Reorganization of gene network for degradation of polycyclic aromatic hydrocarbons (PAHs) in Pseudomonas aeruginosa PAO1 under several conditions.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28685384", "kind": "science-record", "revision": 3, "content_hash": "sha256:751e88323a1fee69f147b63dcb01d21e04bb2f8f0c0cf789fe12f0eab23d73a7", "created_at": "2026-11-01T15:40:27Z", "updated_at": "2026-11-01T21:20:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Reorganization of gene network for degradation of polycyclic aromatic hydrocarbons (PAHs) in Pseudomonas aeruginosa PAO1 under several conditions.", "doi": "10.1007/s13353-017-0402-9", "pmid": "28685384", "authors": ["Shaomin Yan", "Guang Wu"], "journal": "Journal of applied genetics", "year": 2017, "abstract": "Although polycyclic aromatic hydrocarbons (PAHs) are harmful to human health, their elimination from the environment is not easy. Biodegradation of PAHs is promising since many bacteria have the ability to use hydrocarbons as their sole carbon and energy sources for growth. Of various microorganisms that can degrade PAHs, Pseudomonas aeruginosa is particularly important, not only because it causes a series of diseases including infection in cystic fibrosis patients, but also because it is a model bacterium in various studies. The genes that are responsible for degrading PAHs have been identified in P. aeruginosa, however, no gene acts alone as various stresses often initiate different metabolic pathways, quorum sensing, biofilm formation, antibiotic tolerance, etc. Therefore, it is important to study how PAH degradation genes behave under different conditions. In this study, we apply network analysis to investigating how 46 PAH degradation genes reorganized among 5549 genes in P. aeruginosa PAO1 under nine different conditions using publicly available gene coexpression data from GEO. The results provide six aspects of novelties: (i) comparing the number of gene clusters before and after stresses, (ii) comparing the membership in each gene cluster before and after stresses, (iii) defining which gene changed its membership together with PAH degradation genes before and after stresses, (iv) classifying membership-changed-genes in terms of category in Pseudomonas Genome Database, (v) postulating unknown gene's function, and (vi) proposing new mechanisms for genes of interests. This study can shed light on understanding of cooperative mechanisms of PAH degradation from the level of entire genes in an organism, and paves the way to conduct the similar studies on other genes.", "claims": [{"id": "claim-method", "statement": "Network analysis was conducted using iGraph R package (http://igraph.org/) and Pajek (de Nooy et al. 2011).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28685384", "locator": "sections[6] \"Network analysis, heatmap and dendrogram\" paragraph 2", "quote": "Network analysis was conducted using iGraph R package (http://igraph.org/) and Pajek (de Nooy et al. 2011)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available microarray data were obtained from GEO", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28685384", "locator": "sections[3] \"Data\" paragraph 2", "quote": "Publicly available microarray data were obtained from GEO"}], "state": "complete"}], "gaps": []}, "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:28685384"], "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:GSE10304"], "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:GSE10304"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28685384", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s13353-017-0402-9", "sha256": "sha256:68e006218f17fdac882bde9ddfb155f3ddd29eb1bc1b9a0ae0d344ccf5658eb9", "bytes": 46312, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s13353-017-0402-9", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5655620", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE10304", "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=GSE10304", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE10304", "version": null, "note": "Publicly available microarray data were obtained from GEO", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available microarray data were obtained from GEO", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM142279", "GSM142280", "GSM142281", "GSM142282", "GSM260373", "GSM260374", "GSM260375", "GSM260376"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "84", "taxon": "Pseudomonas aeruginosa", "title": "Gene expression in AES-2 clonal isolates of Pseudomonas aeruginosa", "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:GSE10604", "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=GSE10604", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE10604", "version": null, "note": "Publicly available microarray data were obtained from GEO", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available microarray data were obtained from GEO", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM267248", "GSM267249", "GSM267250", "GSM267251", "GSM267252", "GSM267253", "GSM267254", "GSM267255", "GSM267256", "GSM267257", "GSM267258", "GSM267259"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "84", "taxon": "Pseudomonas aeruginosa", "title": "Microarray Analysis of