← All .science files
pmid:31804459
SKA3 Promotes tumor growth by regulating CDK2/P53 phosphorylation in hepatocellular carcinoma.
Yuchen Hou · Ziming Wang · Shanzhou Huang · Chengjun Sun · Jingya Zhao · Jiayu Shi · Zhongqiu Li · Zekang Wang · Xiaoshun He · Nga Lei Tam · Linwei Wu
Cell death & disease · 2019 doi:10.1038/s41419-019-2163-3
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 · 2 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 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 · 1 field
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 · 433 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 134 items
[3] object · 15 fields
structure object · 15 fields
sample_accessions array · 91 items
[4] object · 15 fields
structure object · 15 fields
sample_accessions array · 75 items
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 32 items
[0] array · 4 items
[1] array · 2 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
[9] array · 5 items
[10] array · 5 items
[11] array · 5 items
[12] array · 5 items
[13] array · 5 items
[14] array · 5 items
[15] array · 5 items
[16] array · 5 items
[17] array · 5 items
[18] array · 5 items
[19] array · 5 items
[20] array · 5 items
[21] array · 5 items
[22] array · 5 items
[23] array · 5 items
[24] array · 5 items
[25] array · 5 items
[26] array · 5 items
[27] array · 5 items
[28] array · 5 items
[29] array · 5 items
[30] array · 5 items
[31] array · 5 items
[6] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 12 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
[6] array · 7 items
[7] array · 7 items
[8] array · 7 items
[9] array · 7 items
[10] array · 7 items
[11] array · 7 items
[7] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 12 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
[6] array · 7 items
[7] array · 7 items
[8] array · 7 items
[9] array · 7 items
[10] array · 7 items
[11] array · 7 items
gaps array · 8 items
analysis object · 4 fields
methods array · 4 items
[0] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 1 field
data_shapes array · 1 item
evidence object · 3 fields
[1] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[2] object · 10 fields
dsl_operations array · 3 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 · 3 items
missing_operations array · 0 items
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 · 3 items
assets array · 5 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 · 13 items
assays array · 6 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 3 items
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
[2] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
[3] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
[4] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[5] 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:31804459", "kind": "science-record", "revision": 8, "content_hash": "sha256:8b2015795e2d521cf7a17814b00ed195c589be5363afc600292b02cadac900e3", "created_at": "2026-11-01T15:40:53Z", "updated_at": "2026-11-01T22:44:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "SKA3 Promotes tumor growth by regulating CDK2/P53 phosphorylation in hepatocellular carcinoma.", "doi": "10.1038/s41419-019-2163-3", "pmid": "31804459", "authors": ["Yuchen Hou", "Ziming Wang", "Shanzhou Huang", "Chengjun Sun", "Jingya Zhao", "Jiayu Shi", "Zhongqiu Li", "Zekang Wang", "Xiaoshun He", "Nga Lei Tam", "Linwei Wu"], "journal": "Cell death & disease", "year": 2019, "abstract": "Spindle and kinetochore-related complex subunit 3 (SKA3) is a component of the spindle and kinetochore-related complexes and is essential for accurate timing of late mitosis. However, the relationship between SKA3 and hepatocellular carcinoma (HCC) has not yet been fully elucidated. Gene expression omnibus (GEO) (GSE62232, GSE45436, GSE6764, and GSE36376) and The Cancer Atlas (TCGA) datasets were analyzed to identify differential expression genes. Cell proliferation ability