← All .science files
pmid:33575221
The Autophagy Related Gene CHAF1B Is a Relevant Prognostic and Diagnostic Biomarker in Hepatocellular Carcinoma.
Zunni Zhang · Yalong Zhang · Wuning Mo
Frontiers in oncology · 2020 doi:10.3389/fonc.2020.626175
Paper
complete
Experiment
partial
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 · 3 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 · 1 item
data object · 3 fields
assets array · 9 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 557 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 161 items
[3] object · 15 fields
structure object · 15 fields
sample_accessions array · 125 items
[4] object · 15 fields
structure object · 15 fields
sample_accessions array · 167 items
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 19 items
[0] array · 7 items
[1] array · 7 items
[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 · 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
[6] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 7 items
[0] array · 4 items
[1] array · 4 items
[2] array · 3 items
[3] array · 3 items
[4] array · 4 items
[5] array · 3 items
[6] array · 3 items
[7] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 7 items
[0] array · 2 items
[1] array · 4 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[8] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 6 items
[0] array · 3 items
[1] array · 6 items
[2] array · 7 items
[3] array · 7 items
[4] array · 7 items
[5] array · 7 items
gaps array · 8 items
analysis object · 4 fields
methods array · 4 items
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 1 item
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
[2] object · 10 fields
dsl_operations array · 6 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[3] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
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 · 0 items
missing_operations array · 1 item
capability object · 4 fields
data object · 6 fields
accessions array · 4 items
resolved_accessions array · 4 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 6 items
steps array · 0 items
must_build object · 5 fields
dsl_operations array · 1 item
[0] object · 3 fields
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 · 14 items
assays array · 2 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
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33575221", "kind": "science-record", "revision": 7, "content_hash": "sha256:a3f928ff9537b3ab0a94f0b1a796ae26e2ead303b4809c9725439ca2cd9b30ac", "created_at": "2026-11-01T15:41:25Z", "updated_at": "2026-11-01T22:03:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The Autophagy Related Gene CHAF1B Is a Relevant Prognostic and Diagnostic Biomarker in Hepatocellular Carcinoma.", "doi": "10.3389/fonc.2020.626175", "pmid": "33575221", "authors": ["Zunni Zhang", "Yalong Zhang", "Wuning Mo"], "journal": "Frontiers in oncology", "year": 2020, "abstract": "The role of autophagy in tumors is complex; based on known interactions between autophagy and hepatocellular carcinoma (HCC) pathogenesis, we hypothesized that autophagy-related genes (ARGs) may play an important role in HCC. The ARGs were obtained from the Human Autophagy Database and the Gene Set Enrichment Analysis. Based on the area under the curve (AUC) value >0.9 with p <0.0001 and Student's T-test analysis with p <0.0001, differently expressed autophagy-related genes (DEARGs) with high diagnostic efficiency were found. Besides that, we searched in the PubMed database to find novel DEARGs associated with HCC. Then the DEARGs were validated in the GSE25097, GSE54236, GSE76427, GSE64041, Oncomine, and Human Protein Atlas datasets. Finally, survival