← All .science files
pmid:29861410
RankProd Combined with Genetic Algorithm Optimized Artificial Neural Network Establishes a Diagnostic and Prognostic Prediction Model that Revealed C1QTNF3 as a Biomarker for Prostate Cancer.
Qi Hou · Zhi-Tong Bing · Cheng Hu · Mao-Yin Li · Ke-Hu Yang · Zu Mo · Xiang-Wei Xie · Ji-Lin Liao · Yan Lu · Shigeo Horie · Ming-Wu Lou
EBioMedicine · 2018 doi:10.1016/j.ebiom.2018.05.010
Paper
complete
Experiment
complete
Data
partial
Analysis
partial
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 11 items
claims array · 3 items
[0] object · 6 fields
[1] object · 6 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 8 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 743 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 24 items
[3] object · 15 fields
structure object · 15 fields
sample_accessions array · 89 items
[4] object · 15 fields
structure object · 15 fields
sample_accessions array · 94 items
[5] object · 15 fields
structure object · 15 fields
sample_accessions array · 148 items
[6] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 14 items
[0] array · 5 items
[1] array · 7 items
[2] array · 8 items
[3] array · 8 items
[4] array · 8 items
[5] array · 8 items
[6] array · 8 items
[7] array · 8 items
[8] array · 8 items
[9] array · 8 items
[10] array · 8 items
[11] array · 8 items
[12] array · 8 items
[13] array · 8 items
[7] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 16 items
[0] array · 4 items
[1] array · 4 items
[2] array · 4 items
[3] array · 4 items
[4] array · 4 items
[5] array · 4 items
[6] array · 4 items
[7] array · 4 items
[8] array · 4 items
[9] array · 4 items
[10] array · 4 items
[11] array · 4 items
[12] array · 4 items
[13] array · 4 items
[14] array · 4 items
[15] array · 4 items
gaps array · 10 items
analysis object · 4 fields
methods array · 2 items
[0] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
targets array · 0 items
gaps array · 1 item
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 1 item
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 5 items
resolved_accessions array · 5 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 4 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 15 items
assays array · 4 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 3 items
[2] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 3 items
[3] object · 11 fields
required_operations array · 1 item
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29861410", "kind": "science-record", "revision": 7, "content_hash": "sha256:4f749ba3726c3d054d776fb70015d8272dcec2e573c9e4375349c4e6c53bd2a1", "created_at": "2026-11-01T15:40:34Z", "updated_at": "2026-11-01T21:21:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "RankProd Combined with Genetic Algorithm Optimized Artificial Neural Network Establishes a Diagnostic and Prognostic Prediction Model that Revealed C1QTNF3 as a Biomarker for Prostate Cancer.", "doi": "10.1016/j.ebiom.2018.05.010", "pmid": "29861410", "authors": ["Qi Hou", "Zhi-Tong Bing", "Cheng Hu", "Mao-Yin Li", "Ke-Hu Yang", "Zu Mo", "Xiang-Wei Xie", "Ji-Lin Liao", "Yan Lu", "Shigeo Horie", "Ming-Wu Lou"], "journal": "EBioMedicine", "year": 2018, "abstract": "Prostate cancer (PCa) is the most commonly diagnosed cancer in males in the Western world. Although prostate-specific antigen (PSA) has been widely used as a biomarker for PCa diagnosis, its results can be controversial. Therefore, new biomarkers are needed to enhance the clinical management of PCa. From publicly available microarray data, differentially expressed genes (DEGs) were identified by meta-analysis with RankProd. Genetic algorithm optimized artificial neural network (GA-ANN) was introduced to establish a diagnostic prediction model and to filter candidate genes. The diagnostic and prognostic capability of the prediction model and candidate genes were investigated in both GEO and TCGA datasets. Candidate genes were further validated by qPCR, Western Blot and Tissue microarray. By RankProd meta-analyses, 2306 significantly up- and 1311 down-regulated probes were found in 133 cases and 30 controls microarray data. The overall accuracy rate of the PCa diagnostic prediction model, consisting