← All .science files
pmid:31533842
Identification of key DNA methylation-driven genes in prostate adenocarcinoma: an integrative analysis of TCGA methylation data.
Ning Xu · Yu-Peng Wu · Zhi-Bin Ke · Ying-Chun Liang · Hai Cai · Wen-Ting Su · Xuan Tao · Shao-Hao Chen · Qing-Shui Zheng · Yong Wei · Xue-Yi Xue
Journal of translational medicine · 2019 doi:10.1186/s12967-019-2065-2
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
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 · 1 item
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 · 11 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 47 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 136 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 15 items
[0] array · 2 items
[1] array · 2 items
[2] array · 2 items
[3] array · 1 item
[4] array · 2 items
[5] array · 2 items
[6] array · 2 items
[7] array · 2 items
[8] array · 2 items
[9] array · 2 items
[10] array · 2 items
[11] array · 1 item
[12] array · 2 items
[13] array · 2 items
[14] array · 2 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 23 items
[0] array · 8 items
[1] array · 1 item
[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 · 1 item
[13] array · 8 items
[14] array · 8 items
[15] array · 8 items
[16] array · 8 items
[17] array · 8 items
[18] array · 8 items
[19] array · 8 items
[20] array · 8 items
[21] array · 8 items
[22] array · 8 items
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 9 items
[0] array · 5 items
[1] array · 5 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
[6] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 9 items
[0] array · 6 items
[1] array · 6 items
[2] array · 6 items
[3] array · 6 items
[4] array · 6 items
[5] array · 6 items
[6] array · 6 items
[7] array · 6 items
[8] array · 6 items
[7] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 20 items
[0] array · 7 items
[1] array · 1 item
[2] array · 7 items
[3] array · 7 items
[4] array · 7 items
[5] array · 7 items
[6] array · 7 items
[7] array · 7 items
[8] array · 7 items
[9] array · 1 item
[10] array · 7 items
[11] array · 7 items
[12] array · 7 items
[13] array · 7 items
[14] array · 7 items
[15] array · 7 items
[16] array · 7 items
[17] array · 7 items
[18] array · 7 items
[19] array · 7 items
[8] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 23 items
[0] array · 7 items
[1] array · 1 item
[2] array · 7 items
[3] array · 7 items
[4] array · 7 items
[5] array · 7 items
[6] array · 7 items
[7] array · 7 items
[8] array · 7 items
[9] array · 7 items
[10] array · 7 items
[11] array · 7 items
[12] array · 1 item
[13] array · 7 items
[14] array · 7 items
[15] array · 7 items
[16] array · 7 items
[17] array · 7 items
[18] array · 7 items
[19] array · 7 items
[20] array · 7 items
[21] array · 7 items
[22] array · 7 items
[9] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 15 items
[0] array · 2 items
[1] array · 2 items
[2] array · 2 items
[3] array · 1 item
[4] array · 2 items
[5] array · 2 items
[6] array · 2 items
[7] array · 2 items
[8] array · 2 items
[9] array · 2 items
[10] array · 2 items
[11] array · 1 item
[12] array · 2 items
[13] array · 2 items
[14] array · 2 items
[10] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 23 items
[0] array · 8 items
[1] array · 1 item
[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 · 1 item
[13] array · 8 items
[14] array · 8 items
[15] array · 8 items
[16] array · 8 items
[17] array · 8 items
[18] array · 8 items
[19] array · 8 items
[20] array · 8 items
[21] array · 8 items
[22] array · 8 items
gaps array · 4 items
analysis object · 4 fields
methods array · 2 items
[0] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 0 items
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 · 3 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 2 items
resolved_accessions array · 2 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 3 items
assets array · 10 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 · 8 items
assays array · 3 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[2] object · 11 fields
required_operations array · 3 items
