← All .science files
pmid:34222240
CBX4 Provides an Alternate Mode of Colon Cancer Development via Potential Influences on Circadian Rhythm and Immune Infiltration.
Wangzhi Wei · Wei Zhao · Yu Zhang
Frontiers in cell and developmental biology · 2021 doi:10.3389/fcell.2021.669254
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 · 3 items
claims array · 2 items
[0] object · 6 fields
[1] 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 · 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 · 6 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 290 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 177 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 31 items
[0] array · 2 items
[1] array · 2 items
[2] array · 3 items
[3] array · 1 item
[4] array · 4 items
[5] array · 4 items
[6] array · 4 items
[7] array · 4 items
[8] array · 4 items
[9] array · 4 items
[10] array · 4 items
[11] array · 4 items
[12] array · 4 items
[13] array · 4 items
[14] array · 4 items
[15] array · 4 items
[16] array · 4 items
[17] array · 4 items
[18] array · 4 items
[19] array · 4 items
[20] array · 4 items
[21] array · 4 items
[22] array · 4 items
[23] array · 4 items
[24] array · 4 items
[25] array · 4 items
[26] array · 4 items
[27] array · 4 items
[28] array · 4 items
[29] array · 4 items
[30] array · 4 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 30 items
[0] array · 2 items
[1] array · 2 items
[2] array · 4 items
[3] array · 4 items
[4] array · 6 items
[5] array · 6 items
[6] array · 6 items
[7] array · 6 items
[8] array · 6 items
[9] array · 6 items
[10] array · 6 items
[11] array · 6 items
[12] array · 6 items
[13] array · 6 items
[14] array · 6 items
[15] array · 6 items
[16] array · 6 items
[17] array · 6 items
[18] array · 6 items
[19] array · 6 items
[20] array · 6 items
[21] array · 6 items
[22] array · 6 items
[23] array · 6 items
[24] array · 6 items
[25] array · 6 items
[26] array · 6 items
[27] array · 6 items
[28] array · 6 items
[29] array · 6 items
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 20 items
[0] array · 2 items
[1] array · 2 items
[2] array · 3 items
[3] array · 3 items
[4] array · 9 items
[5] array · 9 items
[6] array · 9 items
[7] array · 9 items
[8] array · 9 items
[9] array · 9 items
[10] array · 9 items
[11] array · 9 items
[12] array · 9 items
[13] array · 9 items
[14] array · 9 items
[15] array · 9 items
[16] array · 9 items
[17] array · 9 items
[18] array · 9 items
[19] array · 9 items
gaps array · 4 items
analysis object · 4 fields
methods array · 1 item
[0] 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 · 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 · 1 item
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 · 1 item
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 · 8 items
assays array · 1 item
[0] object · 11 fields
required_operations array · 1 item
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34222240", "kind": "science-record", "revision": 6, "content_hash": "sha256:94a29da3d6dbd65691a91143721ae529d9e3157a4e7016edf4ef79b4a5b88ebe", "created_at": "2026-11-01T15:41:42Z", "updated_at": "2026-11-01T21:25:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "CBX4 Provides an Alternate Mode of Colon Cancer Development via Potential Influences on Circadian Rhythm and Immune Infiltration.", "doi": "10.3389/fcell.2021.669254", "pmid": "34222240", "authors": ["Wangzhi Wei", "Wei Zhao", "Yu Zhang"], "journal": "Frontiers in cell and developmental biology", "year": 2021, "abstract": "The circadian machinery is critical for the normal physiological functions and cellular processes. Circadian rhythm disruption has been associated with immune suppression which leads to higher cancer risk, suggesting a putative tumor protective role of circadian clock homeostasis. CBX4, as an epigenetic