of a 15-gene signature, reached up to 100% in both the training and test dataset. The prediction model also showed good results for the diagnosis (AUC = 0.953) and prognosis (AUC of 5 years overall survival time = 0.808) of PCa in the TCGA database. The expression levels of three genes, FABP5, C1QTNF3 and LPHN3, were validated by qPCR. C1QTNF3 high expression was further validated in PCa tissue by Western Blot and Tissue microarray. In the GEO datasets, C1QTNF3 was a good predictor for the diagnosis of PCa (GSE6956: AUC = 0.791; GSE8218: AUC = 0.868; GSE26910: AUC = 0.972). In the TCGA database, C1QTNF3 was significantly associated with PCa patient recurrence free survival (P < .001, AUC = 0.57). In this study, we have developed a diagnostic and prognostic prediction model for PCa. C1QTNF3 was revealed as a promising biomarker for PCa. This approach can be applied to other high-throughput data from different platforms for the discovery of oncogenes or biomarkers in different kinds of diseases.", "claims": [{"id": "claim-method", "statement": "In order to integrate microarray data from different platforms, meta-analysis was carried out by RankProd.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29861410", "locator": "sections[4] \"Individual Participant Data Processing\" paragraph 2", "quote": "In order to integrate microarray data from different platforms, meta-analysis was carried out by RankProd."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GSE6956 is composed of 69 primary prostate tumors and 18 non-tumor prostate tissues (Platform: GPL571 Affymetrix Human Genome U133A 2.0 Array).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29861410", "locator": "sections[13] \"Raw Microarray Data and Overall Processing Methodology Description\" paragraph 2", "quote": "GSE6956 is composed of 69 primary prostate tumors and 18 non-tumor prostate tissues (Platform: GPL571 Affymetrix Human Genome U133A 2.0 Array)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Differentially expressed genes were identified by RankProd meta-analysis using publicly available microarray data.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29861410", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "From publicly available microarray data, differentially expressed genes (DEGs) were identified by meta-analysis with RankProd."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Differentially expressed genes were identified by RankProd meta-analysis using publicly available microarray data.", "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:29861410"], "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:GSE21032"], "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:GSE21032"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29861410", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.ebiom.2018.05.010", "sha256": "sha256:123f9837abe8a4354d49922dc7880c4cb9542fc0451b7470cdb9e91db3276f82", "bytes": 38839, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.ebiom.2018.05.010", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6021271", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE21032", "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=GSE21032", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE21032", "version": null, "note": "GSE6956 is composed of 69 primary prostate tumors and 18 non-tumor prostate tissues (Platform: GPL571 Affymetrix Human Genome U133A 2.0 Array).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "GSE6956 is composed of 69 primary prostate tumors and 18 non-tumor prostate tissues (Platform: GPL571 Affymetrix Human Genome U133A 2.0 Array).