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:31533842", "kind": "science-record", "revision": 8, "content_hash": "sha256:ebdb40b431903c5096aa491f9d48b47cc2e280a970c341b112e2c35c81068514", "created_at": "2026-11-01T15:40:49Z", "updated_at": "2026-11-01T22:44:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key DNA methylation-driven genes in prostate adenocarcinoma: an integrative analysis of TCGA methylation data.", "doi": "10.1186/s12967-019-2065-2", "pmid": "31533842", "authors": ["Ning Xu", "Yu-Peng Wu", "Zhi-Bin Ke", "Ying-Chun Liang", "Hai Cai", "Wen-Ting Su", "Xuan Tao", "Shao-Hao Chen", "Qing-Shui Zheng", "Yong Wei", "Xue-Yi Xue"], "journal": "Journal of translational medicine", "year": 2019, "abstract": "BACKGROUND: Prostate cancer (PCa) remains the second leading cause of deaths due to cancer in the United States in men. The aim of this study was to perform an integrative epigenetic analysis of prostate adenocarcinoma to explore the epigenetic abnormalities involved in the development and progression of prostate adenocarcinoma. The key DNA methylation-driven genes were also identified.\nMETHODS: Methylation and RNA-seq data were downloaded for The Cancer Genome Atlas (TCGA). Methylation and gene expression data from TCGA were incorporated and analyzed using MethylMix package. Methylation data from the Gene Expression Omnibus (GEO) were assessed by R package limma to obtain differentially methylated genes. Pathway analysis was performed on genes identified by MethylMix criteria using ConsensusPathDB. Gene Ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were also applied for the identification of pathways in which DNA methylation-driven genes significantly enriched. The protein-protein interaction (PPI) network and module analysis in Cytoscape software were used to find the hub genes. Two methylation profile (GSE112047 and GSE76938) datasets were utilized to validate screened hub genes. Immunohistochemistry of these hub genes were evaluated by the Human Protein Atlas.\nRESULTS: A total of 553 samples in TCGA database, 32 samples in GSE112047 and 136 samples in GSE76938 were included in this study. There were a total of 266 differentially methylated genes were identified by MethylMix. Plus, a total of 369 differentially methylated genes and 594 differentially methylated genes were identified by the R package limma in GSE112047 and GSE76938, respectively. GO term enrichment analysis suggested that DNA methylation-driven genes significantly enriched in oxidation-reduction process, extracellular exosome, electron carrier activity, response to reactive oxygen species, and aldehyde dehydrogenase [NAD(P)+] activity. KEGG pathway analysis found DNA methylation-driven genes significantly enriched in five pathways including drug metabolism-cytochrome P450, phenylalanine metabolism, histidine metabolism, glutathione metabolism, and tyrosine metabolism. The validated hub genes were MAOB and RTP4.\nCONCLUSIONS: Methylated hub genes, including MAOB and RTP4, can be regarded as novel biomarkers for accurate PCa diagnosis and treatment. Further studies are needed to draw more attention to the roles of these hub genes in the occurrence and development of PCa.", "claims": [{"id": "claim-data-access", "statement": "All data was obtained from The Cancer Genome Atlas (TCGA, https://tcga-data.nci.nih.gov/tcga/) and Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31533842", "locator": "sections[28] \"notes\" paragraph 1", "quote": "All data was obtained from The Cancer Genome Atlas (TCGA, https://tcga-data.nci.nih.gov/tcga/) and Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/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:31533842"], "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:GSE112047"], "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:GSE112047"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31533842", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12967-019-2065-2", "sha256": "sha256:3b7a2e077e4a1421fbc11f0e304d7ae8c22939048006a114333f67d24bed3fb6", "bytes": 