analysis of CHAF1B in HCC and correlations of clinico-pathological characteristics and CHAF1B were performed based on the TCGA database. The mRNA and protein expression of 531 ARGs were analyzed and validated in eight independent cohorts. First, 18 DEARGs with high diagnostic efficiency were selected from the TCGA database, and nine of them were identified that had not previously been associated with HCC. These nine DEARGs were validated in the GSE25097, GSE54236, GSE76427, GSE64041, Oncomine, and Human Protein Atlas datasets. Additionally, we found that CHAF1B was associated with overall survival and relapse free survival at one, three, and five years. Furthermore, the univariate and multivariate Cox analyses revealed that the high expression of CHAF1B was an independent risk factor in HCC patients. This research demonstrated that CHAF1B was a novel diagnostic and prognostic signature biomarker that could be potentially useful for predicting the development of HCC and may provide new insights for HCC tumorigenesis and treatments.", "claims": [{"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33575221", "locator": "sections[16] \"Data Availability Statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:33575221"], "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:GSE25097"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE25097"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33575221", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2020.626175", "sha256": "sha256:5fb70e054b5162e0fe950cb202759319cfacbda993821657377162416cfef831", "bytes": 26954, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2020.626175", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7870991", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE25097", "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=GSE25097", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25097", "version": null, "note": "The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM616704", "GSM616705", "GSM616706", "GSM616707", "GSM616708", "GSM616709", "GSM616710", "GSM616711", "GSM616712", "GSM616713", "GSM616714", "GSM616715", "GSM616716", "GSM616717", "GSM616718", "GSM616719", "GSM616720", "GSM616721", "GSM616722", "GSM616723", "GSM616724", "GSM616725", "GSM616726", "GSM616727", "GSM616728", "GSM616729", "GSM616730", "GSM616731", "GSM616732", "GSM616733", "GSM616734", "GSM616735", "GSM616736", "GSM616737", "GSM616738", "GSM616739", "GSM616740", "GSM616741", "GSM616742", "GSM616743", "GSM616744", "GSM616745", "GSM616746", "GSM616747", "GSM616748", "GSM616749", "GSM616750", "GSM616751", "GSM616752", "GSM616753", "GSM616754", "GSM616755", "GSM616756", "GSM616757", "GSM616758", "GSM616759", "GSM616760", "GSM616761", "GSM616762", "GSM616763", "GSM616764", "GSM616765", "GSM616766", "GSM616767", "GSM616768", "GSM616769", "GSM616770", "GSM616771", "GSM616772", "GSM616773", "GSM616774", "GSM616775", "GSM616776", "GSM616777", "GSM616778", "GSM616779", "GSM616780", "GSM616781", "GSM616782", "GSM616783", "GSM616784", "GSM616785", "GSM616786", "GSM616787", "GSM616788", "GSM616789", "GSM616790", "GSM616791", "GSM616792", "GSM616793", "GSM616794", "GSM616795", "GSM616796", "GSM616797", "GSM616798", "GSM616799", "GSM616800", "GSM616801", "GSM616802", "GSM616803", "GSM616804", "GSM616805", "GSM616806", "GSM616807", "GSM616808", "GSM616809", "GSM616810", "GSM616811", "GSM616812", "GSM616813", "GSM616814", "GSM616815", "GSM616816", "GSM616817", "GSM616818", "GSM616819", "GSM616820", "GSM616821", "GSM616822", "GSM616823", "GSM616824", "GSM616825", "GSM616826", "GSM616827", "GSM616828", "GSM616829", "GSM616830", "GSM616831", "GSM616832", "GSM616833", "GSM616834", "GSM616835", "GSM616