", "GSM703554", "GSM703555", "GSM703556", "GSM703557", "GSM703558", "GSM703559", "GSM703560", "GSM703561", "GSM703562", "GSM703563", "GSM703564", "GSM703565", "GSM703566", "GSM703567", "GSM703568", "GSM703569", "GSM703570", "GSM703571", "GSM703572", "GSM703573", "GSM703574", "GSM703575", "GSM703576", "GSM703577", "GSM703578", "GSM703579", "GSM703580", "GSM703581", "GSM703582", "GSM703583", "GSM703584", "GSM703585", "GSM703586", "GSM703587", "GSM703588", "GSM703589", "GSM703590", "GSM703591", "GSM703592", "GSM703593", "GSM703594", "GSM703595", "GSM703596", "GSM703597", "GSM703598", "GSM703599", "GSM703600", "GSM703601", "GSM703602", "GSM703603", "GSM703604", "GSM703605", "GSM703606", "GSM703607", "GSM703608", "GSM703609", "GSM703610", "GSM703611", "GSM703612", "GSM703613", "GSM703614", "GSM703615", "GSM703616", "GSM703617", "GSM703618", "GSM703619", "GSM703620", "GSM703621", "GSM703622", "GSM703623", "GSM703624", "GSM703625", "GSM703626", "GSM703627", "GSM703628", "GSM703629", "GSM703630", "GSM703631", "GSM703632", "GSM703633", "GSM703634", "GSM703635", "GSM703636", "GSM703637", "GSM703638", "GSM703639", "GSM703640", "GSM703641"], "sample_count": 98, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from ALL diagnosis and relapse pediatric acute lymphoblastic leukemia cases", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE3910", "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=GSE3910", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE3910", "version": null, "note": "All relevant data are within the paper. The microarray datasets used in this study are publicly available in Gene Expression Omnibus database GEO and ArrayExpress databases.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All relevant data are within the paper. The microarray datasets used in this study are publicly available in Gene Expression Omnibus database GEO and ArrayExpress databases.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM89501", "GSM89502", "GSM89503", "GSM89504", "GSM89505", "GSM89506", "GSM89507", "GSM89508", "GSM89509", "GSM89510", "GSM89511", "GSM89512", "GSM89513", "GSM89514", "GSM89515", "GSM89516", "GSM89517", "GSM89518", "GSM89519", "GSM89520", "GSM89521", "GSM89522", "GSM89523", "GSM89524", "GSM89525", "GSM89526", "GSM89527", "GSM89528", "GSM89529", "GSM89530", "GSM89531", "GSM89532", "GSM89533", "GSM89534", "GSM89535", "GSM89536", "GSM89537", "GSM89538", "GSM89539", "GSM89540", "GSM89541", "GSM89542", "GSM89543", "GSM89544", "GSM89545", "GSM89546", "GSM89547", "GSM89548", "GSM89549", "GSM89550", "GSM89551", "GSM89552", "GSM89553", "GSM89554", "GSM89555", "GSM89556", "GSM89557", "GSM89558", "GSM89559", "GSM89560", "GSM89561", "GSM89562", "GSM89563", "GSM89564", "GSM89565", "GSM89566", "GSM89567", "GSM89568", "GSM89569", "GSM89570"], "sample_count": 70, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "35 patients at diagnosis and relapse", "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:28183295:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3e709a7ba9bbc9e72543e83318c9e0e8b2f51537cd22ceb34d6bcb9508a2af8a", "bytes": 1144, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#Tab1", "version": null, "note": "The top 20 most significantly upregulated probes identified by RankProd in relapsed childhood ALL (pfp < 0.01; FC > 1), 1000 permutation", "structure": {"pmcid": "PMC5301337", "section_index": 9, "section_title": "Meta-analysis of differentially expressed probes", "row_count": 21, "column_count": 5}, "table": {"label": "Table 1", "caption": "The top 20 most significantly upregulated probes identified by RankProd in relapsed childhood ALL (pfp < 0.01; FC > 1), 1000 permutation", "rows": [["Probe", "Gene", "FC:(class1/class2)", "pfp", "p.value"], ["202917_s_at", "S100A8", "1.8713", "0", "0"], ["203949_at", "MPO", "2.0051", "0", "0"], ["201427_s_at", "SEPP1", "1.6536", "0", "0"], ["213975_s_at", "LYZ", "1.6129", "0", "0"], ["205000_at", "DDX3Y", "1.1483", "0", "0"], ["204971_at", "CSTA", "1.757", "0", "0"], ["209160_at", "AKR1C3", "1.6693", "0", "0"], ["209170_s_at", "GPM6B", "1.3387", "0", "0"], ["204409_s_at", "EIF1AY", "1.2661", "0", "0"], ["201291_s_at", "TOP2A", "1.8054", "0", "0"], ["204304_s_at", "PROM1", "1.1579", "0", "0"], ["201669_s_at", "MARCKS", "1.4776", "0", "0"], ["202018_s_at", "LTF", "1.6698", "0", "0"], ["211657_at", "CEACAM6", "1.3632", "0", "0"], ["212077_at", "CALD1", "1.5944", "0", "0"], ["221731_x_at", "VCAN", "1.3855", "0", "0"], ["214039_s_at", "LAPTM4B", "1.1776", "0", "0"], ["204620_s_at", "VCAN", "1.434", "0", "0"], ["200665_s_at", "SPARC", "1.4726", "0", "0"], ["209687_at", "CXCL12", "1.7029", "0", "0"]], "row_count": 21, "column_count": 5, "numeric_cells": 82, "header_rows": 1, "locator": "section[9]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:28183295:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2a512a87dc10d74dfeb9a341b91cf8893aeabf67735296d2c7343db6dd3dfbce", "bytes": 1059, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[2]#Tab2", "version": null, "note": "The top 20 most significantly downregulated probes identified by RankProd in relapsed