33636, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12967-019-2065-2", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6751626", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE112047", "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=GSE112047", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE112047", "version": null, "note": "All data was obtained from The Cancer Genome Atlas (TCGA, https://tcga-data.nci.nih.gov/tcga/) and Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data was obtained from The Cancer Genome Atlas (TCGA, https://tcga-data.nci.nih.gov/tcga/) and Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3053769", "GSM3053770", "GSM3053771", "GSM3053772", "GSM3053773", "GSM3053774", "GSM3053775", "GSM3053776", "GSM3053777", "GSM3053778", "GSM3053779", "GSM3053780", "GSM3053781", "GSM3053782", "GSM3053783", "GSM3053784", "GSM3053785", "GSM3053786", "GSM3053787", "GSM3053788", "GSM3053789", "GSM3053790", "GSM3053791", "GSM3053792", "GSM3053793", "GSM3053794", "GSM3053795", "GSM3053796", "GSM3053797", "GSM3053798", "GSM3053799", "GSM3053800", "GSM3053801", "GSM3053802", "GSM3053803", "GSM3053804", "GSM3053805", "GSM3053806", "GSM3053807", "GSM3053808", "GSM3053809", "GSM3053810", "GSM3053811", "GSM3053812", "GSM3053813", "GSM3053814", "GSM3053815"], "sample_count": 47, "group_sizes": null, "group_sizes_basis": null, "platform": "13534", "taxon": "Homo sapiens", "title": "Genome-Wide DNA methylation analysis of tumor and adjacent normal prostate tissues", "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:GSE76938", "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=GSE76938", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE76938", "version": null, "note": "All data was obtained from The Cancer Genome Atlas (TCGA, https://tcga-data.nci.nih.gov/tcga/) and Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data was obtained from The Cancer Genome Atlas (TCGA, https://tcga-data.nci.nih.gov/tcga/) and Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2041110", "GSM2041111", "GSM2041112", "GSM2041113", "GSM2041114", "GSM2041115", "GSM2041116", "GSM2041117", "GSM2041118", "GSM2041119", "GSM2041120", "GSM2041121", "GSM2041122", "GSM2041123", "GSM2041124", "GSM2041125", "GSM2041126", "GSM2041127", "GSM2041128", "GSM2041129", "GSM2041130", "GSM2041131", "GSM2041132", "GSM2041133", "GSM2041134", "GSM2041135", "GSM2041136", "GSM2041137", "GSM2041138", "GSM2041139", "GSM2041140", "GSM2041141", "GSM2041142", "GSM2041143", "GSM2041144", "GSM2041145", "GSM2041146", "GSM2041147", "GSM2041148", "GSM2041149", "GSM2041150", "GSM2041151", "GSM2041152", "GSM2041153", "GSM2041154", "GSM2041155", "GSM2041156", "GSM2041157", "GSM2041158", "GSM2041159", "GSM2041160", "GSM2041161", "GSM2041162", "GSM2041163", "GSM2041164", "GSM2041165", "GSM2041166", "GSM2041167", "GSM2041168", "GSM2041169", "GSM2041170", "GSM2041171", "GSM2041172", "GSM2041173", "GSM2041174", "GSM2041175", "GSM2041176", "GSM2041177", "GSM2041178", "GSM2041179", "GSM2041180", "GSM2041181", "GSM2041182", "GSM2041183", "GSM2041184", "GSM2041185", "GSM2041186", "GSM2041187", "GSM2041188", "GSM2041189", "GSM2041190", "GSM2041191", "GSM2041192", "GSM2041193", "GSM2041194", "GSM2041195", "GSM2041196", "GSM2041197", "GSM2041198", "GSM2041199", "GSM2041200", "GSM2041201", "GSM2041202", "GSM2041203", "GSM2041204", "GSM2041205", "GSM2041206", "GSM2041207", "GSM2041208", "GSM2041209", "GSM2041210", "GSM2041211", "GSM2041212", "GSM2041213", "GSM2041214", "GSM2041215", "GSM2041216", "GSM2041217", "GSM2041218", "GSM2041219", "GSM2041220", "GSM2041221", "GSM2041222", "GSM2041223", "GSM2041224", "GSM2041225", "GSM2041226", "GSM2041227", "GSM2041228", "GSM2041229", "GSM2041230", "GSM2041231", "GSM2041232", "GSM2041233", "GSM2041234", "GSM2041235", "GSM2041236", "GSM2041237", "GSM2041238", "GSM2041239", "GSM2041240", "GSM2041241", "GSM2041242", "GSM2041243", "GSM2041244", "GSM2041245"], "sample_count": 136, "group_sizes": null, "group_sizes_basis": null, "platform": "13534", "taxon": "Homo sapiens", "title": "Illumina M450 profiling of human prostate cancer tissue and benign prostate