836", "GSM616837", "GSM616838", "GSM616839", "GSM616840", "GSM616841", "GSM616842", "GSM616843", "GSM616844", "GSM616845", "GSM616846", "GSM616847", "GSM616848", "GSM616849", "GSM616850", "GSM616851", "GSM616852", "GSM616853", "GSM616854", "GSM616855", "GSM616856", "GSM616857", "GSM616858", "GSM616859", "GSM616860", "GSM616861", "GSM616862", "GSM616863", "GSM616864", "GSM616865", "GSM616866", "GSM616867", "GSM616868", "GSM616869", "GSM616870", "GSM616871", "GSM616872", "GSM616873", "GSM616874", "GSM616875", "GSM616876", "GSM616877", "GSM616878", "GSM616879", "GSM616880", "GSM616881", "GSM616882", "GSM616883", "GSM616884", "GSM616885", "GSM616886", "GSM616887", "GSM616888", "GSM616889", "GSM616890", "GSM616891", "GSM616892", "GSM616893", "GSM616894", "GSM616895", "GSM616896", "GSM616897", "GSM616898", "GSM616899", "GSM616900", "GSM616901", "GSM616902", "GSM616903", "GSM616904", "GSM616905", "GSM616906", "GSM616907", "GSM616908", "GSM616909", "GSM616910", "GSM616911", "GSM616912", "GSM616913", "GSM616914", "GSM616915", "GSM616916", "GSM616917", "GSM616918", "GSM616919", "GSM616920", "GSM616921", "GSM616922", "GSM616923", "GSM616924", "GSM616925", "GSM616926", "GSM616927", "GSM616928", "GSM616929", "GSM616930", "GSM616931", "GSM616932", "GSM616933", "GSM616934", "GSM616935", "GSM616936", "GSM616937", "GSM616938", "GSM616939", "GSM616940", "GSM616941", "GSM616942", "GSM616943", "GSM616944", "GSM616945", "GSM616947", "GSM616948", "GSM616950", "GSM616952", "GSM616953", "GSM616955", "GSM616957", "GSM616959", "GSM616961", "GSM616963", "GSM616965", "GSM616966", "GSM616968", "GSM616970", "GSM616972", "GSM616973", "GSM616975", "GSM616977", "GSM616978", "GSM616980", "GSM616982", "GSM616984", "GSM616986", "GSM616987", "GSM616989", "GSM616990", "GSM616992", "GSM616994", "GSM616995", "GSM616996", "GSM616997", "GSM616998", "GSM616999", "GSM617000", "GSM617001", "GSM617002", "GSM617003", "GSM617004", "GSM617005", "GSM617006", "GSM617007", "GSM617008", "GSM617009", "GSM617010", "GSM617011", "GSM617012", "GSM617013", "GSM617304", "GSM617305", "GSM617306", "GSM617307", "GSM617308", "GSM617309", "GSM617310", "GSM617311", "GSM617312", "GSM617313", "GSM617314", "GSM617315", "GSM617316", "GSM617317", "GSM617318", "GSM617319", "GSM617320", "GSM617321", "GSM617322", "GSM617323", "GSM617324", "GSM617325", "GSM617326", "GSM617327", "GSM617328", "GSM617329", "GSM617330", "GSM617331", "GSM617332", "GSM617333", "GSM617334", "GSM617335", "GSM617336", "GSM617337", "GSM617338", "GSM617339", "GSM617340", "GSM617341", "GSM617342", "GSM617343", "GSM617344", "GSM617345", "GSM617346", "GSM617347", "GSM617348", "GSM617349", "GSM617350", "GSM617351", "GSM617352", "GSM617353", "GSM617354", "GSM617355", "GSM617356", "GSM617357", "GSM617358", "GSM617359", "GSM617360", "GSM617361", "GSM617362", "GSM617363", "GSM617364", "GSM617365", "GSM617366", "GSM617367", "GSM617368", "GSM617369", "GSM617370", "GSM617371", "GSM617372", "GSM617373", "GSM617374", "GSM617375", "GSM617376", "GSM617377", "GSM617378", "GSM617379", "GSM617380", "GSM617381", "GSM617382", "GSM617383", "GSM617384", "GSM617385", "GSM617386", "GSM617387", "GSM617388", "GSM617389", "GSM617390", "GSM617391", "GSM617392", "GSM617393", "GSM617394", "GSM617395", "GSM617396", "GSM617397", "GSM617398", "GSM617399", "GSM617400", "GSM617401", "GSM617402", "GSM617403", "GSM617404", "GSM617405", "GSM617406", "GSM617407", "GSM617408", "GSM617409", "GSM617410", "GSM617411", "GSM617412", "GSM617413", "GSM617414", "GSM617415", "GSM617416", "GSM617417", "GSM617418", "GSM617419", "GSM617420", "GSM617421", "GSM617422", "GSM617423", "GSM617424", "GSM617425", "GSM617426", "GSM617427", "GSM617428", "GSM617429", "GSM617430", "GSM617431", "GSM617432", "GSM617433", "GSM617434", "GSM617435", "GSM617436", "GSM617437", "GSM617438", "GSM617439", "GSM617440", "GSM617441", "GSM617442", "GSM617443", "GSM617444", "GSM617445", "GSM617446", "GSM617447", "GSM617448", "GSM617449", "GSM617450", "GSM617451", "GSM617452", "GSM617453", "GSM617454", "GSM617455", "GSM617456", "GSM617457", "GSM617458", "GSM617459", "GSM617460", "GSM617461", "GSM617462", "GSM617463", "GSM617464", "GSM617465", "GSM617466", "GSM617467", "GSM617468", "GSM617469", "GSM617470", "GSM617471", "GSM617472", "GSM617473", "GSM617474", "GSM617475", "GSM617476", "GSM617477", "GSM617478", "GSM617479", "GSM617480", "GSM617481", "GSM617482", "GSM617483", "GSM617484", "GSM617485", "GSM617486", "GSM617487", "GSM617488", "GSM617489", "GSM617490", "GSM617491", "GSM617492", "GSM617493", "GSM617494", "GSM617495", "GSM617496", "GSM617497", "GSM617498", "GSM617499", "GSM617500", "GSM617501", "GSM617502", "GSM617503", "GSM617504", "GSM617505", "GSM617506", "GSM617507", "GSM617508", "GSM617509", "GSM617510", "GSM617511", "GSM617512", "GSM617513", "GSM617514", "GSM617515", "GSM617516", "GSM617517", "GSM617518", "GSM617519", "GSM617520", "GSM617521", "GSM617522", "GSM617523", "GSM617524", "GSM617525", "GSM617526", "GSM617527", "GSM617528", "GSM617529", "GSM617530", "GSM617531", "GSM617532", "GSM617533", "GSM617534", "GSM617535", "GSM617536", "GSM617537", "GSM617538", "GSM617539", "GSM617540", "GSM617541", "GSM617542", "GSM617543", "GSM617544", "GSM617545", "GSM617546", "GSM617547", "GSM617548", "GSM617549", "GSM617550", "GSM617551", "GSM617552", "GSM617553", "GSM617554", "GSM617555", "GSM617556", "GSM617557", "GSM617558", "GSM617559", "GSM617560", "GSM617561", "GSM617562", "GSM617563", "GSM617564", "GSM617565", "GSM617566", "GSM617567", "GSM617568", "GSM617569", "GSM617570", "GSM617571"], "sample_count": 557, "group_sizes": null, "group_sizes_basis": null, "platform": "10687", "taxon": "Homo sapiens", "title": "Study of gene expression of human liver Hepatocellular carcinoma", "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:GSE54236", "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=GSE54236", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE54236", "version": null, "note": "The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1310570", "GSM1310571", "GSM1310572", "GSM1310573", "GSM1310574", "GSM1310575", "GSM1310576", "GSM1310577", "GSM1310578", "GSM1310579", "GSM1310580", "GSM1310581", "GSM1310582", "GSM1310583", "GSM1310584", "GSM1310585", "GSM1310586", "GSM1310587", "GSM1310588", "GSM1310589", "GSM1310590", "GSM1310591", "GSM1310592", "GSM1310593", "GSM1310594", "GSM1310595", "GSM1310596", "GSM1310597", "GSM1310598", "GSM1310599", "GSM1310600", "GSM1310601", "GSM1310602", "GSM1310603", "GSM1310604", "GSM1310605", "GSM1310606", "GSM1310607", "GSM1310608", "GSM1310609", "GSM1310610", "GSM1310611", "GSM1310612", "GSM1310613", "GSM1310614", "GSM1310615", "GSM1310616", "GSM1310617", "GSM1310618", "GSM1310619", "GSM1310620", "GSM1310621", "GSM1310622", "GSM1310623", "GSM1310624", "GSM1310625", "GSM1310626", "GSM1310627", "GSM1310628", "GSM1310629", "GSM1310630", "GSM1310631", "GSM1310632", "GSM1310633", "GSM1310634", "GSM1310635", "GSM1310636", "GSM1310637", "GSM1310638", "GSM1310639", "GSM1310640", "GSM1310641", "GSM1310642", "GSM1310643", "GSM1310644", "GSM1310645", "GSM1310646", "GSM1310647", "GSM1310648", "GSM1310649", "GSM1310650", "GSM1310651", "GSM1310652", "GSM1310653", "GSM1310654", "GSM1310655", "GSM1310656", "GSM1310657", "GSM1310658", "GSM1310659", "GSM1310660", "GSM1310661", "GSM1310662", "GSM1310663", "GSM1310664", "GSM1310665", "GSM1310666", "GSM1310667", "GSM1310668", "GSM1310669", "GSM1310670", "GSM1310671", "GSM1310672", "GSM1310