regulator, has been explored for its involvement in tumorigenesis. However, little is known about the correlation between CBX4 and circadian rhythm disruption in colon cancer as well as the potential impact on the tumor immunity. A significant upregulation of CBX4 was identified in the TCGA colon adenocarcinoma (COAD) samples when compared with the normal controls (p < 0.001). This differential expression was confirmed at the protein level using colon adenocarcinoma tissue array (p < 0.01). CBX4 was up-regulated in the recurred/progressed colon cancer cases compared with the disease-free samples (p < 0.01), suggesting CBX4 as a potential predictor for poor prognosis. With regard to nodular metastasis, CBX4 was found to be associated with early onset of metastatic diseases but not late progression. The circadian rhythm is orchestrated by the alternating activation and suppression of the CLOCK/ARNTL-driven positive loop and the PER/CRY-controlled negative loop. In COAD, CBX4 was negatively correlated with CLOCK (p < 0.001), and positively correlated with PER1 (p < 0.001), PER3 (p < 0.01), and CRY2 (p < 0.001) as well as NR1D1 (p < 0.001), a critical negative regulator of the circadian clock. These interactions consistently impacted on patient survival based on the colorectal cancer cohorts GSE17536 and GSE14333 of PrognoScan. CBX4 showed significant negative correlations with infiltrating B cells (p < 0.05) and CD4+ T cells (p < 0.01), and positive correlations with myeloid derived suppressor cells (MDSCs) (p < 0.05) and cancer associated fibroblast (CAFs) (p < 0.001), as well as a low immunoscore. Moreover, CBX4 displayed significant correlations with diverse immune metagenes. PER1 and PER3, consistent with their coordinated expression with CBX4, also had strong correlations with these gene representatives in COAD, suggesting a potential interaction of CBX4 with the circadian machinery. Our studies implicate that CBX4 may contribute to colon cancer development via potential influence on circadian rhythm and immune infiltration. These findings provide new insights into deciphering the function of CBX4, and may contribute to the development of new targeting strategies.", "claims": [{"id": "claim-method", "statement": "For each optimal cutpoint, patients are dichotomized and survival difference between high and low expression groups is calculated by log-rank test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34222240", "locator": "sections[7] \"PrognoScan Survival Analysis\" paragraph 2", "quote": "For each optimal cutpoint, patients are dichotomized and survival difference between high and low expression groups is calculated by log-rank test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study are available in online repositories. These data were derived from the following publicly available resources:\n1.TIMER: https://cistrome.shinyapps.io/timer/,2.UALCAN: Ualcan.path.uab.edu/analysis3.STRING: https://string-db.org/cgi/input?sessionId=bnvX D8cMolD6&input_page_active_form=multiple_identifiers4.cBioportal: https://www.cbioportal.org/5.GEPIA: http://gepia.cancer-pku.cn6.PrognoScan: http://dna00.bio.kyutech.ac.jp/PrognoScan/7.ESTIMATE: http:// bioinformatics.mdanderson.org/estimate/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34222240", "locator": "sections[18] \"Data Availability Statement\" paragraphs 1-3", "quote": "The datasets presented in this study are available in online repositories. These data were derived from the following publicly available resources:\n1.TIMER: https://cistrome.shinyapps.io/timer/,2.UALCAN: Ualcan.path.uab.edu/analysis3.STRING: https://string-db.org/cgi/input?sessionId=bnvX D8cMolD6&input_page_active_form=multiple_identifiers4.cBioportal: https://www.cbioportal.org/5.GEPIA: http://gepia.cancer-pku.cn6.PrognoScan: http://dna00.bio.kyutech.ac.jp/PrognoScan/7.ESTIMATE: http:// bioinformatics.mdanderson.org/estimate/."