tissue", "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:31533842:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2dbe3c51f56448581f0f08bd69acc6208cbe1499e7336694efe6bca871d2c3c5", "bytes": 526, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Clinical dada of prostate cancer patients from TCGA", "structure": {"pmcid": "PMC6751626", "section_index": 3, "section_title": "Identification of DNA methylation-driven genes", "row_count": 15, "column_count": 2}, "table": {"label": "Table 1", "caption": "Clinical dada of prostate cancer patients from TCGA", "rows": [["Characteristic", "Total"], ["Cohort sizea", "500"], ["Mean age, years", "61.01 ± 6.823"], ["T stage"], ["pT2a", "13 (2.6%)"], ["pT2b", "10 (2%)"], ["pT2c", "165 (33%)"], ["pT3a", "159 (31.8%)"], ["pT3b", "136 (27.2%)"], ["pT4", "10 (2%)"], ["Unknown", "7 (1.4%)"], ["N stage"], ["N0", "348 (69.6%)"], ["N1", "79 (15.8%)"], ["Unknown", "73 (14.6%)"]], "row_count": 15, "column_count": 2, "numeric_cells": 12, "header_rows": 1, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:31533842:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:08c7727aa2306ea4ff63707933ff230eff0d2703a6ceddc00743aa89f76143b3", "bytes": 2481, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[2]#Tab2", "version": null, "note": "Top 10 hypomethylated genes and hypermethylated genes in patients with prostate cancer", "structure": {"pmcid": "PMC6751626", "section_index": 3, "section_title": "Identification of DNA methylation-driven genes", "row_count": 23, "column_count": 8}, "table": {"label": "Table 2", "caption": "Top 10 hypomethylated genes and hypermethylated genes in patients with prostate cancer", "rows": [["Gene", "Normal mean", "Tumor mean", "Log FC", "p value", "Adjust p", "Cor", "Cor p value"], ["Top 10 hypomethylated genes"], ["TAF1D", "0.298851771", "0.17046481", "− 0.809956148", "5.12E−22", "1.61E−19", "− 0.515133904", "3.62E−35"], ["TMEM87A", "0.36898334", "0.219989007", "− 0.746124244", "2.40E−22", "7.57E−20", "− 0.415783216", "2.80E−22"], ["KLK2", "0.42230197", "0.252663444", "− 0.741058027", "2.34E−25", "7.36E−23", "− 0.424469057", "3.03E−23"], ["MARS", "0.661117252", "0.407190703", "− 0.69920154", "2.88E−18", "9.08E−16", "− 0.402813221", "6.87E−21"], ["SLC10A5", "0.682378547", "0.421046571", "-0.696592477", "1.19E−16", "3.76E−14", "− 0.320114016", "2.36E−13"], ["KLK3", "0.528659515", "0.348234132", "− 0.602281232", "2.38E−22", "7.50E−20", "− 0.352378214", "4.92E−16"], ["MPC2", "0.847716806", "0.573604393", "− 0.563526315", "3.24E−22", "1.02E−19", "− 0.509873152", "2.25E−34"], ["ALDH1A3", "0.390659331", "0.266302408", "− 0.552845598", "6.96E−20", "2.19E−17", "− 0.500862763", "4.78E−33"], ["CLDN8", "0.556942422", "0.387056997", "− 0.524982157", "1.24E−14", "3.91E−12", "− 0.339347771", "6.50E−15"], ["PMEPA1", "0.427234317", "0.301507194", "− 0.50283511", "1.93E−21", "6.07E−19", "− 0.559861766", "1.65E−42"], ["Top 10 hypermethylated genes"], ["HIST1H2BH", "0.073047", "0.264894", "1.858512", "1.40E−15", "4.41E−13", "− 0.37138", "9.15E−18"], ["FAM200A", "0.052277", "0.163374", "1.643934", "1.78E−18", "5.60E−16", "− 0.32491", "9.86E−14"], ["ZFP36L2", "0.101664", "0.293078", "1.527482", "1.59E−13", "5.02E−11", "− 0.47382", "2.72E−29"], ["WFDC2", "0.125846", "0.347072", "1.463575", "2.89E−24", "9.09E−22", "− 0.46874", "1.27E−28"], ["SMIM10", "0.169555", "0.460955", "1.44287", "1.29E−18", "4.06E−16", "− 0.52098", "4.58E−36"], ["RIPPLY2", "0.06161", "0.166659", "1.435669", "4.35E−23", "1.37E−20", "− 0.33215", "2.57E−14"], ["RTP4", "0.102519", "0.273692", "1.416666", "4.91E−19", "1.55E−16", "− 0.51074", "1.67E−34"], ["FBXO27", "0.048294", "0.126663", "1.391093", "3.13E−12", "9.85E−10", "− 0.64419", "7.67E−60"], ["ZNF492", "0.057359", "0.147069", "1.358401", "3.63E−20", "1.14E−17", "− 0.33472", "1.58E−14"], ["HPDL", "0.14249", "0.356177", "1.321732", "5.48E−20", "1.73E−17", "− 0.54417", "8.31E−40"]], "row_count": 23, "column_count": 8, "numeric_cells": 149, "header_rows": 1, "locator": "section[3]/table-wrap[2]#Tab2"}}, {"id": "asset:table:pmid:31533842:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3df6af4ea6ff618a0418ebb6e6e4cdfbf90e8d91680705a305bd2caba5ae3a88", "bytes": 