673", "GSM1310674", "GSM1310675", "GSM1310676", "GSM1310677", "GSM1310678", "GSM1310679", "GSM1310680", "GSM1310681", "GSM1310682", "GSM1310683", "GSM1310684", "GSM1310685", "GSM1310686", "GSM1310687", "GSM1310688", "GSM1310689", "GSM1310690", "GSM1310691", "GSM1310692", "GSM1310693", "GSM1310694", "GSM1310695", "GSM1310696", "GSM1310697", "GSM1310698", "GSM1310699", "GSM1310700", "GSM1310701", "GSM1310702", "GSM1310703", "GSM1310704", "GSM1310705", "GSM1310706", "GSM1310707", "GSM1310708", "GSM1310709", "GSM1310710", "GSM1310711", "GSM1310712", "GSM1310713", "GSM1310714", "GSM1310715", "GSM1310716", "GSM1310717", "GSM1310718", "GSM1310719", "GSM1310720", "GSM1310721", "GSM1310722", "GSM1310723", "GSM1310724", "GSM1310725", "GSM1310726", "GSM1310727", "GSM1310728", "GSM1310729", "GSM1310730"], "sample_count": 161, "group_sizes": null, "group_sizes_basis": null, "platform": "6480", "taxon": "Homo sapiens", "title": "Prospective gene expression analysis of human RNA samples from Hepatocellular Carcinoma in relation with growth rate and survival", "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:GSE64041", "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=GSE64041", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE64041", "version": null, "note": "The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2052455", "GSM2052456", "GSM2052457", "GSM2052458", "GSM2052459", "GSM2052460", "GSM2052461", "GSM2052462", "GSM2052463", "GSM2052464", "GSM2052465", "GSM2052466", "GSM2052467", "GSM2052468", "GSM2052469", "GSM2052470", "GSM2052471", "GSM2052472", "GSM2052473", "GSM2052474", "GSM2052475", "GSM2052476", "GSM2052477", "GSM2052478", "GSM2052479", "GSM2052480", "GSM2052481", "GSM2052482", "GSM2052483", "GSM2052484", "GSM2052485", "GSM2052486", "GSM2052487", "GSM2052488", "GSM2052489", "GSM2052490", "GSM2052491", "GSM2052492", "GSM2052493", "GSM2052494", "GSM2052495", "GSM2052496", "GSM2052497", "GSM2052498", "GSM2052499", "GSM2052500", "GSM2052501", "GSM2052502", "GSM2052503", "GSM2052504", "GSM2052505", "GSM2052506", "GSM2052507", "GSM2052508", "GSM2052509", "GSM2052510", "GSM2052511", "GSM2052512", "GSM2052513", "GSM2052514", "GSM2052515", "GSM2052516", "GSM2052517", "GSM2052518", "GSM2052519", "GSM2052520", "GSM2052521", "GSM2052522", "GSM2052523", "GSM2052524", "GSM2052525", "GSM2052526", "GSM2052527", "GSM2052528", "GSM2052529", "GSM2052530", "GSM2052531", "GSM2052532", "GSM2052533", "GSM2052534", "GSM2052535", "GSM2052536", "GSM2052537", "GSM2052538", "GSM2052539", "GSM2052540", "GSM2052541", "GSM2052542", "GSM2052543", "GSM2052544", "GSM2052545", "GSM2052546", "GSM2052547", "GSM2052548", "GSM2052549", "GSM2052550", "GSM2052551", "GSM2052552", "GSM2052553", "GSM2052554", "GSM2052555", "GSM2052556", "GSM2052557", "GSM2052558", "GSM2052559", "GSM2052560", "GSM2052561", "GSM2052562", "GSM2052563", "GSM2052564", "GSM2052565", "GSM2052566", "GSM2052567", "GSM2052568", "GSM2052569", "GSM2052570", "GSM2052571", "GSM2052572", "GSM2052573", "GSM2052574", "GSM2052575", "GSM2052576", "GSM2052577", "GSM2052578", "GSM2052579"], "sample_count": 125, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Gene expression profiling in paired human hepatocellular carcinoma and liver parenchyma biopsies and normal liver