childhood ALL (pfp < 0.01; FC < 1), 1000 permutation", "structure": {"pmcid": "PMC5301337", "section_index": 9, "section_title": "Meta-analysis of differentially expressed probes", "row_count": 19, "column_count": 5}, "table": {"label": "Table 2", "caption": "The top 20 most significantly downregulated probes identified by RankProd in relapsed childhood ALL (pfp < 0.01; FC < 1), 1000 permutation", "rows": [["Probe", "Gene", "FC:(class1/class2)", "pfp", "p.value"], ["209480_at", "HLA-DQB1", "0.8503", "0", "0"], ["219737_s_at", "PCDH9", "0.5924", "0", "0"], ["210432_s_at", "SCN3A", "0.6362", "0", "0"], ["203038_at", "PTPRK", "0.8517", "0", "0"], ["206637_at", "P2RY14", "0.7417", "0", "0"], ["204897_at", "PTGER4", "0.6231", "0", "0"], ["221728_x_at", "XIST", "0.9313", "0", "0"], ["212592_at", "IGJ", "0.7981", "0", "0"], ["221841_s_at", "KLF4", "0.6573", "0", "0"], ["203910_at", "ARHGAP29", "0.8594", "0", "0"], ["206864_s_at", "HRK", "0.6284", "0", "0"], ["210448_s_at", "P2RX5", "0.6183", "0", "0"], ["214218_s_at", "XIST", "0.9554", "0", "0"], ["201005_at", "CD9", "0.7092", "0", "0"], ["210517_s_at", "AKAP12", "0.8163", "0", "0"], ["205081_at", "CRIP1", "0.605", "0", "0"], ["204439_at", "IFI44L", "0.7068", "0", "0"], ["205289_at", "BMP2", "0.7267", "0", "0"]], "row_count": 19, "column_count": 5, "numeric_cells": 76, "header_rows": 1, "locator": "section[9]/table-wrap[2]#Tab2"}}], "gaps": ["asset:data:geo:GSE18497 not downloaded", "asset:data:geo:GSE18497 licence not read", "asset:data:geo:GSE28460 not downloaded", "asset:data:geo:GSE28460 licence not read", "asset:data:geo:GSE3910 not downloaded", "asset:data:geo:GSE3910 licence not read"]}, "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": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-2", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "hierarchical clustering"}}, {"id": "method-3", "family": null, "specific": null, "label": "RankProd", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "Meta-analysis was performed on the three datasets using the RankProd package [14] to identify the upregulated and downregulated genes between relapsed ALL and matched samples at diagnosis. The microarray datasets used in this study are publicly available in Gene Expression Omnibus database GEO and ArrayExpress databases."}}], "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": ["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": "R1", "reachable": true, "accessions": ["GSE28460", "GSE18497", "GSE3910"], "resolved_accessions": ["GSE28460", "GSE18497", "GSE3910"], "statements": ["All relevant data are within the paper. The microarray datasets used in this study are publicly available in Gene Expression Omnibus database GEO and ArrayExpress databases."], "basis": "The paper names GSE28460, GSE18497, GSE3910 in Gene Expression Omnibus database GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:28183295", "data:geo:GSE18497", "asset:table:pmid:28183295:1", "asset:table:pmid:28183295:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE18497"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:30:27Z", "independence": "same_provider"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 116707, "completion_tokens": 4749, "cached_tokens": 2104}}, "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:28183295", "type": "paper", "label": "pmid:28183295"}, {"id": "source:pmid:28183295", "type": "manuscript", "label": "PMID 28183295 full text"}, {"id": "data:geo:GSE18497", "type": "dataset", "label": "GEO GSE18497"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28183295", "type": "paper", "label": "pmid:28183295"}, {"id": "source:pmid:28183295", "type": "manuscript", "label": "PMID 28183295 full text"}, {"id": "data:geo:GSE18497", "type": "dataset", "label": "GEO GSE18497"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28183295", "type": "extraction", "used": ["source:pmid:28183295"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE18497", "type": "accession_resolution", "used": ["data:geo:GSE18497"], "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:28183295", "parent_hash": "sha256:5660122b5623d6113d6822b2c05b271883c9ccfb71b94088891fcba62b0f733b", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE18497 licence not read", "asset:data:geo:GSE18497 not downloaded", "asset:data:geo:GSE28460 licence not read", "asset:data:geo:GSE28460 not downloaded", "asset:data:geo:GSE3910 licence not read", "asset:data:geo:GSE3910 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["eywords \"acute lymphoblastic leukemia\", and \"microarray\", a total of 280 and 275 microarray datasets", "a\", and \"microarray\", a total of 280 and 275 microarray datasets were found listed in Gene Expressio", "Methods Meta-analysis of multiple microarray datasets Meta-analysis was performed on the", "and to increase the specificity. Individual microarray data analysis of differentially expressed pr"], "order_basis": "paper_text_order:931", "id": "assay:1"}, {"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": 0.8, "evidence": ["limma"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}