1644, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#Tab3", "version": null, "note": "The top 8 GO terms enriched by the 266 DNA methylation driven genes in prostate cancer", "structure": {"pmcid": "PMC6751626", "section_index": 4, "section_title": "Gene ontology terms analysis of DNA methylation-driven genes obtained from TCGA database", "row_count": 9, "column_count": 5}, "table": {"label": "Table 3", "caption": "The top 8 GO terms enriched by the 266 DNA methylation driven genes in prostate cancer", "rows": [["Category", "Term", "Count", "p value", "Genes"], ["BP", "GO:0055114 ~ oxidation–reduction process", "25", "2.13E−06", "STEAP4, ME3, OXA1L, GLUD1, DUOX1, PAH, HPDL, ALDH3A1, ALDH1A3, GPX3, HAAO, FASN, GPX7, DHCR24, FAXDC2, MAOB, CRYZ, CDO1, RDH5, CYBA, CYP27A1, AKR1B1, TMLHE, AOX1, CYBRD1"], ["CC", "GO:0070062 ~ extracellular exosome", "66", "6.38E−06", "STEAP4, RARRES2, RPS2, SYNGR2, CANT1, GSTM2, DES, APOD, GPX3, LTF, PI15, ZDHHC1, BST2, CFTR, EEF2, CD40, CD38, KRT17, KRT15, TMEM106A, CYBRD1, HSPB1, SERPINB1, NEU1, CSTA, MFAP4, WFDC2, GSTP1, ACP5, PAH, CD74, B3GNT8, KRT5, ITGB8, KRT7, ALDH1A3, ENTPD5, FASN, RPL3, HAAO, ANGPTL1, RPL7A, MARS, BHMT2, S100A16, LGALS3, KLK2, KLK3, HIST1H2BH, MAOB, KLK1, CRYZ, ANXA2, PROM1, ORM1, ACSM1, C1ORF116, PKP1, PHB2, RAB34, AKR1B1, CAPG, AOX1, ALDH2, SLC46A3, PON3"], ["MF", "GO:0009055 ~ electron carrier activity", "7", "0.001504105", "ACOX2, CYBA, AOX1, AKR1B1, MAOB, ALDH2, HAAO"], ["BP", "GO:0000302 ~ response to reactive oxygen species", "5", "0.0019364", "CYBA, APOD, GPX3, GPX7, GSTP1"], ["MF", "GO:0004030 ~ aldehyde dehydrogenase [NAD(P)+] activity", "3", "0.002720156", "ALDH1A3, ALDH2, ALDH3A1"], ["MF", "GO:0004602 ~ glutathione peroxidase activity", "4", "0.002838234", "GSTM2, GPX3, GPX7, GSTP1"], ["BP", "GO:0042178 ~ xenobiotic catabolic process", "3", "0.003748861", "GSTM1, GSTM2, CRYZ"], ["BP", "GO:0060349 ~ bone morphogenesis", "4", "0.005820424", "SP5, LTF, ACP5, RIPPLY2"]], "row_count": 9, "column_count": 5, "numeric_cells": 26, "header_rows": 1, "locator": "section[4]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:31533842:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9acd3658af768b7d3242dc33133afa1705f1e1fb800d1bff03ce876e21775e97", "bytes": 1161, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#Tab4", "version": null, "note": "Pathway enriched by the 266 DNA methylation driven genes", "structure": {"pmcid": "PMC6751626", "section_index": 5, "section_title": "KEGG pathway analysis of DNA methylation-driven genes obtained from TCGA", "row_count": 9, "column_count": 6}, "table": {"label": "Table 4", "caption": "Pathway enriched by the 266 DNA methylation driven genes", "rows": [["Pathway", "External_id", "Members_input_overlap", "p-value", "q-value", "Size"], ["Drug metabolism—cytochrome P450", "hsa00982", "AOX1; GSTM1; GSTM2; ALDH3A1; MAOB; GSTP1; ALDH1A3", "6.59E−05", "0.003828899", "70"], ["Phenylalanine metabolism", "hsa00360", "PAH; MAOB; ALDH3A1; ALDH1A3", "9.23E−05", "0.003828899", "17"], ["Histidine metabolism", "hsa00340", "MAOB; ALDH3A1; ALDH2; ALDH1A3", "0.000320403", "0.008864472", "23"], ["Glutathione metabolism", "hsa00480", "GSTM1; GSTM2; GPX3; GSTP1; GPX7", "0.00114281", "0.023713299", "54"], ["Tyrosine metabolism", "hsa00350", "AOX1; ALDH3A1; ALDH1A3; MAOB", "0.001836818", "0.030491186", "36"], ["Tryptophan metabolism", "hsa00380", "MAOB; HAAO; ALDH2; AOX1", "0.002722806", "0.037665486", "40"], ["Metabolism of xenobiotics by cytochrome P450", "hsa00980", "GSTM1; GSTM2; ALDH3A1; GSTP1; ALDH1A3", "0.00433977", "0.051457275", "74"], ["Chemical carcinogenesis", "hsa05204", "GSTM1; GSTM2; ALDH3A1; GSTP1; ALDH1A3", "0.007094498", "0.073605418", "82"]], "row_count": 9, "column_count": 6, "numeric_cells": 34, "header_rows": 1, "locator": "section[5]/table-wrap[1]#Tab4"}}, {"id": "asset:table:pmid:31533842:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0eae6c3c3988cf053c9a0974aa260bf8cdc9c504b5ca94a3c09037214297af5b", "bytes": 1886, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#Tab5", "version": null, "note": "GO