biopsies.", "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:GSE76427", "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=GSE76427", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE76427", "version": null, "note": "The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2011285", "GSM2011286", "GSM2011287", "GSM2011288", "GSM2011289", "GSM2011290", "GSM2011291", "GSM2011292", "GSM2011293", "GSM2011294", "GSM2011295", "GSM2011296", "GSM2011297", "GSM2011298", "GSM2011299", "GSM2011300", "GSM2011301", "GSM2011302", "GSM2011303", "GSM2011304", "GSM2011305", "GSM2011306", "GSM2011307", "GSM2011308", "GSM2011309", "GSM2011310", "GSM2011311", "GSM2011312", "GSM2011313", "GSM2011314", "GSM2011315", "GSM2011316", "GSM2011317", "GSM2011318", "GSM2011319", "GSM2011320", "GSM2011321", "GSM2011322", "GSM2011323", "GSM2011324", "GSM2011325", "GSM2011326", "GSM2011327", "GSM2011328", "GSM2011329", "GSM2011330", "GSM2011331", "GSM2011332", "GSM2011333", "GSM2011334", "GSM2011335", "GSM2011336", "GSM2011337", "GSM2011338", "GSM2011339", "GSM2011340", "GSM2011341", "GSM2011342", "GSM2011343", "GSM2011344", "GSM2011345", "GSM2011346", "GSM2011347", "GSM2011348", "GSM2011349", "GSM2011350", "GSM2011351", "GSM2011352", "GSM2011353", "GSM2011354", "GSM2011355", "GSM2011356", "GSM2011357", "GSM2011358", "GSM2011359", "GSM2011360", "GSM2011361", "GSM2011362", "GSM2011363", "GSM2011364", "GSM2011365", "GSM2011366", "GSM2011367", "GSM2011368", "GSM2011369", "GSM2011370", "GSM2011371", "GSM2011372", "GSM2011373", "GSM2011374", "GSM2011375", "GSM2011376", "GSM2011377", "GSM2011378", "GSM2011379", "GSM2011380", "GSM2011381", "GSM2011382", "GSM2011383", "GSM2011384", "GSM2011385", "GSM2011386", "GSM2011387", "GSM2011388", "GSM2011389", "GSM2011390", "GSM2011391", "GSM2011392", "GSM2011393", "GSM2011394", "GSM2011395", "GSM2011396", "GSM2011397", "GSM2011398", "GSM2011399", "GSM2011400", "GSM2011401", "GSM2011402", "GSM2011403", "GSM2011404", "GSM2011405", "GSM2011406", "GSM2011407", "GSM2011408", "GSM2011409", "GSM2011410", "GSM2011411", "GSM2011412", "GSM2011413", "GSM2011414", "GSM2011415", "GSM2011416", "GSM2011417", "GSM2011418", "GSM2011419", "GSM2011420", "GSM2011421", "GSM2011422", "GSM2011423", "GSM2011424", "GSM2011425", "GSM2011426", "GSM2011427", "GSM2011428", "GSM2011429", "GSM2011430", "GSM2011431", "GSM2011432", "GSM2011433", "GSM2011434", "GSM2011435", "GSM2011436", "GSM2011437", "GSM2011438", "GSM2011439", "GSM2011440", "GSM2011441", "GSM2011442", "GSM2011443", "GSM2011444", "GSM2011445", "GSM2011446", "GSM2011447", "GSM2011448", "GSM2011449", "GSM2011450", "GSM2011451"], "sample_count": 167, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Microarray expression data for tumor and adjacent non-tumor tissues from hepatocellular carcinoma patients", "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:33575221:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3153c8233143021d15cd2b2f6c2776b0970e8feb3faaf3b3bc62864591668e5f", "bytes": 1418, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T1", "version": null, "note": "The expression and ROC analysis of ARGs in TCGA database.", "structure": {"pmcid": "PMC7870991", "section_index": 11, "section_title": "The Selection of DEARGs From the TCGA Database", "row_count": 19, "column_count": 7}, "table": {"label": "Table 1", "caption": "The expression and ROC analysis of ARGs in TCGA database.", "rows": [["No", "Gene symbol", "Mean expression in HCC", "Mean expression in control", "p-value", "AUC", "ARG reported for HCC in PubMed"], ["1", "BIRC5", "1338.476", "54.1224", "<0.0001", "0.973", "≥1"], ["2", "CDKN2A", "881.9568", "38.5714", "<0.0001", "0.951", "≥1"], ["3", "CLN3", "1761.56", "612.4694", "<0.0001", "0.941", "≥1"], ["4", "RAB24", "452.9378", "155.8163", "<0.0001", "0.937", "≥1"], ["5", "LSM4", "5,100.578", "1861", "<0.0001", "0.936", "0"], ["6", "PEA15", "6082.446", "1,897.633", "<0.0001", "0.935", "≥1"], ["7", "SNRPB", "7362.876", "2,341.878", "<0.0001", "0.932", "≥1"], ["8", "SNAPIN", "1,500.478", "653.102", "<0.0001", "0.923", "0"], ["9", "CHAF1B", "369.5108", "40.9388", "<0.0001", "0.922", "0"], ["10", "HSP90AB1", "53