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM525575", "GSM525576", "GSM525577", "GSM525578", "GSM525579", "GSM525580", "GSM525581", "GSM525582", "GSM525583", "GSM525584", "GSM525585", "GSM525586", "GSM525587", "GSM525588", "GSM525589", "GSM525590", "GSM525591", "GSM525592", "GSM525593", "GSM525594", "GSM525595", "GSM525596", "GSM525597", "GSM525598", "GSM525599", "GSM525600", "GSM525601", "GSM525602", "GSM525603", "GSM525604", "GSM525605", "GSM525606", "GSM525607", "GSM525608", "GSM525609", "GSM525610", "GSM525611", "GSM525612", "GSM525613", "GSM525614", "GSM525615", "GSM525616", "GSM525617", "GSM525618", "GSM525619", "GSM525620", "GSM525621", "GSM525622", "GSM525623", "GSM525624", "GSM525625", "GSM525626", "GSM525627", "GSM525628", "GSM525629", "GSM525630", "GSM525631", "GSM525632", "GSM525633", "GSM525634", "GSM525635", "GSM525636", "GSM525637", "GSM525638", "GSM525639", "GSM525640", "GSM525641", "GSM525642", "GSM525643", "GSM525644", "GSM525645", "GSM525646", "GSM525647", "GSM525648", "GSM525649", "GSM525650", "GSM525651", "GSM525652", "GSM525653", "GSM525654", "GSM525655", "GSM525656", "GSM525657", "GSM525658", "GSM525659", "GSM525660", "GSM525661", "GSM525662", "GSM525663", "GSM525664", "GSM525665", "GSM525666", "GSM525667", "GSM525668", "GSM525669", "GSM525670", "GSM525671", "GSM525672", "GSM525673", "GSM525674", "GSM525675", "GSM525676", "GSM525677", "GSM525678", "GSM525679", "GSM525680", "GSM525681", "GSM525682", "GSM525683", "GSM525684", "GSM525685", "GSM525686", "GSM525687", "GSM525688", "GSM525689", "GSM525690", "GSM525691", "GSM525692", "GSM525693", "GSM525694", "GSM525695", "GSM525696", "GSM525697", "GSM525698", "GSM525699", "GSM525700", "GSM525701", "GSM525702", "GSM525703", "GSM525704", "GSM525705", "GSM525706", "GSM525707", "GSM525708", "GSM525709", "GSM525710", "GSM525711", "GSM525712", "GSM525713", "GSM525714", "GSM525715", "GSM525716", "GSM525717", "GSM525718", "GSM525719", "GSM525720", "GSM525721", "GSM525722", "GSM525723", "GSM525724", "GSM525725", "GSM525726", "GSM525727", "GSM525728", "GSM525729", "GSM525730", "GSM525731", "GSM525732", "GSM525733", "GSM525734", "GSM525735", "GSM525736", "GSM525737", "GSM525738", "GSM525739", "GSM525740", "GSM525741", "GSM525742", "GSM525743", "GSM525744", "GSM525745", "GSM525746", "GSM525747", "GSM525748", "GSM525749", "GSM525750", "GSM525751", "GSM525752", "GSM525753", "GSM525754", "GSM525755", "GSM525756", "GSM525757", "GSM525758", "GSM525759", "GSM525760", "GSM525761", "GSM525762", "GSM525763", "GSM525764", "GSM525765", "GSM525766", "GSM525767", "GSM525768", "GSM525769", "GSM525770", "GSM525771", "GSM525772", "GSM525773", "GSM525774", "GSM525775", "GSM525776", "GSM525777", "GSM525778", "GSM525779", "GSM525780", "GSM525781", "GSM525782", "GSM525783", "GSM525784", "GSM525785", "GSM525786", "GSM525787", "GSM525788", "GSM525789", "GSM525790", "GSM525791", "GSM525792", "GSM525793", "GSM525794", "GSM525795", "GSM525796", "GSM525797", "GSM525798", "GSM525799", "GSM525800", "GSM525801", "GSM525802", "GSM525803", "GSM525804", "GSM525805", "GSM526134", "GSM526135", "GSM526136", "GSM526137", "GSM526138", "GSM526139", "GSM526140", "GSM526141", "GSM526142", "GSM526143", "GSM526144", "GSM526145", "GSM526146", "GSM526147", "GSM526148", "GSM526149", "GSM526150", "GSM526151", "GSM526152", "GSM526153", "GSM526154", "GSM526155", "GSM526156", "GSM526157", "GSM526158", "GSM526159", "GSM526160", "GSM526161", "GSM526162", "GSM526163", "GSM526164", "GSM526165", "GSM526166", "GSM526167", "GSM526168", "GSM526169", "GSM526170", "GSM526171", "GSM526172", "GSM526173", "GSM526174", "GSM526175", "GSM526176", "GSM526177", "GSM526178", "GSM526179", "GSM526180", "GSM526181", "GSM526182", "GSM526183", "GSM526184", "GSM526185", "GSM526186", "GSM526187", "GSM526188", "GSM526189", "GSM526190", "GSM526191", "GSM526192", "GSM526193", "GSM526194", "GSM526195", "GSM526196", "GSM526197", "GSM526198", "GSM526199", "GSM526200", "GSM526201", "GSM526202", "GSM526203", "GSM526204", "GSM526205", "GSM526206", "GSM526207", "GSM526208", "GSM526209", "GSM526210", "GSM526211", "GSM526212", "GSM526213", "GSM526214", "GSM526215", "GSM526216", "GSM526217", "GSM526218", "GSM526219", "GSM526220", "GSM526221", "GSM526222", "GSM526223", "GSM526224", "GSM526225", "GSM526226", "GSM526227", "GSM526228", "GSM526229", "GSM526230", "GSM526231", "GSM526232", "GSM526233", "GSM526234", "GSM526235", "GSM526236", "GSM526237", "GSM526238", "GSM526239", "GSM526240", "GSM526241", "GSM526242", "GSM526243", "GSM526244", "GSM526245", "GSM526246", "GSM526247", "GSM526248", "GSM526249", "GSM526250", "GSM526251", "GSM526252", "GSM526253", "GSM526254", "GSM526255", "GSM526256", "GSM526257", "GSM526258", "GSM526259", "GSM526260", "GSM526261", "GSM526262", "GSM526263", "GSM526264", "GSM526265", "GSM526266", "GSM526267