terms enriched in GSE112047 and GSE76938 datasets", "structure": {"pmcid": "PMC6751626", "section_index": 8, "section_title": "Gene ontology terms analysis of DNA methylation-driven genes obtained from GEO database", "row_count": 20, "column_count": 7}, "table": {"label": "Table 5", "caption": "GO terms enriched in GSE112047 and GSE76938 datasets", "rows": [["Gene set", "Description", "Size", "Expect", "Ratio", "p value", "FDR"], ["GSE112047"], ["GO:0045595", "Regulation of cell differentiation", "1699", "28.866", "2.1479", "5.48E−09", "0.0001"], ["GO:0031012", "Extracellular matrix", "496", "8.4271", "3.3226", "3.00E−08", "0.0002"], ["GO:0007155", "Cell adhesion", "1369", "23.259", "2.1067", "5.21E−07", "0.0016"], ["GO:0061061", "Muscle structure development", "610", "10.364", "2.7982", "6.40E−07", "0.0016"], ["GO:0030182", "Neuron differentiation", "1313", "22.308", "2.1069", "9.19E−07", "0.0016"], ["GO:0005540", "Hyaluronic acid binding", "22", "0.3738", "16.052", "1.3596E−06", "0.0021"], ["GO:2000026", "Regulation of multicellular organismal development", "1908", "32.417", "1.82", "3.8179E−06", "0.0046"], ["GSE76938"], ["GO:0043062", "Extracellular structure organization", "400", "11.623", "2.8392", "7.43E−08", "0"], ["GO:0031012", "Extracellular matrix", "496", "14.412", "3.1223", "1.20E−11", "1.56E−08"], ["GO:0021953", "Central nervous system neuron differentiation", "179", "5.2012", "4.2298", "1.19E−08", "7.73E−06"], ["GO:0001505", "Regulation of neurotransmitter levels", "335", "9.7341", "2.9792", "1.70E−07", "0.0001"], ["GO:0045165", "Cell fate commitment", "249", "7.2352", "3.3171", "2.86E−07", "0.0001"], ["GO:1990351", "Transporter complex", "332", "9.6469", "2.9025", "4.73E−07", "0.0001"], ["GO:0050769", "Positive regulation of neurogenesis", "447", "12.989", "2.5407", "9.50E−07", "0.0002"], ["GO:0043025", "Neuronal cell body", "486", "14.122", "2.4076", "2.17E−06", "0.0004"], ["GO:0005201", "Extracellular matrix structural constituent", "158", "4.591", "3.7029", "3.55E−06", "0.0005"], ["GO:0042391", "Regulation of membrane potential", "414", "12.03", "2.4938", "4.34E−06", "0.0005"]], "row_count": 20, "column_count": 7, "numeric_cells": 104, "header_rows": 1, "locator": "section[8]/table-wrap[1]#Tab5"}}, {"id": "asset:table:pmid:31533842:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d4ad6e7f78008a5ce445327d815af1332406b13f456c7bd44ea91ed79ba86b80", "bytes": 1915, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#Tab6", "version": null, "note": "Pathways enriched in GSE112047 and GSE76938 datasets", "structure": {"pmcid": "PMC6751626", "section_index": 9, "section_title": "KEGG pathway analysis of DNA methylation-driven genes obtained from GEO", "row_count": 23, "column_count": 7}, "table": {"label": "Table 6", "caption": "Pathways enriched in GSE112047 and GSE76938 datasets", "rows": [["Gene set", "Description", "Size", "Expect", "Ratio", "p value", "FDR"], ["GSE112047"], ["hsa04728", "Dopaminergic synapse", "131", "2.3422", "3.8426", "0.0005", "0.1734"], ["hsa05033", "Nicotine addiction", "40", "0.7152", "5.5931", "0.0054", "0.5917"], ["hsa05031", "Amphetamine addiction", "68", "1.2158", "4.1126", "0.0072", "0.5917"], ["hsa05146", "Amoebiasis", "96", "1.7164", "3.4957", "0.0073", "0.5917"], ["hsa04512", "ECM-receptor interaction", "82", "1.4661", "3.4104", "0.0154", "0.8913"], ["hsa05323", "Rheumatoid arthritis", "90", "1.6091", "3.1073", "0.0222", "0.8913"], ["hsa00604", "Glycosphingolipid biosynthesis", "15", "0.2682", "7.4574", "0.0286", "0.8913"], ["hsa04933", "AGE-RAGE signaling pathway in diabetic complications", "99", "1.77", "2.8248", "0.0318", "0.8913"], ["hsa00380", "Tryptophan metabolism", "40", "0.7152", "4.1948", "0.0341", "0.8913"], ["hsa00360", "Phenylalanine metabolism", "17", "0.3039", "6.5801", "0.0362", "0.8913"], ["GSE76938"], ["hsa05033", "Nicotine addiction", "40", "1.1993", "9.1721", "1.47E−08", "4.8E−06"], ["hsa05032", "Morphine addiction", "91", "2.7284", "4.7647", "2.68E−06", "0.0004"], ["hsa04723", "Retrograde endocannabinoid