311.34", "1,8807.98", "<0.0001", "0.921", "≥1"], ["11", "TP73", "179.7297", "11.7347", "<0.0001", "0.919", "≥1"], ["12", "CDC37", "6,337.065", "3,175.347", "<0.0001", "0.915", "≥1"], ["13", "VPS33A", "1,028.641", "436.1837", "<0.0001", "0.914", "0"], ["14", "ZKSCAN3", "415.427", "105.9796", "<0.0001", "0.912", "0"], ["15", "PACS2", "1,691.941", "690.2245", "<0.0001", "0.909", "0"], ["16", "CTSA", "16,048.41", "6072.959", "<0.0001", "0.908", "0"], ["17", "CAPN10", "611.6297", "241.0612", "<0.0001", "0.905", "0"], ["18", "VPS28", "8,330.284", "3,233.408", "<0.0001", "0.904", "0"]], "row_count": 19, "column_count": 7, "numeric_cells": 116, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:33575221:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:11ba0424dad4ccc03f60fa1ddbbad3794f779db85da10c4c8d15041841568c71", "bytes": 422, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[2]#T2", "version": null, "note": "The expression of DEARGs in Oncomine database.", "structure": {"pmcid": "PMC7870991", "section_index": 11, "section_title": "The Selection of DEARGs From the TCGA Database", "row_count": 7, "column_count": 4}, "table": {"label": "Table 2", "caption": "The expression of DEARGs in Oncomine database.", "rows": [["", "Gene symbol", "FC", "P-value"], ["Chen Liver", "SNAPIN", "1.589", "1.38E-15"], ["LSM4", "1.735", "2.47E-15"], ["CHAF1B", "1.311", "0.023"], ["Wumbach Liver", "SNAPIN", "1.39", "0.002"], ["LSM4", "1.642", "7.24E-4"], ["CHAF1B", "1.223", "0.044"]], "row_count": 7, "column_count": 4, "numeric_cells": 12, "header_rows": 1, "locator": "section[11]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:33575221:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:876495c52c0fff6c92cc044aace278288e7788c127443c8cb5b154b23c66ef98", "bytes": 758, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T3", "version": null, "note": "The association between CHAF1B and clinico-pathological variable in TCGA.", "structure": {"pmcid": "PMC7870991", "section_index": 12, "section_title": "Prognostic Significance", "row_count": 7, "column_count": 5}, "table": {"label": "Table 3", "caption": "The association between CHAF1B and clinico-pathological variable in TCGA.", "rows": [["Variables", "CHAF1B mRNA expression"], ["", "High (n = 122)", "Low (n = 243)", "p-value"], ["Gender", "MaleFemale", "73(59.8%)49(40.2%)", "172(70.2%)71(29.2%)", "0.036"], ["Tumor status", "With tumorTumor freeNA", "44(36.1%)70(57.4%)8(6.6%)", "65((26.7%)160(65.8%)18(7.4%)", "0.189"], ["AJCC stage", "T1/T2T3/T4/T5NA", "81(66.4%)41(33.6%)0", "190(78.2%)52(21.4%)1", "0.02"], ["Neoplasm histologic grade", "G1/G2G3/G4NA", "55(45.1%)66(54.1%)1", "172(70.8%)67(27.6%)4", "<0.001"], ["Living status", "AliveDead", "69(56.6%)53((43.4%)", "167(68.7%)76(31.3%)", "0.022"]], "row_count": 7, "column_count": 5, "numeric_cells": 17, "header_rows": 2, "locator": "section[12]/table-wrap[1]#T3"}}, {"id": "asset:table:pmid:33575221:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:af64fd7254e8864ea1eea213662b8027f54c13374933dcd8b60be38f5dbe0712", "bytes": 699, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#T4", "version": null, "note": "Univariate and multivariate Cox regression analysis of variables associated with the OS of HCC patients in TCGA.", "structure": {"pmcid": "PMC7870991", "section_index": 12, "section_title": "Prognostic Significance", "row_count": 6, "column_count": 7}, "table": {"label": "Table 4", "caption": "Univariate and multivariate Cox regression analysis of variables associated with the OS of HCC patients in TCGA.", "rows": [["Variables OS", "Univariate analysis", "Multivariate analysis"], ["HR", "95%CI", "p", "HR", "95%CI", "p"], ["Male vs