", "GSM526268", "GSM526269", "GSM526270", "GSM526271", "GSM526272", "GSM526273", "GSM526274", "GSM526275", "GSM526276", "GSM526277", "GSM526278", "GSM526279", "GSM526280", "GSM526281", "GSM526282", "GSM526283", "GSM526284", "GSM526285", "GSM526286", "GSM526287", "GSM526288", "GSM526289", "GSM526290", "GSM526291", "GSM526292", "GSM526293", "GSM526294", "GSM526295", "GSM526296", "GSM526297", "GSM526298", "GSM526299", "GSM526300", "GSM526301", "GSM526302", "GSM526303", "GSM526304", "GSM526305", "GSM526306", "GSM526307", "GSM526308", "GSM526309", "GSM526310", "GSM526311", "GSM526312", "GSM526313", "GSM526314", "GSM526315", "GSM526316", "GSM526317", "GSM526318", "GSM526419", "GSM526420", "GSM526421", "GSM526422", "GSM526423", "GSM526424", "GSM526425", "GSM526426", "GSM526427", "GSM526428", "GSM526429", "GSM526430", "GSM526431", "GSM526432", "GSM526433", "GSM526434", "GSM526435", "GSM526436", "GSM526437", "GSM526438", "GSM526439", "GSM526440", "GSM526441", "GSM526442", "GSM526443", "GSM526444", "GSM526445", "GSM526446", "GSM526447", "GSM526448", "GSM526449", "GSM526450", "GSM526451", "GSM526452", "GSM526453", "GSM526454", "GSM526455", "GSM526456", "GSM526457", "GSM526458", "GSM526459", "GSM526460", "GSM526461", "GSM526462", "GSM526463", "GSM526464", "GSM526465", "GSM526466", "GSM526467", "GSM526468", "GSM526469", "GSM526470", "GSM526471", "GSM526472", "GSM526473", "GSM526474", "GSM526475", "GSM526476", "GSM526477", "GSM526478", "GSM526479", "GSM526480", "GSM526481", "GSM526482", "GSM526483", "GSM526484", "GSM526485", "GSM526486", "GSM526487", "GSM526488", "GSM526489", "GSM526490", "GSM526491", "GSM526492", "GSM526493", "GSM526494", "GSM526495", "GSM526496", "GSM526497", "GSM526498", "GSM526499", "GSM526500", "GSM526501", "GSM526502", "GSM526503", "GSM526504", "GSM526505", "GSM526506", "GSM526507", "GSM526508", "GSM526509", "GSM526510", "GSM526511", "GSM526512", "GSM526513", "GSM526514", "GSM526515", "GSM526516", "GSM526517", "GSM526518", "GSM526519", "GSM526520", "GSM526521", "GSM526522", "GSM526523", "GSM526524", "GSM526525", "GSM526526", "GSM526527", "GSM526528", "GSM526529", "GSM526530", "GSM526531", "GSM526532", "GSM526533", "GSM526534", "GSM526535", "GSM526536", "GSM526537", "GSM526538", "GSM526539", "GSM526540", "GSM526541", "GSM526542", "GSM526543", "GSM526544", "GSM526545", "GSM526546", "GSM526547", "GSM526548", "GSM526549", "GSM526550", "GSM526551", "GSM526552", "GSM526553", "GSM526554", "GSM526555", "GSM526556", "GSM526557", "GSM526558", "GSM526559", "GSM526560", "GSM527858", "GSM527859", "GSM527860", "GSM527861", "GSM527862", "GSM527863", "GSM527864", "GSM527865", "GSM527866", "GSM527867", "GSM527868", "GSM527869", "GSM527870", "GSM527871", "GSM527872", "GSM527873", "GSM527874", "GSM527875", "GSM527876", "GSM527877", "GSM527878", "GSM527879", "GSM527880", "GSM527881", "GSM527882", "GSM527883", "GSM527884", "GSM527885", "GSM527886", "GSM527887", "GSM527888", "GSM527889", "GSM527890", "GSM527891", "GSM527892", "GSM527893", "GSM527894", "GSM527895", "GSM527896", "GSM527897", "GSM527898", "GSM527899", "GSM527900", "GSM527901", "GSM527902", "GSM527903", "GSM527904", "GSM527905", "GSM527906", "GSM527907", "GSM527908", "GSM527909", "GSM527910", "GSM527911", "GSM527912", "GSM527913", "GSM527914", "GSM527915", "GSM527916", "GSM527917", "GSM527918", "GSM527919", "GSM527920", "GSM527921", "GSM527922", "GSM527923", "GSM527924", "GSM527925", "GSM527926", "GSM527927", "GSM527928", "GSM527929", "GSM527930", "GSM527931", "GSM527932", "GSM527933", "GSM527934", "GSM527935", "GSM527936", "GSM527937", "GSM527938", "GSM527939", "GSM527940", "GSM527941", "GSM527942", "GSM527943", "GSM527944", "GSM527945", "GSM527946", "GSM527947", "GSM527948", "GSM527949", "GSM527950", "GSM527951", "GSM527952", "GSM527953", "GSM527954", "GSM527955", "GSM527956", "GSM527957", "GSM527958", "GSM527959", "GSM527960", "GSM527961", "GSM527962", "GSM527963", "GSM527965", "GSM527966", "GSM527968", "GSM527970", "GSM527971", "GSM527972", "GSM527973", "GSM527974", "GSM527975", "GSM527977", "GSM527979", "GSM527980", "GSM527982", "GSM527984", "GSM527985", "GSM527986", "GSM527987", "GSM527988", "GSM527989", "GSM527990", "GSM527991", "GSM527992", "GSM527993", "GSM527994", "GSM527995", "GSM527996", "GSM527997", "GSM527998", "GSM527999", "GSM528000", "GSM528001", "GSM528002", "GSM528003", "GSM528004", "GSM528005", "GSM528006", "GSM528007", "GSM528008", "GSM528009", "GSM528010", "GSM528011", "GSM528012", "GSM528013", "GSM528014", "GSM528015", "GSM528016", "GSM528017", "GSM528018", "GSM528019", "GSM528020", "GSM528021", "GSM528022", "GSM528023", "GSM528024", "GSM528025", "GSM528026", "GSM528027", "GSM528028", "GSM528029", "GSM528030", "GSM528031", "GSM528032", "GSM528033", "GSM528034", "GSM528035", "GSM528036", "GSM528037", "GSM528038", "GSM528039", "GSM528040", "GSM528041", "GSM528042", "GSM528043", "GSM528044", "GSM528045", "GSM528046", "GSM528047", "GSM528048", "GSM528049"], "sample_count": 743, "group_sizes": null, "group_sizes_basis": null, "platform": "10264;8227;5188;4091", "taxon": "Homo sapiens", "title": "Integrative genomic profiling of human prostate cancer", "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:GSE26910", "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=GSE26910", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26910", "version": null, "note": "GSE6956 is composed of 69 primary prostate tumors and 18 non-tumor prostate tissues (Platform: GPL571 Affymetrix Human Genome U133A 2.0 Array).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "GSE6956 is composed of 69 primary prostate tumors and 18 non-tumor prostate tissues (Platform: GPL571 Affymetrix Human Genome U133A 2.0 Array).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM662756", "GSM662757", "GSM662758", "GSM662759", "GSM662760", "GSM662761", "GSM662762", "GSM662763", "GSM662764", "GSM662765", "GSM662766", "GSM662767", "GSM662768", "GSM662769", "GSM662770", "GSM662771", "GSM662772", "GSM662773", "GSM662774", "GSM662775", "GSM662776", "GSM662777", "GSM662778", "GSM662779"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Stromal molecular signatures of breast and prostate cancer", "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:GSE6956", "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=GSE6956", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE6956", "version": null, "note": "GSE6956 is composed of 69 primary prostate tumors and 18 non-tumor prostate tissues (Platform: GPL571 Affymetrix Human Genome U133A 2.0 Array).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "GSE6956 is composed of 69 primary prostate tumors and 18 non-tumor prostate tissues (Platform: GPL571 Affymetrix Human Genome U133A 2.0 Array).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM160343", "GSM160344", "GSM160345", "GSM160346", "GSM160347", "GSM160348", "GSM160349", "GSM160350", "GSM160351", "GSM160352", "GSM160353", "GSM160354", "GSM160355", "GSM160356", "GSM160357", "GSM160358", "GSM160359", "GSM160360", "GSM160361", "GSM160362", "GSM160363", "GSM160364", "GSM160365", "GSM160366", "GSM160367", "GSM160368", "GSM160369", "GSM160370", "GSM160371", "GSM160372", "GSM160373", "GSM160374", "GSM160375", "GSM160376", "GSM160377", "GSM160378", "GSM160379", "GSM160380", "GSM160381", "GSM160382", "GSM160383", "GSM160384", "GSM160385", "GSM160386", "GSM160387", "GSM160388", "GSM160389", "GSM160390", "GSM160391", "GSM160392", "GSM160393", "GSM160394", "GSM160395", "GSM160396", "GSM160397", "GSM160398", "GSM160399", "GSM160400", "GSM160401", "GSM160402", "GSM160403", "GSM160404", "GSM160405", "GSM160406", "GSM160407", "GSM160408", "GSM160409", "GSM160410", "GSM160411", "GSM160412", "GSM160413", "GSM160414", "GSM160415", "GSM160416", "GSM160417", "GSM160418", "GSM160419", "GSM160420", "GSM160421", "GSM160422", "GSM160423", "GSM160424", "GSM160425", "GSM160426", "GSM160427", "GSM160428", "GSM160429", "GSM160430", "GSM160431"], "sample_count": 89, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Tumor Immunobiological Differences in Prostate Cancer between African-American and European-American Men", "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:GSE70769", "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=GSE70769", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE70769", "version": null, "note": "GSE6956 is composed of 69 primary prostate tumors and 18 non-tumor prostate tissues (Platform: GPL571 Affymetrix Human Genome U133A 2.0 Array).