was analyzed using Cell Counting Kit-8 (CCK8) assay and plate clone formation assay, while scratch wound healing assay and transwell assay were used to analyze cell invasion. The role of SKA3 in vivo was explored using subcutaneous xenotransplantation model and lung metastasis model. Bioinformatics analysis found that hepatocellular carcinoma patients with high levels of expression of SKA3 have a poor prognosis. Similarly, immunohistochemical staining of 236 samples of tumors also found higher SKA3 expression in them, than in adjacent normal liver tissues. Significant levels of inhibition of in vivo and in vitro tumor proliferation and invasion result from the downregulation of SKA3. Mechanistically, SKA3 was found to affect tumor progression through the cell cycle and P53 signaling pathway as shown by the gene enrichment analysis (GSEA). G2/M phase arrest and severe apoptosis was also found to result from SKA3 knockdown, as shown by the inhibition of CDK2/p53 phosphorylation together with downregulation of BAX/Bcl-2 expression in HCC cells. Overall, these findings uncover the role of SKA3 in regulating the apoptosis and proliferation of hepatocellular carcinoma cells. This study was able to uncover new information on the tumorigenesis mechanism in hepatocellular carcinoma.", "claims": [{"id": "claim-method", "statement": "We acquired HCC expression data from GEO (datasets GSE62232, GSE45436, GSE36376, and GSE6764; http://www.ncbi.nlm.nih.gov/geo) and TCGA (http://gdc.cancer.gov/) databases. Log2 conversion was performed for all data in data standardization. EdgeR package was used to analyse gene differential expression for the data in count form. Limma package was used for the data in GEO database.\nWe selected genes whose |logFC (fold change)| > 1 and p-value < 0.05 as differential expression genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31804459", "locator": "sections[4] \"Data analysis of public databases\" paragraphs 1-3", "quote": "We acquired HCC expression data from GEO (datasets GSE62232, GSE45436, GSE36376, and GSE6764; http://www.ncbi.nlm.nih.gov/geo) and TCGA (http://gdc.cancer.gov/) databases. Log2 conversion was performed for all data in data standardization. EdgeR package was used to analyse gene differential expression for the data in count form. Limma package was used for the data in GEO database.\nWe selected genes whose |logFC (fold change)| > 1 and p-value < 0.05 as differential expression genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study can be obtained from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31804459", "locator": "sections[33] \"notes\" paragraph 1", "quote": "The datasets used and/or analyzed during the current study can be obtained from the corresponding author on reasonable request."}], "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:31804459"], "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:GSE36376"], "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": {"log2fc_threshold": "es were selected using |logFC| > 1 and p-value < 0"}, "inputs": ["data:geo:GSE36376"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31804459", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41419-019-2163-3", "sha256": "sha256:21b73cc9181442dd03fd12343bad4c54a234655278766656342383d42c81827f", "bytes": 41245, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41419-019-2163-3", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6895034", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE36376", "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=GSE36376", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE36376", "version": null, "note": "The datasets used and/or analyzed during the current study can be obtained from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study can be obtained