}], "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:34222240"], "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:GSE14333"], "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:GSE14333"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34222240", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fcell.2021.669254", "sha256": "sha256:e2401c46a7a75c65cd1940d70aea2784d36a7f81ff4ed2524a471b29e6725b01", "bytes": 57324, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fcell.2021.669254", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8253160", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE14333", "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=GSE14333", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14333", "version": null, "note": "The datasets presented in this study are available in online repositories. These data were derived from the following publicly available resources:\n1.TIMER: https://cistrome.shinyapps.io/timer/,2.UALCAN: Ualcan.path.uab.edu/analysis3.STRING: https://string-db.org/cgi/input?sessionId=bnvX D8cMolD6&input_page_active_form=multiple_identifiers4.cBioportal: https://www.cbioportal.org/5.GEPIA: http://gepia.cancer-pku.cn6.PrognoScan: http://dna00.bio.kyutech.ac.jp/PrognoScan/7.ESTIMATE: http:// bioinformatics.mdanderson.org/estimate/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study are available in online repositories. These data were derived from the following publicly available resources:\n1.TIMER: https://cistrome.shinyapps.io/timer/,2.UALCAN: Ualcan.path.uab.edu/analysis3.STRING: https://string-db.org/cgi/input?sessionId=bnvX D8cMolD6&input_page_active_form=multiple_identifiers4.cBioportal: https://www.cbioportal.org/5.GEPIA: http://gepia.cancer-pku.cn6.PrognoScan: http://dna00.bio.kyutech.ac.jp/PrognoScan/7.ESTIMATE: http:// bioinformatics.mdanderson.org/estimate/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM358341", "GSM358342", "GSM358343", "GSM358344", "GSM358345", "GSM358346", "GSM358347", "GSM358348", "GSM358349", "GSM358350", "GSM358351", "GSM358352", "GSM358353", "GSM358354", "GSM358355", "GSM358356", "GSM358357", "GSM358358", "GSM358359", "GSM358360", "GSM358361", "GSM358362", "GSM358363", "GSM358364", "GSM358365", "GSM358366", "GSM358367", "GSM358368", "GSM358369", "GSM358370", "GSM358371", "GSM358372", "GSM358373", "GSM358374", "GSM358375", "GSM358376", "GSM358377", "GSM358378", "GSM358379", "GSM358380", "GSM358381", "GSM358382", "GSM358383", "GSM358384", "GSM358385", "GSM358386", "GSM358387", "GSM358388", "GSM358389", "GSM358390", "GSM358391", "GSM358392", "GSM358393", "GSM358394", "GSM358395", "GSM358396", "GSM358397", "GSM358398", "GSM358399", "GSM358400", "GSM358401", "GSM358402", "GSM358403", "GSM358404", "GSM358405", "GSM358406", "GSM358407", "GSM358408", "GSM358409", "GSM358410", "GSM358411", "GSM358412", "GSM358413", "GSM358414", "GSM358415", "GSM358416", "GSM358417", "GSM358418", "GSM358419", "GSM358420", "GSM358421", "GSM358422", "GSM358423", "GSM358424", "GSM358425", "GSM358426", "GSM358427", "GSM358428", "GSM358429", "GSM358430", "GSM358431", "GSM358432", "GSM358433", "GSM358434", "GSM358435", "GSM358436", "GSM358437", "GSM358438", "GSM358439", "GSM358440", "GSM358441", "GSM358442", "GSM358443", "GSM358444", "GSM358445", "GSM358446", "GSM358447", "GSM358448", "GSM358449", "GSM358450", "GSM358451", "GSM358452", "GSM358453", "GSM358454", "GSM358455", "GSM358456", "GSM358457", "GSM358458", "GSM358459", "GSM358460", "GSM358461", "GSM358462", "GSM358463", "GSM358464", "GSM358465", "GSM358466", "GSM358467", "GSM358468", "GSM358469", "GSM358470", "GSM358471", "GSM358472", "GSM358473", "GSM358474", "GSM358475", "GSM358476", "GSM358477", "GSM358478", "GSM358479", "GSM358480