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "GSE6956 is composed of 69 primary prostate tumors and 18 non-tumor prostate tissues (Platform: GPL571 Affymetrix Human Genome U133A 2.0 Array).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1817906", "GSM1817907", "GSM1817908", "GSM1817909", "GSM1817910", "GSM1817911", "GSM1817912", "GSM1817913", "GSM1817914", "GSM1817915", "GSM1817916", "GSM1817917", "GSM1817918", "GSM1817919", "GSM1817920", "GSM1817921", "GSM1817922", "GSM1817923", "GSM1817924", "GSM1817925", "GSM1817926", "GSM1817927", "GSM1817928", "GSM1817929", "GSM1817930", "GSM1817931", "GSM1817932", "GSM1817933", "GSM1817934", "GSM1817935", "GSM1817936", "GSM1817937", "GSM1817938", "GSM1817939", "GSM1817940", "GSM1817941", "GSM1817942", "GSM1817943", "GSM1817944", "GSM1817945", "GSM1817946", "GSM1817947", "GSM1817948", "GSM1817949", "GSM1817950", "GSM1817951", "GSM1817952", "GSM1817953", "GSM1817954", "GSM1817955", "GSM1817956", "GSM1817957", "GSM1817958", "GSM1817959", "GSM1817960", "GSM1817961", "GSM1817962", "GSM1817963", "GSM1817964", "GSM1817965", "GSM1817966", "GSM1817967", "GSM1817968", "GSM1817969", "GSM1817970", "GSM1817971", "GSM1817972", "GSM1817973", "GSM1817974", "GSM1817975", "GSM1817976", "GSM1817977", "GSM1817978", "GSM1817979", "GSM1817980", "GSM1817981", "GSM1817982", "GSM1817983", "GSM1817984", "GSM1817985", "GSM1817986", "GSM1817987", "GSM1817988", "GSM1817989", "GSM1817990", "GSM1817991", "GSM1817992", "GSM1817993", "GSM1817994", "GSM1817995", "GSM1817996", "GSM1817997", "GSM1817998", "GSM1817999"], "sample_count": 94, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Prostate cancer stratification using molecular profiles [Stockholm ExpressionArray]", "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:GSE8218", "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=GSE8218", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE8218", "version": null, "note": "GSE6956 is composed of 69 primary prostate tumors and 18 non-tumor prostate tissues (Platform: GPL571 Affymetrix Human Genome U133A 2.0 Array).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "GSE6956 is composed of 69 primary prostate tumors and 18 non-tumor prostate tissues (Platform: GPL571 Affymetrix Human Genome U133A 2.0 Array).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM203261", "GSM203262", "GSM203263", "GSM203264", "GSM203265", "GSM203266", "GSM203267", "GSM203268", "GSM203269", "GSM203270", "GSM203271", "GSM203272", "GSM203273", "GSM203274", "GSM203275", "GSM203276", "GSM203277", "GSM203278", "GSM203279", "GSM203280", "GSM203281", "GSM203282", "GSM203283", "GSM203284", "GSM203285", "GSM203286", "GSM203287", "GSM203288", "GSM203289", "GSM203290", "GSM203291", "GSM203292", "GSM203293", "GSM203294", "GSM203295", "GSM203296", "GSM203297", "GSM203298", "GSM203299", "GSM203300", "GSM203301", "GSM203302", "GSM203303", "GSM203304", "GSM203305", "GSM203306", "GSM203307", "GSM203308", "GSM203309", "GSM203310", "GSM203311", "GSM203312", "GSM203313", "GSM203314", "GSM203315", "GSM203316", "GSM203317", "GSM203318", "GSM203319", "GSM203320", "GSM203321", "GSM203322", "GSM203323", "GSM203324", "GSM203325", "GSM203326", "GSM203327", "GSM203328", "GSM203329", "GSM203330", "GSM203331", "GSM203332", "GSM203333", "GSM203334", "GSM203335", "GSM203336", "GSM203337", "GSM203338", "GSM203339", "GSM203340", "GSM203341", "GSM203342", "GSM203343", "GSM203344", "GSM203345", "GSM203346", "GSM203347", "GSM203348", "GSM203349", "GSM203350", "GSM203351", "GSM203352", "GSM203353", "GSM203354", "GSM203355", "GSM203356", "GSM203357", "GSM203358", "GSM203359", "GSM203360", "GSM203361", "GSM203362", "GSM203363", "GSM203364", "GSM203365", "GSM203366", "GSM203367", "GSM203368", "GSM203369", "GSM203370", "GSM203371", "GSM203372", "GSM203373", "GSM203374", "GSM203375", "GSM203376", "GSM203377", "GSM203378", "GSM203379", "GSM203380", "GSM203381", "GSM203382", "GSM203383", "GSM203384", "GSM203385", "GSM203386", "GSM203387", "GSM203388", "GSM203389", "GSM203390", "GSM203391", "GSM203392", "GSM203393", "GSM203394", "GSM203395", "GSM203396", "GSM203397", "GSM203398", "GSM203399", "GSM203400", "GSM203401", "GSM203402", "GSM203403", "GSM203404", "GSM203405", "GSM203406", "GSM203407", "GSM203408"], "sample_count": 148, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Gene expression data from prostate cancer samples", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:29861410:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1a154edd7869ecc2360a665fffcc5ae4301da218b1e6f672e88466cc1efe4f64", "bytes": 1442, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#t0005", "version": null, "note": "Table of parameter of ANN, accuracy rate of prediction and number of genes filtered from GA-ANN.", "structure": {"pmcid": "PMC6021271", "section_index": 16, "section_title": "GA-ANN Screening for Candidate PCa Biomarker Genes", "row_count": 14, "column_count": 8}, "table": {"label": "Table 1", "caption": "Table of parameter of ANN, accuracy rate of prediction and number of genes filtered from GA-ANN.", "rows": [["Nodes of Input layer", "popu = 100, gen = 50", "popu = 50, gen = 50", "popu = 20, gen = 50", "15-gene signature"], ["S = 1000", "S = 478", "S = 229", "S = 122", "S = 54", "S = 27", ""], ["Training(normal/tumor)", "100(22/78)", "100(20/80)", "100(19/81)", "100(16/84)", "100(17/83)", "100(21/79)", "100(22/78)"], ["Testing(normal/tumor)", "63(8/55)", "63(10/53)", "63(11/52)", "63(14/49)", "63(13/50)", "63(9/54)", "63(8/55)"], ["Testing results of ANN", "", "", "", "", "", "", ""], ["Normal(accuracy rate)", "8(100%)", "9(90%)", "11(100%)", "14(100%)", "10(76.92%)", "9(100%)", "8(100%)"], ["Tumor(accuracy rate)", "55(100%)", "52(98.11%)", "52(100%)", "49(100%)", "50(100%)", "54(100%)", "55(100%)"], ["Time cost for modeling", "23.525 s", "4.3524 s", "2.5428 s", "3.2448 s", "1.3416 s", "1.9032 s", "1.326 s"], ["Testing results of GA-ANN", "", "", "", "", "", "", ""], ["Normal(accuracy rate)", "8(100%)", "10(100%)", "11(100%)", "14(100%)", "13(100%)", "9(100%)", ""], ["Tumor(accuracy rate)", "55(100%)", "52(98.11%)", "52(100%)", "48(97.96%)", "50(100%)", "54(100%)", ""], ["Time cost for modeling", "3.822 s", "1.5132 s", "0.96721 s", "0.93601 s", "0.5616 s", "0.6864 s", ""], ["Iterations", "2", "3", "3", "6", "3", "6", "6"], ["Candidate genes", "478", "229", "122", "54", "27", "15", ""]], "row_count": 14, "column_count": 8, "numeric_cells": 76, "header_rows": 2, "locator": "section[16]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:29861410:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:72ed323e5d7203d0baf51ff0b0d66fc71cd19d5809ef500a374398b6a207ae29", "bytes": 1063, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[2]#t0010", "version": null, "note": "The P values, HR and coefficients of 15 genes in overall survival prediction model for the TCGA cohort.", "structure": {"pmcid": "PMC6021271", "section_index": 16, "section_title": "GA-ANN Screening for Candidate PCa Biomarker Genes", "row_count": 16, "column_count": 4}, "table": {"label": "Table 2", "caption": "The P values, HR and coefficients of 15 genes in overall survival prediction model for the TCGA cohort.", "rows": [["Gene symbol", "P value", "HR (95% CI)", "Coefficient"], ["FKRP", "0.727", "1.032 (0.865–1.231)", "0.031"], ["SEL1L", "0.580", "1.073(0.837–1.375)", "0.070"], ["IGFALS", "0.742", "1.027(0.877–1.202)", "0.026"], ["PNMA2", "0.801", "1.015(0.901–1.144)", "0.015"], ["ARHGAP8", "0.693", "1.015(0.944–1.090)", "0.014"], ["PHF3", "0.284", "1.093(0.929–1.287)", "0.089"], ["HMG20B", "0.338", "1.205(0.822–1.766)", "0.187"], ["LPHN3", "0.869", "0.991(0.895–1.098)", "−0.009"], ["NPY", "0.372", "0.989(0.966–1.013)", "−0.011"], ["EPHB2", "0.225", "0.925(0.815–1.049)", "−0.078"], ["NNMT", "0.670", "0.991(0.950–1.034)", "−0.009"], ["C1QTNF3", "0.247", "0.940(0.848–1.043)", "−0.061"], ["FABP5", "0.485", "0.986(0.947–1.026)", "−0.014"], ["MTRR", "0.144", "1.069(0.978–1.168)", "0.066"], ["ITPR1", "0.322", "1.028(0.973–1.086)", "0.028"]], "row_count": 16, "column_count": 4, "numeric_cells": 47, "header_rows": 1, "locator": "section[16]/table-wrap[2]#t0010"}}], "gaps": ["asset:data:geo:GSE21032 not downloaded", "asset:data:geo:GSE21032 licence not read", "asset:data:geo:GSE26910 not downloaded", "asset:data:geo:GSE26910 licence not read", "asset:data:geo:GSE6956 not downloaded", "asset:data:geo:GSE6956 licence not read", "asset:data:geo:GSE70769 not downloaded", "asset:data:geo:GSE70769 licence not read", "asset:data:geo:GSE8218 not downloaded", "asset:data:geo:GSE8218 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}, {"id": "method-2", "family": null, "specific": null, "label": "RankProd", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "In order to integrate microarray data from different platforms, meta-analysis was carried out by RankProd."