from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM890128", "GSM890129", "GSM890130", "GSM890131", "GSM890132", "GSM890133", "GSM890134", "GSM890135", "GSM890136", "GSM890137", "GSM890138", "GSM890139", "GSM890140", "GSM890141", "GSM890142", "GSM890143", "GSM890144", "GSM890145", "GSM890146", "GSM890147", "GSM890148", "GSM890149", "GSM890150", "GSM890151", "GSM890152", "GSM890153", "GSM890154", "GSM890155", "GSM890156", "GSM890157", "GSM890158", "GSM890159", "GSM890160", "GSM890161", "GSM890162", "GSM890163", "GSM890164", "GSM890165", "GSM890166", "GSM890167", "GSM890168", "GSM890169", "GSM890170", "GSM890171", "GSM890172", "GSM890173", "GSM890174", "GSM890175", "GSM890176", "GSM890177", "GSM890178", "GSM890179", "GSM890180", "GSM890181", "GSM890182", "GSM890183", "GSM890184", "GSM890185", "GSM890186", "GSM890187", "GSM890188", "GSM890189", "GSM890190", "GSM890191", "GSM890192", "GSM890193", "GSM890194", "GSM890195", "GSM890196", "GSM890197", "GSM890198", "GSM890199", "GSM890200", "GSM890201", "GSM890202", "GSM890203", "GSM890204", "GSM890205", "GSM890206", "GSM890207", "GSM890208", "GSM890209", "GSM890210", "GSM890211", "GSM890212", "GSM890213", "GSM890214", "GSM890215", "GSM890216", "GSM890217", "GSM890218", "GSM890219", "GSM890220", "GSM890221", "GSM890222", "GSM890223", "GSM890224", "GSM890225", "GSM890226", "GSM890227", "GSM890228", "GSM890229", "GSM890230", "GSM890231", "GSM890232", "GSM890233", "GSM890234", "GSM890235", "GSM890236", "GSM890237", "GSM890238", "GSM890239", "GSM890240", "GSM890241", "GSM890242", "GSM890243", "GSM890244", "GSM890245", "GSM890246", "GSM890247", "GSM890248", "GSM890249", "GSM890250", "GSM890251", "GSM890252", "GSM890253", "GSM890254", "GSM890255", "GSM890256", "GSM890257", "GSM890258", "GSM890259", "GSM890260", "GSM890261", "GSM890262", "GSM890263", "GSM890264", "GSM890265", "GSM890266", "GSM890267", "GSM890268", "GSM890269", "GSM890270", "GSM890271", "GSM890272", "GSM890273", "GSM890274", "GSM890275", "GSM890276", "GSM890277", "GSM890278", "GSM890279", "GSM890280", "GSM890281", "GSM890282", "GSM890283", "GSM890284", "GSM890285", "GSM890286", "GSM890287", "GSM890288", "GSM890289", "GSM890290", "GSM890291", "GSM890292", "GSM890293", "GSM890294", "GSM890295", "GSM890296", "GSM890297", "GSM890298", "GSM890299", "GSM890300", "GSM890301", "GSM890302", "GSM890303", "GSM890304", "GSM890305", "GSM890306", "GSM890307", "GSM890308", "GSM890309", "GSM890310", "GSM890311", "GSM890312", "GSM890313", "GSM890314", "GSM890315", "GSM890316", "GSM890317", "GSM890318", "GSM890319", "GSM890320", "GSM890321", "GSM890322", "GSM890323", "GSM890324", "GSM890325", "GSM890326", "GSM890327", "GSM890328", "GSM890329", "GSM890330", "GSM890331", "GSM890332", "GSM890333", "GSM890334", "GSM890335", "GSM890336", "GSM890337", "GSM890338", "GSM890339", "GSM890340", "GSM890341", "GSM890342", "GSM890343", "GSM890344", "GSM890345", "GSM890346", "GSM890347", "GSM890348", "GSM890349", "GSM890350", "GSM890351", "GSM890352", "GSM890353", "GSM890354", "GSM890355", "GSM890356", "GSM890357", "GSM890358", "GSM890359", "GSM890360", "GSM890361", "GSM890362", "GSM890363", "GSM890364", "GSM890365", "GSM890366", "GSM890367", "GSM890368", "GSM890369", "GSM890370", "GSM890371", "GSM890372", "GSM890373", "GSM890374", "GSM890375", "GSM890376", "GSM890377", "GSM890378", "GSM890379", "GSM890380", "GSM890381", "GSM890382", "GSM890383", "GSM890384", "GSM890385", "GSM890386", "GSM890387", "GSM890388", "GSM890389", "GSM890390", "GSM890391", "GSM890392", "GSM890393", "GSM890394", "GSM890395", "GSM890396", "GSM890397", "GSM890398", "GSM890399", "GSM890400", "GSM890401", "GSM890402", "GSM890403", "GSM890404", "GSM890405", "GSM890406", "GSM890407", "GSM890408", "GSM890409", "GSM890410", "GSM890411", "GSM890412", "GSM890413", "GSM890414", "GSM890415", "GSM890416", "GSM890417", "GSM890418", "GSM890419", "GSM890420", "GSM890421", "GSM890422", "GSM890423", "GSM890424", "GSM890425", "GSM890426", "GSM890427", "GSM890428", "GSM890429", "GSM890430", "GSM890431", "GSM890432", "GSM890433", "GSM890434", "GSM890435", "GSM890436", "GSM890