", "GSM358481", "GSM358482", "GSM358483", "GSM358484", "GSM358485", "GSM358486", "GSM358487", "GSM358488", "GSM358489", "GSM358490", "GSM358491", "GSM358492", "GSM358493", "GSM358494", "GSM358495", "GSM358496", "GSM358497", "GSM358498", "GSM358499", "GSM358500", "GSM358501", "GSM358502", "GSM358503", "GSM358504", "GSM358505", "GSM358506", "GSM358507", "GSM358508", "GSM358509", "GSM358510", "GSM358511", "GSM358512", "GSM358513", "GSM358514", "GSM358515", "GSM358516", "GSM358517", "GSM358518", "GSM358519", "GSM358520", "GSM358521", "GSM358522", "GSM358523", "GSM358524", "GSM358525", "GSM358526", "GSM358527", "GSM358528", "GSM358529", "GSM358530", "GSM358531", "GSM358532", "GSM358533", "GSM358534", "GSM358535", "GSM358536", "GSM358537", "GSM358538", "GSM358539", "GSM358540", "GSM358541", "GSM358542", "GSM358543", "GSM358544", "GSM358545", "GSM358546", "GSM358547", "GSM358548", "GSM358549", "GSM358550", "GSM358551", "GSM358552", "GSM358553", "GSM358554", "GSM358555", "GSM358556", "GSM358557", "GSM358558", "GSM358559", "GSM358560", "GSM358561", "GSM358562", "GSM358563", "GSM358564", "GSM358565", "GSM358566", "GSM358567", "GSM358568", "GSM358569", "GSM358570", "GSM358571", "GSM358572", "GSM358573", "GSM358574", "GSM358575", "GSM358576", "GSM358577", "GSM358578", "GSM358579", "GSM358580", "GSM358581", "GSM358582", "GSM358583", "GSM358584", "GSM358585", "GSM358586", "GSM358587", "GSM358588", "GSM358589", "GSM358590", "GSM358591", "GSM358592", "GSM358593", "GSM358594", "GSM358595", "GSM358596", "GSM358597", "GSM358598", "GSM358599", "GSM358600", "GSM358601", "GSM358602", "GSM358603", "GSM358604", "GSM358605", "GSM358606", "GSM358607", "GSM358608", "GSM358609", "GSM358610", "GSM358611", "GSM358612", "GSM358613", "GSM358614", "GSM358615", "GSM358616", "GSM358617", "GSM358618", "GSM358619", "GSM358620", "GSM358621", "GSM358622", "GSM358623", "GSM358624", "GSM358625", "GSM358626", "GSM358627", "GSM358628", "GSM358629", "GSM358630"], "sample_count": 290, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from 290 primary colorectal cancers", "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:GSE17536", "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=GSE17536", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE17536", "version": null, "note": "The datasets presented in this study are available in online repositories. These data were derived from the following publicly available resources:\n1.TIMER: https://cistrome.shinyapps.io/timer/,2.UALCAN: Ualcan.path.uab.edu/analysis3.STRING: https://string-db.org/cgi/input?sessionId=bnvX D8cMolD6&input_page_active_form=multiple_identifiers4.cBioportal: https://www.cbioportal.org/5.GEPIA: http://gepia.cancer-pku.cn6.PrognoScan: http://dna00.bio.kyutech.ac.jp/PrognoScan/7.ESTIMATE: http:// bioinformatics.mdanderson.org/estimate/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study are available in online repositories. These data were derived from the following publicly available resources:\n1.TIMER: https://cistrome.shinyapps.io/timer/,2.UALCAN: Ualcan.path.uab.edu/analysis3.STRING: https://string-db.org/cgi/input?sessionId=bnvX D8cMolD6&input_page_active_form=multiple_identifiers4.cBioportal: https://www.cbioportal.org/5.GEPIA: http://gepia.cancer-pku.cn6.PrognoScan: http://dna00.bio.kyutech.ac.jp/PrognoScan/7.ESTIMATE: http:// bioinformatics.mdanderson.org/estimate/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM437093", "GSM437094", "GSM437095", "GSM437096", "GSM437097", "GSM437098", "GSM437099", "GSM437100", "GSM437101", "GSM437102", "GSM437103", "GSM437104", "GSM437105", "GSM437106", "GSM437107", "GSM437108", "GSM437109", "GSM437110", "GSM437111", "GSM437112", "GSM437113", "GSM437114", "GSM437115", "GSM437116", "GSM437117", "GSM437118", "GSM437119", "GSM437120", "GSM437121", "GSM437122", "GSM437123", "GSM437124", "GSM437125", "GSM437126", "GSM437127", "GSM437128", "GSM437129", "GSM437130", "GSM437131", "GSM437132", "GSM437133", "GSM437134", "GSM437135", "GSM437136", "GSM437137", "GSM437138", "GSM437139", "GSM437140", "GSM437141", "GSM437142", "GSM437143", "GSM437144", "GSM437145", "GSM437146", "GSM437147", "GSM437148", "GSM437149", "GSM437150", "GSM437151", "GSM437152", "GSM437153", "GSM437154", "GSM437155", "GSM437156", "GSM437157", "GSM437158", "GSM437159", "GSM437160", "GSM437161", "GSM437162", "GSM437163", "GSM437164", "GSM437165", "GSM437166", "GSM437167", "GSM437168", "GSM437169", "GSM437170", "GSM437171", "GSM437172", "GSM437173", "GSM437174", "GSM437175", "GSM437176", "GSM437177", "GSM437178", "GSM437179", "GSM437180", "GSM437181", "GSM437182", "GSM437183", "GSM437184", "GSM437185", "GSM437186", "GSM437187", "GSM437188", "GSM437189", "GSM437190", "GSM437191", "GSM437192", "GSM437193", "GSM437194", "GSM437195", "GSM437196", "GSM437197", "GSM437198", "GSM437199", "GSM437200", "GSM437201", "GSM437202", "GSM437203", "GSM437204", "GSM437205", "GSM437206", "GSM437207", "GSM437208", "GSM437209", "GSM437210", "GSM437211", "GSM437212", "GSM437213", "GSM437214", "GSM437215", "GSM437216", "GSM437217", "GSM437218", "GSM437219", "GSM437220", "GSM437221", "GSM437222", "GSM437223", "GSM437224", "GSM437225", "GSM437226", "GSM437227", "GSM437228", "GSM437229", "GSM437230", "GSM437231", "GSM437232", "GSM437233", "GSM437234", "GSM437235", "GSM437236", "GSM437237", "GSM437238", "GSM437239", "GSM437240", "GSM437241", "GSM437242", "GSM437243", "GSM437244", "GSM437245", "GSM437246", "GSM437247", "GSM437248", "GSM437249", "GSM437250", "GSM437251", "GSM437252", "GSM437253", "GSM437254", "GSM437255", "GSM437256", "GSM437257", "GSM437258", "GSM437259", "GSM437260", "GSM437261", "GSM437262", "GSM437263", "GSM437264", "GSM437265", "GSM437266", "GSM437267", "GSM437268", "GSM437269"], "sample_count": 177, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Metastasis Gene Expression Profile Predicts Recurrence and Death in Colon Cancer Patients (Moffitt Samples)", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:34222240:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:012291b587899e470b8fe15de63c9610c38d335df1d53342e74c49cab31e7899", "bytes": 1274, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#T1", "version": null, "note": "Correlations between CBX4 and gene representatives of various functional cell subsets in COAD determined by TIMER2.0.", "structure": {"pmcid": "PMC8253160", "section_index": 10, "section_title": "Statistical Analyses", "row_count": 31, "column_count": 4}, "table": {"label": "TABLE 1", "caption": "Correlations between CBX4 and gene representatives of various functional cell subsets in COAD determined by TIMER2.0.", "rows": [["", "Colon adenocarcinoma (COAD)"], ["", ""], ["Cell type", "Gene marker", "CBX4 Correlation (TIMER 2.0)"], [""], ["", "", "Purity-adjusted partial", "P Value"], ["", "", "spearman’s rho value", ""], ["T cell exhaustion", "PD-1(PDCD1)", "0.152", "**"], ["", "CTLA4", "0.093", "0.062"], ["", "LAG3", "0.138", "**"], ["", "TIM-3 (HAVCR2)", "0.066", "0.182"], ["Regulatory T cells", "FOXP3", "0.127", "*"], ["", "TGFβ (TGFB1)", "0.225", "***"], ["", "L1CAM", "0.469", "***"], ["", "PTGIR", "0.238", "***"], ["", "ITGA4", "0.016", "0.743"], ["Th1 cells", "T-bet (TBX21)", "0.119", "*"], ["", "STAT1", "0.197", "***"], ["", "STAT4", "0.02", "0.687"], ["", "IFN-γ (IFNG)", "0.076", "0.126"], ["Th2 cells", "GATA3", "0.197", "***"], ["", "STAT6", "0.253", "***"], ["Th17 cells", "IL-6R", "0.203", "***"], ["", "STAT3", "0.221", "***"], ["", "RORγt (RORC)", "-0.035", "0.479"], ["", "IL-17A", "-0.071", "0.154"], ["Macrophage", "CD68", "0.174", "***"], ["MDSC", "CD11b (ITGAM)", "0.139", "**"], ["", "IL-4R", "0.286", "***"], ["", "CD33", "−0.006", "0.902"], ["", "CD14", "0.126", "*"], ["", "S100A9", "−0.007", "0.881"]], "row_count": 