}}], "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": ["pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pathway_enrichment."}, "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": ["GSE6956", "GSE8218", "GSE26910", "GSE21032", "GSE70769"], "resolved_accessions": ["GSE6956", "GSE8218", "GSE26910", "GSE21032", "GSE70769"], "statements": ["GSE6956 is composed of 69 primary prostate tumors and 18 non-tumor prostate tissues (Platform: GPL571 Affymetrix Human Genome U133A 2.0 Array)."], "basis": "The paper names GSE6956, GSE8218, GSE26910, GSE21032, GSE70769 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": ["pathway_enrich"], "assets": ["source:pmid:29861410", "data:geo:GSE21032", "asset:table:pmid:29861410:1", "asset:table:pmid:29861410:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE21032"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:34:39Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 80897, "completion_tokens": 4569, "cached_tokens": 2096}}, "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:29861410", "type": "paper", "label": "pmid:29861410"}, {"id": "source:pmid:29861410", "type": "manuscript", "label": "PMID 29861410 full text"}, {"id": "data:geo:GSE21032", "type": "dataset", "label": "GEO GSE21032"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29861410", "type": "paper", "label": "pmid:29861410"}, {"id": "source:pmid:29861410", "type": "manuscript", "label": "PMID 29861410 full text"}, {"id": "data:geo:GSE21032", "type": "dataset", "label": "GEO GSE21032"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29861410", "type": "extraction", "used": ["source:pmid:29861410"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE21032", "type": "accession_resolution", "used": ["data:geo:GSE21032"], "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:29861410", "parent_hash": "sha256:060373272a4e69e7aa1b963b29bff09b2840f55ecb6cd7ac24a05c4cd1cb993d", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE21032 licence not read", "asset:data:geo:GSE21032 not downloaded", "asset:data:geo:GSE26910 licence not read", "asset:data:geo:GSE26910 not downloaded", "asset:data:geo:GSE6956 licence not read", "asset:data:geo:GSE6956 not downloaded", "asset:data:geo:GSE70769 licence not read", "asset:data:geo:GSE70769 not downloaded", "asset:data:geo:GSE8218 licence not read", "asset:data:geo:GSE8218 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": ["l management of PCa. From publicly available microarray data, differentially expressed genes (DEGs)", "icroarrays were downloaded from the official Affymetrix website. To pre-process Affymetrix microarra", "r validated by qPCR, Western Blot and Tissue microarray. By RankProd meta-analyses, 2306 significant", "obes were found in 133 cases and 30 controls microarray data. The overall accuracy rate of the PCa d"], "order_basis": "paper_text_order:472", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["s. Candidate genes were further validated by qPCR, Western Blot and Tissue microarray. By Rank", "FABP5, C1QTNF3 and LPHN3, were validated by qPCR. C1QTNF3 high expression was further validat", "red adjacent normal tissues were analyzed by qPCR and western blot (Supplementary file 2: Tabl"], "order_basis": "paper_text_order:903", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["didate genes were further validated by qPCR, Western Blot and Tissue microarray. By RankProd meta-anal", "ssion was further validated in PCa tissue by Western Blot and Tissue microarray. In the GEO datasets,", "ent normal tissues were analyzed by qPCR and western blot (Supplementary file 2: Table S2). All fresh"], "order_basis": "paper_text_order:909", "id": "assay:3"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["GO enrichment"], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}