437", "GSM890438", "GSM890439", "GSM890440", "GSM890441", "GSM890442", "GSM890443", "GSM890444", "GSM890445", "GSM890446", "GSM890447", "GSM890448", "GSM890449", "GSM890450", "GSM890451", "GSM890452", "GSM890453", "GSM890454", "GSM890455", "GSM890456", "GSM890457", "GSM890458", "GSM890459", "GSM890460", "GSM890461", "GSM890462", "GSM890463", "GSM890464", "GSM890465", "GSM890466", "GSM890467", "GSM890468", "GSM890469", "GSM890470", "GSM890471", "GSM890472", "GSM890473", "GSM890474", "GSM890475", "GSM890476", "GSM890477", "GSM890478", "GSM890479", "GSM890480", "GSM890481", "GSM890482", "GSM890483", "GSM890484", "GSM890485", "GSM890486", "GSM890487", "GSM890488", "GSM890489", "GSM890490", "GSM890491", "GSM890492", "GSM890493", "GSM890494", "GSM890495", "GSM890496", "GSM890497", "GSM890498", "GSM890499", "GSM890500", "GSM890501", "GSM890502", "GSM890503", "GSM890504", "GSM890505", "GSM890506", "GSM890507", "GSM890508", "GSM890509", "GSM890510", "GSM890511", "GSM890512", "GSM890513", "GSM890514", "GSM890515", "GSM890516", "GSM890517", "GSM890518", "GSM890519", "GSM890520", "GSM890521", "GSM890522", "GSM890523", "GSM890524", "GSM890525", "GSM890526", "GSM890527", "GSM890528", "GSM890529", "GSM890530", "GSM890531", "GSM890532", "GSM890533", "GSM890534", "GSM890535", "GSM890536", "GSM890537", "GSM890538", "GSM890539", "GSM890540", "GSM890541", "GSM890542", "GSM890543", "GSM890544", "GSM890545", "GSM890546", "GSM890547", "GSM890548", "GSM890549", "GSM890550", "GSM890551", "GSM890552", "GSM890553", "GSM890554", "GSM890555", "GSM890556", "GSM890557", "GSM890558", "GSM890559", "GSM890560"], "sample_count": 433, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Gene Expression Profiles of both tumor and adjacent non-tumor liver Identify Hepatocellular Carcinoma Patients at High Risk of Recurrence after Curative Hepatectomy", "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:GSE45436", "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=GSE45436", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE45436", "version": null, "note": "The datasets used and/or analyzed during the current study can be obtained from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study can be obtained from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1100370", "GSM1100371", "GSM1100372", "GSM1100373", "GSM1100374", "GSM1100375", "GSM1100376", "GSM1100377", "GSM1100378", "GSM1100379", "GSM1100380", "GSM1100381", "GSM1100382", "GSM1100383", "GSM1100384", "GSM1100385", "GSM1100386", "GSM1100387", "GSM1100388", "GSM1100389", "GSM1100390", "GSM1100391", "GSM1100392", "GSM1100393", "GSM1100394", "GSM1100395", "GSM1100396", "GSM1100397", "GSM1100398", "GSM1100399", "GSM1100400", "GSM1100401", "GSM1100402", "GSM1100403", "GSM1100404", "GSM1100405", "GSM1100406", "GSM1100407", "GSM1100408", "GSM1100409", "GSM1100410", "GSM1100411", "GSM1100412", "GSM1100413", "GSM1100414", "GSM1100415", "GSM1100416", "GSM1100417", "GSM1100418", "GSM1100419", "GSM1100420", "GSM1100421", "GSM1100422", "GSM1100423", "GSM1100424", "GSM1100425", "GSM1100426", "GSM1100427", "GSM1100428", "GSM1100429", "GSM1100430", "GSM1100431", "GSM1100432", "GSM1100433", "GSM1100434", "GSM1100435", "GSM1100436", "GSM1100437", "GSM1100438", "GSM1100439", "GSM1100440", "GSM1100441", "GSM1100442", "GSM1100443", "GSM1100444", "GSM1100445", "GSM1100446", "GSM1100447", "GSM1100448", "GSM1100449", "GSM1100450", "GSM1100451", "GSM1100452", "GSM1100453", "GSM1100454", "GSM1100455", "GSM1100456", "GSM1104153", "GSM1104154", "GSM1104155", "GSM1104156", "GSM1104157", "GSM1104158", "GSM1104159", "GSM1104160", "GSM1104161", "GSM1104162", "GSM1104163", "GSM1104164", "GSM1104165", "GSM1104166", "GSM1104167", "GSM1104168", "GSM1104169", "GSM1104170", "GSM1104171", "GSM1104172", "GSM1104173", "GSM1104174", "GSM1104175", "GSM1104176", "GSM1104177", "GSM1104178", "GSM1104179", "GSM1104180", "GSM1104181", "GSM1104182", "GSM1104183", "GSM1104184", "GSM1104185", "GSM1104186", "GSM1104187", "GSM1104188", "GSM1104189", "GSM1104190", "GSM1104191", "GSM1104192", "GSM1104193", "GSM1104194", "GSM1104195", "GSM1104196", "GSM1104197", "GSM1104198", "GSM1104199"], "sample_count": 134, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression profiles of human 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:GSE62232", "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=GSE62232", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62232", "version": null, "note": "The datasets used and/or analyzed during the current study can be obtained from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study can be obtained from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1523329", "GSM1523330", "GSM1523331", "GSM1523332", "GSM1523333", "GSM1523334", "GSM1523335", "GSM1523336", "GSM1523337", "GSM1523338", "GSM1523339", "GSM1523340", "GSM1523341", "GSM1523342", "GSM1523343", "GSM1523344", "GSM1523345", "GSM1523346", "GSM1523347", "GSM1523348", "GSM1523349", "GSM1523350", "GSM1523351", "GSM1523352", "GSM1523353", "GSM1523354", "GSM1523355", "GSM1523356", "GSM1523357", "GSM1523358", "GSM1523359", "GSM1523360", "GSM1523361", "GSM1523362", "GSM1523363", "GSM1523364", "GSM1523365", "GSM1523366", "GSM1523367", "GSM1523368", "GSM1523369", "GSM1523370", "GSM1523371", "GSM1523372", "GSM1523373", "GSM1523374", "GSM1523375", "GSM1523376", "GSM1523377", "GSM1523378", "GSM1523379", "GSM1523380", "GSM1523381", "GSM1523382", "GSM1523383", "GSM1523384", "GSM1523385", "GSM1523386", "GSM1523387", "GSM1523388", "GSM1523389", "GSM1523390", "GSM1523391", "GSM1523392", "GSM1523393", "GSM1523394", "GSM1523395", "GSM1523396", "GSM1523397", "GSM1523398", "GSM1523399", "GSM1523400", "GSM1523401", "GSM1523402", "GSM1523403", "GSM1523404", "GSM1523405", "GSM1523406", "GSM1523407", "GSM1523408", "GSM1523409", "GSM1523410", "GSM1523411", "GSM1523412", "GSM1523413", "GSM1523414", "GSM1523415", "GSM1523416", "GSM1523417", "GSM1523418", "GSM1523419"], "sample_count": 91, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Large-scale gene expression profiling of 81 hepatocellular carcinomas", "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:GSE6764", "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=GSE6764", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE6764", "version": null, "note": "The datasets used and/or analyzed during the current study can be obtained from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study can be obtained from the corresponding author on reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM155919", "GSM155920", "GSM155921", "GSM155922", "GSM155923", "GSM155924", "GSM155925", "GSM155926", "GSM155927", "GSM155928", "GSM155929", "GSM155930", "GSM155931", "GSM155932", "GSM155933", "GSM155934", "GSM155935", "GSM155936", "GSM155937", "GSM155938", "GSM155939", "GSM155940", "GSM155941", "GSM155942", "GSM155943", "GSM155944", "GSM155945", "GSM155946", "GSM155947", "GSM155948", "GSM155949", "GSM155950", "GSM155951", "GSM155952", "GSM155953", "GSM155954", "GSM155955", "GSM155956", "GSM155957", "GSM155958", "GSM155959", "GSM155960", "GSM155961", "GSM155962", "GSM155963", "GSM155964", "GSM155965", "GSM155966", "GSM155967", "GSM155968", "GSM155969", "GSM155970", "GSM155971", "GSM155972", "GSM155973", "GSM155974", "GSM155975", "GSM155976", "GSM155977", "GSM155978", "GSM155979", "GSM155980", "GSM155981", "GSM155982", "GSM155983", "GSM155984", "GSM155985", "GSM155986", "GSM155987", "GSM155988", "GSM155989", "GSM155990", "GSM155991", "GSM155992", "GSM155993"], "sample_count": 75, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Genome-wide molecular profiles of HCV-induced dysplasia and hepatocellular carcinoma", "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:31804459:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9f47a98b9d3958c9563d64f4790e683009e6c1341b06682cbb1f5bd38a2bb9d8", "bytes": 1294, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Correlation