female", "0.805", "0.565–1.148", "0.232", "", "", ""], ["AJCC stageT3/T4/T5 vs T1/T2", "2.483", "1.746–3.531", "<0.001", "2.329", "1.629–3.328", "<0.001"], ["Neoplasm histologic gradeG3/G4 vs G1/G2", "1.114", "0.776–1.599", "0.559", "", "", ""], ["CHAF1B expressionHigh vs low", "1.737", "1.221–2.473", "0.002", "1.534", "1.073–2.191", "0.019"]], "row_count": 6, "column_count": 7, "numeric_cells": 20, "header_rows": 2, "locator": "section[12]/table-wrap[2]#T4"}}], "gaps": ["asset:data:geo:GSE25097 not downloaded", "asset:data:geo:GSE25097 licence not read", "asset:data:geo:GSE54236 not downloaded", "asset:data:geo:GSE54236 licence not read", "asset:data:geo:GSE64041 not downloaded", "asset:data:geo:GSE64041 licence not read", "asset:data:geo:GSE76427 not downloaded", "asset:data:geo:GSE76427 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.7, "band": "medium", "quote": "Student's T-test"}}, {"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": 0.8, "band": "high", "quote": "PPI"}}, {"id": "method-3", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.8, "band": "high", "quote": "ROC curve"}}, {"id": "method-4", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "chi-square"}}], "targets": [], "gaps": ["method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["GSE25097", "GSE54236", "GSE76427", "GSE64041"], "resolved_accessions": ["GSE25097", "GSE54236", "GSE76427", "GSE64041"], "statements": ["The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE25097, GSE54236, GSE76427, GSE64041 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": [], "assets": ["source:pmid:33575221", "data:geo:GSE25097", "asset:table:pmid:33575221:1", "asset:table:pmid:33575221:2", "asset:table:pmid:33575221:3", "asset:table:pmid:33575221:4"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE25097"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:24:42Z", "independence": "single_reader"}, "evidence_check": {"method": "absent", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 23497, "completion_tokens": 2582, "cached_tokens": 7944}}, "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:33575221", "type": "paper", "label": "pmid:33575221"}, {"id": "source:pmid:33575221", "type": "manuscript", "label": "PMID 33575221 full text"}, {"id": "data:geo:GSE25097", "type": "dataset", "label": "GEO GSE25097"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33575221", "type": "paper", "label": "pmid:33575221"}, {"id": "source:pmid:33575221", "type": "manuscript", "label": "PMID 33575221 full text"}, {"id": "data:geo:GSE25097", "type": "dataset", "label": "GEO GSE25097"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33575221", "type": "extraction", "used": ["source:pmid:33575221"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE25097", "type": "accession_resolution", "used": ["data:geo:GSE25097"], "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:33575221", "parent_hash": "sha256:e65e63fa74f4b25dadce99ead10874ab9da79af547144ab2e38dc008e610b877", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE25097 licence not read", "asset:data:geo:GSE25097 not downloaded", "asset:data:geo:GSE54236 licence not read", "asset:data:geo:GSE54236 not downloaded", "asset:data:geo:GSE64041 licence not read", "asset:data:geo:GSE64041 not downloaded", "asset:data:geo:GSE76427 licence not read", "asset:data:geo:GSE76427 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "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": ["ps://portal.gdc.cancer.gov), we obtained the RNA-seq data of 49 normal and 370 HCC liver tissue s"], "order_basis": "paper_text_order:2403", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Student's T-test"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}