31, "column_count": 4, "numeric_cells": 47, "header_rows": 6, "locator": "section[10]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:34222240:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6e38d4d806a8a5b5021734793da5c51dd2d69d98c993527ae8439517e78f2b54", "bytes": 1604, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[2]#T3", "version": null, "note": "Correlations between PER1, PER3, and gene representatives of various functional cell subsets in COAD determined by TIMER2.0.", "structure": {"pmcid": "PMC8253160", "section_index": 10, "section_title": "Statistical Analyses", "row_count": 30, "column_count": 6}, "table": {"label": "TABLE 3", "caption": "Correlations between PER1, PER3, and gene representatives of various functional cell subsets in COAD determined by TIMER2.0.", "rows": [["", "Colon Adenocarcinoma (COAD)"], ["", ""], ["Cell type", "Gene marker", "PER1", "PER3"], ["", "", "", ""], ["", "", "spearman’s rho", "P Value", "spearman’s rho", "P Value"], ["T cell exhaustion", "PD-1(PDCD1)", "0.272", "***", "0.246", "***"], ["", "CTLA4", "0.305", "***", "0.259", "***"], ["", "LAG3", "0.309", "***", "0.257", "***"], ["", "TIM-3 (HAVCR2)", "0.258", "***", "0.255", "***"], ["Regulatory T cells", "FOXP3", "0.269", "***", "0.286", "***"], ["", "TGFβ (TGFB1)", "0.34", "***", "0.231", "***"], ["", "L1CAM", "0.189", "***", "0.147", "**"], ["", "PTGIR", "0.315", "***", "0.214", "***"], ["", "ITGA4", "0.205", "***", "0.342", "***"], ["Th1 cells", "T-bet (TBX21)", "0.303", "***", "0.287", "***"], ["", "STAT1", "0.308", "***", "0.351", "***"], ["", "STAT4", "0.224", "***", "0.305", "***"], ["", "IFN-γ (IFNG)", "0.122", "*", "0.209", "***"], ["Th2 cells", "GATA3", "0.245", "***", "0.282", "***"], ["", "STAT6", "0.195", "***", "0.229", "***"], ["Th17 cells", "IL-6R", "0.209", "***", "0.395", "***"], ["", "STAT3", "0.282", "***", "0.406", "***"], ["", "RORγt (RORC)", "−0.087", "0.08", "0.145", "**"], ["", "IL-17A", "−0.231", "***", "−0.072", "0.15"], ["Macrophage", "CD68", "0.254", "***", "0.277", "***"], ["MDSC", "CD11b (ITGAM)", "0.232", "***", "0.244", "***"], ["", "IL-4R", "0.413", "***", "0.354", "***"], ["", "CD33", "0.146", "**", "0.223", "***"], ["", "CD14", "0.239", "***", "0.228", "***"], ["", "S100A9", "0.01", "0.834", "−0.031", "0.539"]], "row_count": 30, "column_count": 6, "numeric_cells": 66, "header_rows": 5, "locator": "section[10]/table-wrap[2]#T3"}}, {"id": "asset:table:pmid:34222240:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3074538aa4559d94f0b5743b6cf3b70f5ddcfc9f83574bbdf9bfe77b618eec69", "bytes": 1419, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#T2", "version": null, "note": "Correlations between CBX4 and gene representatives of various functional cell subsets in COAD determined by GEPIA.", "structure": {"pmcid": "PMC8253160", "section_index": 15, "section_title": "CBX4 Impacts Immunophenotype in Colon Cancer", "row_count": 20, "column_count": 9}, "table": {"label": "TABLE 2", "caption": "Correlations between CBX4 and gene representatives of various functional cell subsets in COAD determined by GEPIA.", "rows": [["Immune markers", "CBX4 Correlation (GEPIA)"], ["", ""], ["", "COAD Tumor", "COAD Normal"], ["", "", ""], ["", "Spearman’s", "p value", "Pearson’s", "p value", "Spearman’s", "p value", "Pearson’s", "p value"], ["PD-1(PDCD1)", "0.17", "**", "0.17", "**", "0.28", "0.079", "0.38", "0.015"], ["LAG3", "0.15", "*", "0.21", "***", "0.15", "0.34", "0.19", "0.24"], ["FOXP3", "0.12", "*", "0.12", "*", "0.2", "0.21", "0.27", "0.089"], ["TGFβ (TGFB1)", "0.27", "***", "0.33", "***", "0.65", "***", "0.71", "***"], ["L1CAM", "0.44", "***", "0.32", "***", "0.15", "0.37", "0.24", "0.14"], ["PTGIR", "0.25", "***", "0.14", "*", "0.16", "0.32", "0.25", "0.11"], ["T-bet (TBX21)", "0.15", "*", "0.15", "*", "0.16", "0.32", "0.2", "0.2"], ["STAT1", "0.24", "***", "0.3", "***", "0.096", "0.55", "−0.09", "0.58"], ["GATA3", "0.19", "**", "0.15", "*", "0.36", "*", "0.41", "**"], ["STAT6", "0.23", "***", "0.19", "**", "0.42", "**", "0.44", "**"], ["IL-6R", "0.22", "***", "0.13", "*", "−0.22", "0.18", "−0.16", "0.33"], ["STAT3", "0.27", "***", "0.25", "***", "0.37", "*", "0.25", "0.11"], ["CD68", "0.18", "**", "0.22", "***", "0.097", "0.55", "0.068", "0.67"], ["CD11b (ITGAM)", "0.2", "***", "0.13", "*", "0.51", "***", "0.4", "**"], ["IL-4R", "0.27", "***", "0.21", "***", "0.2", "0.2", "0.29", "0.064"]], "row_count": 20, "column_count": 9, "numeric_cells": 87, "header_rows": 5, "locator": "section[15]/table-wrap[1]#T2"}}], "gaps": ["asset:data:geo:GSE14333 not downloaded", "asset:data:geo:GSE14333 licence not read", "asset:data:geo:GSE17536 not downloaded", "asset:data:geo:GSE17536 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "For each optimal cutpoint, patients are dichotomized and survival difference between high and low expression groups is calculated by log-rank test."}}], "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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_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": ["GSE17536", "GSE14333"], "resolved_accessions": ["GSE17536", "GSE14333"], "statements": ["The datasets presented in this study are available in online repositories. These data were derived from the following publicly available resources:\n1.TIMER: https://cistrome.shinyapps.io/timer/,2.UALCAN: Ualcan.path.uab.edu/analysis3.STRING: https://string-db.org/cgi/input?sessionId=bnvX D8cMolD6&input_page_active_form=multiple_identifiers4.cBioportal: https://www.cbioportal.org/5.GEPIA: http://gepia.cancer-pku.cn6.PrognoScan: http://dna00.bio.kyutech.ac.jp/PrognoScan/7.ESTIMATE: http:// bioinformatics.mdanderson.org/estimate/."], "basis": "The paper names GSE17536, GSE14333 in PrognoScan and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["logrank_test"], "assets": ["source:pmid:34222240", "data:geo:GSE14333", "asset:table:pmid:34222240:1", "asset:table:pmid:34222240:2", "asset:table:pmid:34222240:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14333"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:32:08Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 45208, "completion_tokens": 2117, "cached_tokens": 784}}, "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:34222240", "type": "paper", "label": "pmid:34222240"}, {"id": "source:pmid:34222240", "type": "manuscript", "label": "PMID 34222240 full text"}, {"id": "data:geo:GSE14333", "type": "dataset", "label": "GEO GSE14333"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34222240", "type": "paper", "label": "pmid:34222240"}, {"id": "source:pmid:34222240", "type": "manuscript", "label": "PMID 34222240 full text"}, {"id": "data:geo:GSE14333", "type": "dataset", "label": "GEO GSE14333"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34222240", "type": "extraction", "used": ["source:pmid:34222240"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14333", "type": "accession_resolution", "used": ["data:geo:GSE14333"], "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:34222240", "parent_hash": "sha256:8ed4a8238df0fe9c90d0e178284418c2a0582c29d138772e85b71b066a054f4a", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE14333 licence not read", "asset:data:geo:GSE14333 not downloaded", "asset:data:geo:GSE17536 licence not read", "asset:data:geo:GSE17536 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["For each optimal cutpoint, patients are dichotomized and survival difference between high and low expression groups is calculated by log-rank test."], "order_basis": "analysis_only", "id": "assay:1"}]}