between SKA3 expressions with clinic-pathological characteristics of HCC.", "structure": {"pmcid": "PMC6895034", "section_index": 3, "section_title": "Clinical patient specimens and information", "row_count": 32, "column_count": 5}, "table": {"label": "Table 1", "caption": "Correlation between SKA3 expressions with clinic-pathological characteristics of HCC.", "rows": [["Clinicopathological Variables", "N", "SKA3 expression", "P-Value"], ["Low (102)", "High (134)"], ["Sex", "", "", "", "0.244"], ["Male", "120", "55", "65", ""], ["Female", "116", "47", "69", ""], ["Age, years", "", "", "", "0.438"], ["<50", "139", "59", "80", ""], ["≥50", "97", "43", "54", ""], ["AFP, ng/L", "", "", "", "8.856e−11"], ["<200", "153", "89", "64", ""], ["≥200", "83", "13", "70", ""], ["HBsAg", "", "", "", "0.398"], ["Negative", "82", "34", "48", ""], ["Positive", "154", "68", "86", ""], ["Tumor size, cm", "", "", "", "3.29e–11"], ["≤5", "138", "84", "54", ""], [">5", "98", "18", "80", ""], ["Tumor nodule number", "", "", "", "8.29e−07"], ["Solitary", "146", "81", "65", ""], ["Multiple (≥2)", "90", "21", "69", ""], ["Cancer embolus", "", "", "", "5.83e−14"], ["Absence", "152", "92", "60", ""], ["Presence", "84", "10", "74", ""], ["TNM stage", "", "", "", "1.6e−05"], ["Early (I & II)", "157", "83", "74", ""], ["Late (III & IV)", "79", "19", "60", ""], ["Differentiation grade", "", "", "", "0.002"], ["Well", "173", "85", "88", ""], ["Poor", "63", "17", "46", ""], ["P53 expression", "", "", "", "0.021"], ["High", "95", "33", "62", ""], ["Low", "141", "69", "72", ""]], "row_count": 32, "column_count": 5, "numeric_cells": 80, "header_rows": 2, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:31804459:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0afa91a3ec149fd18d1d864d734b8ee24212e7d803e2954b2961552b8f661c39", "bytes": 1307, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[26]/table-wrap[1]#Tab2", "version": null, "note": "Univariate and multivariate Cox regression analysis of risk factors associated with overall survival.", "structure": {"pmcid": "PMC6895034", "section_index": 26, "section_title": "Overexpression of SKA3 in HCC patients predicts poor survival", "row_count": 12, "column_count": 7}, "table": {"label": "Table 2", "caption": "Univariate and multivariate Cox regression analysis of risk factors associated with overall survival.", "rows": [["Variables", "Univariate analysis", "Multivariate analysis"], ["HR", "95% CI", "P-Value", "HR", "95% CI", "P-Value"], ["SKA3 expression (high vs. low)", "2.239", "1.574–3.187", "7.59e−06", "1.299", "0.829–2.034", "0.25"], ["Sex (male vs. female)", "0.935", "0.67–1.305", "0.69", "", "", ""], ["Age (≥50 vs. <50)", "0.899", "0.659–1.226", "0.50", "", "", ""], ["HBsAg (positive vs. negative)", "0.944", "0.671–1.329", "0.74", "", "", ""], ["AFP (≥200 ng/ml vs. <200 ng/ml)", "1.797", "1.279–2.525", "7.31e−04", "1.048", "0.692–1.586", "0.83"], ["Tumor size (>5 cm vs. ≤5 cm)", "2.441", "1.742–3.421", "2.19e−07", "1.688", "1.136–2.509", "0.0095"], ["Tumor nodule number (multiple vs. single)", "1.797", "1.284–2.514", "6.27e−04", "1.086", "0.744–1.585", "0.67"], ["Cancer embolus (presence vs. absence)", "2.875", "2.035–4.061", "2.07e−09", "1.878", "1.231–2.866", "0.0035"], ["TNM stage (late vs. early)", "2.095", "1.485–2.956", "2.5e−05", "1.209", "0.804–1.818", "0.36"], ["Differentiation grade (poor vs. well)", "1.545", "1.08–2.211", "0.017", "0.970", "0.648–1.452", "0.88"]], "row_count": 12, "column_count": 7, "numeric_cells": 56, "header_rows": 2, "locator": "section[26]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:31804459:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f84668530aca17eb0cb22a5431bf986381a66a472dc6915f59328b4eb0e643df", "bytes": 1326, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[26]/table-wrap[2]#Tab3", "version": null, "note": "Univariate and multivariate Cox regression analysis of