signaling", "148", "4.4374", "3.3804", "0", "0.0029"], ["hsa04933", "AGE-RAGE signaling pathway in diabetic complications", "99", "2.9682", "4.0428", "0", "0.0029"], ["hsa04080", "Neuroactive ligand-receptor interaction", "277", "8.305", "2.5286", "0.0001", "0.0051"], ["hsa05146", "Amoebiasis", "96", "2.8783", "3.8217", "0.0001", "0.007"], ["hsa04727", "GABAergic synapse", "88", "2.6384", "3.7901", "0.0003", "0.013"], ["hsa04728", "Dopaminergic synapse", "131", "3.9277", "3.0553", "0.0005", "0.0191"], ["hsa05144", "Malaria", "49", "1.4691", "4.7647", "0.0006", "0.0191"], ["hsa04724", "Glutamatergic synapse", "114", "3.418", "3.2183", "0.0006", "0.0191"]], "row_count": 23, "column_count": 7, "numeric_cells": 122, "header_rows": 1, "locator": "section[9]/table-wrap[1]#Tab6"}}, {"id": "asset:table:pmid:31533842:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2dbe3c51f56448581f0f08bd69acc6208cbe1499e7336694efe6bca871d2c3c5", "bytes": 526, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Clinical dada of prostate cancer patients from TCGA", "structure": {"pmcid": "PMC6751626", "section_index": 15, "section_title": "Identification of DNA methylation-driven genes", "row_count": 15, "column_count": 2}, "table": {"label": "Table 1", "caption": "Clinical dada of prostate cancer patients from TCGA", "rows": [["Characteristic", "Total"], ["Cohort sizea", "500"], ["Mean age, years", "61.01 ± 6.823"], ["T stage"], ["pT2a", "13 (2.6%)"], ["pT2b", "10 (2%)"], ["pT2c", "165 (33%)"], ["pT3a", "159 (31.8%)"], ["pT3b", "136 (27.2%)"], ["pT4", "10 (2%)"], ["Unknown", "7 (1.4%)"], ["N stage"], ["N0", "348 (69.6%)"], ["N1", "79 (15.8%)"], ["Unknown", "73 (14.6%)"]], "row_count": 15, "column_count": 2, "numeric_cells": 12, "header_rows": 1, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:31533842:8", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:08c7727aa2306ea4ff63707933ff230eff0d2703a6ceddc00743aa89f76143b3", "bytes": 2481, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[2]#Tab2", "version": null, "note": "Top 10 hypomethylated genes and hypermethylated genes in patients with prostate cancer", "structure": {"pmcid": "PMC6751626", "section_index": 15, "section_title": "Identification of DNA methylation-driven genes", "row_count": 23, "column_count": 8}, "table": {"label": "Table 2", "caption": "Top 10 hypomethylated genes and hypermethylated genes in patients with prostate cancer", "rows": [["Gene", "Normal mean", "Tumor mean", "Log FC", "p value", "Adjust p", "Cor", "Cor p value"], ["Top 10 hypomethylated genes"], ["TAF1D", "0.298851771", "0.17046481", "− 0.809956148", "5.12E−22", "1.61E−19", "− 0.515133904", "3.62E−35"], ["TMEM87A", "0.36898334", "0.219989007", "− 0.746124244", "2.40E−22", "7.57E−20", "− 0.415783216", "2.80E−22"], ["KLK2", "0.42230197", "0.252663444", "− 0.741058027", "2.34E−25", "7.36E−23", "− 0.424469057", "3.03E−23"], ["MARS", "0.661117252", "0.407190703", "− 0.69920154", "2.88E−18", "9.08E−16", "− 0.402813221", "6.87E−21"], ["SLC10A5", "0.682378547", "0.421046571", "-0.696592477", "1.19E−16", "3.76E−14", "− 0.320114016", "2.36E−13"], ["KLK3", "0.528659515", "0.348234132", "− 0.602281232", "2.38E−22", "7.50E−20", "− 0.352378214", "4.92E−16"], ["MPC2", "0.847716806", "0.573604393", "− 0.563526315", "3.24E−22", "1.02E−19", "− 0.509873152", "2.25E−34"], ["ALDH1A3", "0.390659331", "0.266302408", "− 0.552845598", "6.96E−20", "2.19E−17", "− 0.500862763", "4.78E−33"], ["CLDN8", "0.556942422", "0.387056997", "− 0.524982157", "1.24E−14", "3.91E−12", "− 0.339347771", "6.50E−15"], ["PMEPA1", "0.427234317", "0.301507194", "− 0.50283511", "1.93E−21", "6.07E−19", "− 0.559861766", "1.65E−42"], ["Top 10 hypermethylated genes"], ["HIST1H2BH", "0.073047", "0.264894", "1.858512", "1.40E−15", "4.41E−13", "− 0.37138", "9.15E−18"], ["FAM200A", "0.052277", "0.163374", "1.643934", "1.78E−18", "5.60E−16", "− 0.32491", "9.86E−14"], ["ZFP36L2", "0.101664", "0.293078", "1.527482", "1.59E−13", "5.02E−11", "− 0.47382", "2.72E−29"], ["WFDC2", "0.125846", "0.347072", "1.463575", "2.89E−24", "9.09E−22", "− 0.46874", "1.27E−28"], ["SMIM10", "0.169555", "0.460955", "1.44287", "1.29E−18", "4.06E−16", "− 