Toxicogenomic Effects of Ortho-Phenylphenol on Pseudomonas aeruginosa", "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:GSE3090", "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=GSE3090", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE3090", "version": null, "note": "Publicly available microarray data were obtained from GEO", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available microarray data were obtained from GEO", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM68687", "GSM68688", "GSM68689", "GSM68690", "GSM68691", "GSM68692", "GSM68693", "GSM68694", "GSM68695"], "sample_count": 9, "group_sizes": null, "group_sizes_basis": null, "platform": "84", "taxon": "Pseudomonas aeruginosa; Pseudomonas aeruginosa PAO1", "title": "Microarray Analysis of Pseudomonas aeruginosa Reveals Induction of Pyocin Genes in Response to Hydrogen Peroxide", "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:GSE34762", "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=GSE34762", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE34762", "version": null, "note": "Publicly available microarray data were obtained from GEO", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available microarray data were obtained from GEO", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM854792", "GSM854793", "GSM854794", "GSM854795", "GSM854796", "GSM854797", "GSM854798", "GSM854799", "GSM854800", "GSM854801"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "84", "taxon": "Pseudomonas aeruginosa", "title": "Pseudomonas aeruginosa biofilm cells contain ribosome hibernation factors in the dormant antibiotic-tolerant subpopulation", "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:GSE35632", "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=GSE35632", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE35632", "version": null, "note": "Publicly available microarray data were obtained from GEO", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available microarray data were obtained from GEO", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM871963", "GSM871964", "GSM871965", "GSM871966", "GSM871967", "GSM871968", "GSM871969", "GSM871970", "GSM871971", "GSM871972", "GSM871973", "GSM871974", "GSM871975", "GSM871976", "GSM871977", "GSM871978"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "84", "taxon": "Pseudomonas aeruginosa; Pseudomonas aeruginosa PAO1", "title": "Expression of RpoN molecular roadblock in Pseudomonas aeruginosa PAO1 in rich media", "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:GSE39044", "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=GSE39044", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39044", "version": null, "note": "Publicly available microarray data were obtained from GEO", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available microarray data were obtained from GEO", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM954576", "GSM954577", "GSM954578", "GSM954579", "GSM954580", "GSM954581", "GSM954582", "GSM954583"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "84", "taxon": "Pseudomonas aeruginosa PAO1; Pseudomonas aeruginosa", "title": "Regulon of transcriptional regulator PA2449 in Pseduomonas aeruginosa PAO1", "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:GSE52445", "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=GSE52445", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE52445", "version": null, "note": "Publicly available microarray data were obtained from GEO", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available microarray data were obtained from GEO", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1267086", "GSM1267087", "GSM1267088", "GSM1267089", "GSM1267090", "GSM1267091", "GSM1267092", "GSM1267093", "GSM1267094", "GSM1267095", "GSM1267096", "GSM1267097", "GSM1267098", "GSM1267099", "GSM1267100", "GSM1267101", "GSM1267102", "GSM1267103", "GSM1267104", "GSM1267105", "GSM1267106", "GSM1267107", "GSM1267108", "GSM1267109", "GSM1267110", "GSM1267111", "GSM1267112", "GSM1267113"], "sample_count": 28, "group_sizes": null, "group_sizes_basis": null, "platform": "84", "taxon": "Pseudomonas aeruginosa; Pseudomonas aeruginosa PAO1", "title": "High-time-resolution time-series transcriptome data of Pseudomonas aeruginosa PAO1 under two inverted oxygen-availability transitions", "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:GSE6122", "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=GSE6122", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE6122", "version": null, "note": "Publicly available microarray data were obtained from GEO", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available microarray data were obtained from GEO", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM142284", "GSM142285", "GSM142286", "GSM142288", "GSM259816", "GSM259817", "GSM259818", "GSM259819", "GSM259820", "GSM259821", "GSM259822", "GSM259823", "GSM260365", "GSM260366", "GSM260368", "GSM260370", "GSM260371", "GSM260372"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "84", "taxon": "Pseudomonas aeruginosa", "title": "Gene expression in PAO1, clonal AES-1 and non-clonal isolates of Pseudomonas