risk factors associated with disease-free survival.", "structure": {"pmcid": "PMC6895034", "section_index": 26, "section_title": "Overexpression of SKA3 in HCC patients predicts poor survival", "row_count": 12, "column_count": 7}, "table": {"label": "Table 3", "caption": "Univariate and multivariate Cox regression analysis of risk factors associated with disease-free survival.", "rows": [["Variables", "Univariate analysis", "Multivariate analysis"], ["HR", "95% CI", "P-Value", "HR", "95% CI", "P-Value"], ["SKA3expression (high vs. low)", "2.107", "1.54–2.883", "3.18e−06", "1.501", "1.017–2.216", "0.04"], ["Sex (male vs. female)", "1.107", "0.818–1.498", "0.51", "", "", ""], ["Age (≥50 vs. <50)", "0.912", "0.67–1.24", "0.56", "", "", ""], ["HBsAg (positive vs. negative)", "1.441", "1.04–1.998", "0.028", "1.745", "1.234–2.466", "0.0016"], ["AFP (≥200 ng/ml vs. <200 ng/ml)", "1.623", "1.184–2.225", "2.63e−03", "1.042", "0.707–1.536", "0.83"], ["Tumor size (>5 cm vs. ≤5 cm)", "2.098", "1.549–2.84", "1.66e−06", "1.667", "1.174–2.365", "0.0042"], ["Tumor nodule number (multiple vs. single)", "1.517", "1.114–2.066", "8.13e−03", "1.077", "0.76–1.525", "0.68"], ["Cancer embolus (presence vs. absence)", "2.420", "1.766–3.316", "3.88e−08", "2.002", "1.046–3.832", "0.0362"], ["TNM stage (late vs. early)", "1.451", "1.049–2.008", "0.025", "1.051", "0.715–1.547", "0.80"], ["Differentiation grade (poor vs. well)", "1.480", "1.064–2.058", "0.02", "0.909", "0.62–1.333", "0.62"]], "row_count": 12, "column_count": 7, "numeric_cells": 59, "header_rows": 2, "locator": "section[26]/table-wrap[2]#Tab3"}}], "gaps": ["asset:data:geo:GSE36376 not downloaded", "asset:data:geo:GSE36376 licence not read", "asset:data:geo:GSE45436 not downloaded", "asset:data:geo:GSE45436 licence not read", "asset:data:geo:GSE62232 not downloaded", "asset:data:geo:GSE62232 licence not read", "asset:data:geo:GSE6764 not downloaded", "asset:data:geo:GSE6764 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "edger", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {"log2fc_threshold": "es were selected using |logFC| > 1 and p-value < 0"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We acquired HCC expression data from GEO (datasets GSE62232, GSE45436, GSE36376, and GSE6764; http://www.ncbi.nlm.nih.gov/geo) and TCGA (http://gdc.cancer.gov/) databases. Log2 conversion was performed for all data in data standardization. EdgeR package was used to analyse gene differential expression for the data in count form. Limma package was used for the data in GEO database.\nWe selected genes whose |logFC (fold change)| > 1 and p-value < 0.05 as differential expression genes."}}, {"id": "method-2", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox proportional hazards"}}, {"id": "method-3", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "Limma"}}, {"id": "method-4", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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: edger."}, "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": ["GSE62232", "GSE45436", "GSE36376", "GSE6764"], "resolved_accessions": ["GSE62232", "GSE45436", "GSE36376", "GSE6764"], "statements": ["The datasets used and/or analyzed during the current study can be obtained from the corresponding author on reasonable request."], "basis": "The paper names GSE62232, GSE45436, GSE36376, GSE6764 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:31804459", "data:geo:GSE36376", "asset:table:pmid:31804459:1", "asset:table:pmid:31804459:2", "asset:table:pmid:31804459:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE36376"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:17:12Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 33212, "completion_tokens": 1530, "cached_tokens": 792}}, "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:31804459", "type": "paper", "label": "pmid:31804459"}, {"id": "source:pmid:31804459", "type": "manuscript", "label": "PMID 