0.52098", "4.58E−36"], ["RIPPLY2", "0.06161", "0.166659", "1.435669", "4.35E−23", "1.37E−20", "− 0.33215", "2.57E−14"], ["RTP4", "0.102519", "0.273692", "1.416666", "4.91E−19", "1.55E−16", "− 0.51074", "1.67E−34"], ["FBXO27", "0.048294", "0.126663", "1.391093", "3.13E−12", "9.85E−10", "− 0.64419", "7.67E−60"], ["ZNF492", "0.057359", "0.147069", "1.358401", "3.63E−20", "1.14E−17", "− 0.33472", "1.58E−14"], ["HPDL", "0.14249", "0.356177", "1.321732", "5.48E−20", "1.73E−17", "− 0.54417", "8.31E−40"]], "row_count": 23, "column_count": 8, "numeric_cells": 149, "header_rows": 1, "locator": "section[3]/table-wrap[2]#Tab2"}}], "gaps": ["asset:data:geo:GSE112047 not downloaded", "asset:data:geo:GSE112047 licence not read", "asset:data:geo:GSE76938 not downloaded", "asset:data:geo:GSE76938 licence not read"]}, "analysis": {"state": "complete", "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": 1.0, "band": "reordered", "quote": "“For the data from TCGA, the R package MethylMix was applied to perform an analysis integrating gene expression data and methylation data.” “For the data from GEO, the R package limma was applied to perform analysis to identify the DMEs.”"}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}], "targets": [], "gaps": []}, "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": ["GSE112047", "GSE76938"], "resolved_accessions": ["GSE112047", "GSE76938"], "statements": ["All data was obtained from The Cancer Genome Atlas (TCGA, https://tcga-data.nci.nih.gov/tcga/) and Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/)."], "basis": "The paper names GSE112047, GSE76938 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:31533842", "data:geo:GSE112047", "asset:table:pmid:31533842:1", "asset:table:pmid:31533842:2", "asset:table:pmid:31533842:3", "asset:table:pmid:31533842:4", "asset:table:pmid:31533842:5", "asset:table:pmid:31533842:6", "asset:table:pmid:31533842:7", "asset:table:pmid:31533842:8"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE112047"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:16:11Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 28932, "completion_tokens": 2326, "cached_tokens": 9736}}, "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:31533842", "type": "paper", "label": "pmid:31533842"}, {"id": "source:pmid:31533842", "type": "manuscript", "label": "PMID 31533842 full text"}, {"id": "data:geo:GSE112047", "type": "dataset", "label": "GEO GSE112047"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31533842", "type": "paper", "label": "pmid:31533842"}, {"id": "source:pmid:31533842", "type": "manuscript", "label": "PMID 31533842 full text"}, {"id": "data:geo:GSE112047", "type": "dataset", "label": "GEO GSE112047"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31533842", "type": "extraction", "used": ["source:pmid:31533842"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE112047", "type": "accession_resolution", "used": ["data:geo:GSE112047"], "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:31533842", "parent_hash": "sha256:bd4b80bfdd20d2198c76e1df20abee6dfd2d1ff1dcdbaf7a2bd4654e74b72d10", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE112047 licence not read", "asset:data:geo:GSE112047 not downloaded", "asset:data:geo:GSE76938 licence not read", "asset:data:geo:GSE76938 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["re also identified. METHODS: Methylation and RNA-seq data were downloaded for The Cancer Genome A"], "order_basis": "paper_text_order:499", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ere utilized to validate screened hub genes. Immunohistochemistry of these hub genes were evaluated by the Hum"], "order_basis": "paper_text_order:1347", "id": "assay:2"}, {"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": 1.0, "evidence": ["“For the data from TCGA, the R package MethylMix was applied to perform an analysis integrating gene expression data and methylation data.” “For the data from GEO, the R package limma was applied to perform analysis to identify the DMEs.”"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}