aeruginosa", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE65882", "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=GSE65882", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65882", "version": null, "note": "Publicly available microarray data were obtained from GEO", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available microarray data were obtained from GEO", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1608059", "GSM1608060", "GSM1608061", "GSM1608062", "GSM1608067", "GSM1608068", "GSM1608069", "GSM1608070", "GSM1608071", "GSM1608072"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "84", "taxon": "Pseudomonas aeruginosa", "title": "Identification of genes involved with P. aeruginosa biofilms", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE7402", "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=GSE7402", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE7402", "version": null, "note": "Publicly available microarray data were obtained from GEO", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available microarray data were obtained from GEO", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM178564", "GSM178565", "GSM178566", "GSM178567", "GSM178568", "GSM68692", "GSM68693", "GSM68694", "GSM68695"], "sample_count": 9, "group_sizes": null, "group_sizes_basis": null, "platform": "84", "taxon": "Pseudomonas aeruginosa; Pseudomonas aeruginosa PAO1", "title": "Toxicogenomic analysis of sodium sodium hypochlorite antimicrobial mechanisms in Pseudomonas aeruginosa", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE10304 not downloaded", "asset:data:geo:GSE10304 licence not read", "asset:data:geo:GSE10604 not downloaded", "asset:data:geo:GSE10604 licence not read", "asset:data:geo:GSE3090 not downloaded", "asset:data:geo:GSE3090 licence not read", "asset:data:geo:GSE34762 not downloaded", "asset:data:geo:GSE34762 licence not read", "asset:data:geo:GSE35632 not downloaded", "asset:data:geo:GSE35632 licence not read", "asset:data:geo:GSE39044 not downloaded", "asset:data:geo:GSE39044 licence not read", "asset:data:geo:GSE52445 not downloaded", "asset:data:geo:GSE52445 licence not read", "asset:data:geo:GSE6122 not downloaded", "asset:data:geo:GSE6122 licence not read", "asset:data:geo:GSE65882 not downloaded", "asset:data:geo:GSE65882 licence not read", "asset:data:geo:GSE7402 not downloaded", "asset:data:geo:GSE7402 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Network analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Network analysis was conducted using iGraph R package (http://igraph.org/) and Pajek (de Nooy et al. 2011)."}}], "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 (Network analysis), 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": ["GSE3090", "GSE7402", "GSE52445", "GSE10604", "GSE35632", "GSE34762", "GSE65882", "GSE6122", "GSE10304", "GSE39044"], "resolved_accessions": ["GSE3090", "GSE7402", "GSE52445", "GSE10604", "GSE35632", "GSE34762", "GSE65882", "GSE6122", "GSE10304", "GSE39044"], "statements": ["Publicly available microarray data were obtained from GEO"], "basis": "The paper names GSE3090, GSE7402, GSE52445, GSE10604, GSE35632, GSE34762, GSE65882, GSE6122, GSE10304, GSE39044 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:28685384", "data:geo:GSE10304"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE10304"]}, "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": null, "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 0, "usage": {}}, "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:28685384", "type": "paper", "label": "pmid:28685384"}, {"id": "source:pmid:28685384", "type": "manuscript", "label": "PMID 28685384 full text"}, {"id": "data:geo:GSE10304", "type": "dataset", "label": "GEO GSE10304"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28685384", "type": "paper", "label": "pmid:28685384"}, {"id": "source:pmid:28685384", "type": "manuscript", "label": "PMID 28685384 full text"}, {"id": "data:geo:GSE10304", "type": "dataset", "label": "GEO GSE10304"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28685384", "type": "extraction", "used": ["source:pmid:28685384"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE10304", "type": "accession_resolution", "used": ["data:geo:GSE10304"], "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:28685384", "parent_hash": "sha256:dd22d0d8cba8eca95a9fcafbaaa22e9c3c9c599e70f2c868d002a4788dacbeeb", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE10304 licence not read", "asset:data:geo:GSE10304 not downloaded", "asset:data:geo:GSE10604 licence not read", "asset:data:geo:GSE10604 not downloaded", "asset:data:geo:GSE3090 licence not read", "asset:data:geo:GSE3090 not downloaded", "asset:data:geo:GSE34762 licence not read", "asset:data:geo:GSE34762 not downloaded", "asset:data:geo:GSE35632 licence not read", "asset:data:geo:GSE35632 not downloaded", "asset:data:geo:GSE39044 licence not read", "asset:data:geo:GSE39044 not downloaded", "asset:data:geo:GSE52445 licence not read", "asset:data:geo:GSE52445 not downloaded", "asset:data:geo:GSE6122 licence not read", "asset:data:geo:GSE6122 not downloaded", "asset:data:geo:GSE65882 licence not read", "asset:data:geo:GSE65882 not downloaded", "asset:data:geo:GSE7402 licence not read", "asset:data:geo:GSE7402 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"]}