31804459 full text"}, {"id": "data:geo:GSE36376", "type": "dataset", "label": "GEO GSE36376"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31804459", "type": "paper", "label": "pmid:31804459"}, {"id": "source:pmid:31804459", "type": "manuscript", "label": "PMID 31804459 full text"}, {"id": "data:geo:GSE36376", "type": "dataset", "label": "GEO GSE36376"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31804459", "type": "extraction", "used": ["source:pmid:31804459"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE36376", "type": "accession_resolution", "used": ["data:geo:GSE36376"], "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:31804459", "parent_hash": "sha256:1eaa222c4d2b74dee430941ca109a11d546c1cc3a8dc040f78fb202666d23c55", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE36376 licence not read", "asset:data:geo:GSE36376 not downloaded", "asset:data:geo:GSE45436 licence not read", "asset:data:geo:GSE45436 not downloaded", "asset:data:geo:GSE62232 licence not read", "asset:data:geo:GSE62232 not downloaded", "asset:data:geo:GSE6764 licence not read", "asset:data:geo:GSE6764 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["nalysis (GSEA). G2/M phase arrest and severe apoptosis was also found to result from SKA3 knockdown", "s uncover the role of SKA3 in regulating the apoptosis and proliferation of hepatocellular carcinom", "lity was analyzed using Cell Counting Kit-8 (CCK8) assay and plate clone formation assay, whil"], "order_basis": "paper_text_order:569", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["d to analyze cell invasion. The role of SKA3 in vivo was explored using subcutaneous xenotranspla", "tissues. Significant levels of inhibition of in vivo and in vitro tumor proliferation and invasio", "used to measure the mice, and at week 8 the mice were sacrificed. Thereafter, in order to analyze the presenc", "n order to perform cervical dislocation, the mice were euthanized. Then, the xenografts were remove"], "order_basis": "paper_text_order:721", "id": "assay:2"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["on of SKA3 have a poor prognosis. Similarly, immunohistochemical staining of 236 samples of tumors also found", "ographed and preserved. Ki-67 antibodies for immunohistochemistry staining was obtained from Bioss (bs-2130R).", "SKA3 in HCC patients predicts poor survival Immunohistochemical results showed that 134 out of 236 HCC patie", "clinical patients (Fig. 1j, k). We then used immunohistochemical staining to explore the status of P53 in tho"], "order_basis": "paper_text_order:956", "id": "assay:3"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["apoptosis was also found to result from SKA3 knockdown, as shown by the inhibition of CDK2/p53 phos", "boxplots and scatter plots. Cell culture and transfection Human hepatocellular carcinoma cell lines (L", "order to inhibit the expression of SKA3, we transfected three small interfering RNAs (siRNAs) target", "was mixed with pPACKH1 packaging plasmid and transfected into 293TN cells with sh-SKA3/NC. 3 days lat"], "order_basis": "paper_text_order:1454", "id": "assay:4"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["lar carcinoma cell lines (LM3 and HUH7) were cultured in American-type media (ATCC, Manassas, VA) at"], "order_basis": "paper_text_order:4554", "id": "assay:5"}, {"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": ["We acquired HCC expression data from GEO (datasets GSE62232, GSE45436, GSE36376, and GSE6764; http://www.ncbi.nlm.nih.gov/geo) and TCGA (http://gdc.cancer.gov/) databases. Log2 conversion was performed for all data in data standardization. EdgeR package was used to analyse gene differential expression for the data in count form. Limma package was used for the data in GEO database.\nWe selected genes whose |logFC (fold change)| > 1 and p-value < 0.05 as differential expression genes."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}