← All .science files
pmid:33666342
Identification of hub genes associated with neutrophils infiltration in colorectal cancer.
Hao Su · Tianyi Cai · Sen Zhang · Xialin Yan · Leqi Zhou · Zirui He · Pei Xue · Jianwen Li · Minhua Zheng · Xiao Yang · Bo Feng
Journal of cellular and molecular medicine · 2021 doi:10.1111/jcmm.16414
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 · 11 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 · 1 item
data object · 3 fields
assets array · 3 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 917 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 585 items
gaps array · 4 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 1 item
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 · 2 items
resolved_accessions array · 2 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 2 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 · 10 items
assays array · 3 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 · 2 items
[2] 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:33666342", "kind": "science-record", "revision": 7, "content_hash": "sha256:d9c41d8350eef5d486f4614ebac17eca7e61ccdd7be01fa4f3379af134b88330", "created_at": "2026-11-01T15:41:27Z", "updated_at": "2026-11-01T22:03:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of hub genes associated with neutrophils infiltration in colorectal cancer.", "doi": "10.1111/jcmm.16414", "pmid": "33666342", "authors": ["Hao Su", "Tianyi Cai", "Sen Zhang", "Xialin Yan", "Leqi Zhou", "Zirui He", "Pei Xue", "Jianwen Li", "Minhua Zheng", "Xiao Yang", "Bo Feng"], "journal": "Journal of cellular and molecular medicine", "year": 2021, "abstract": "Colorectal cancer (CRC) is the leading cause of cancer-related mortality in the world. Accumulating evidence indicate that tumour infiltrating immune cells participated in cancer progression. Among them, tumour infiltrating neutrophils (TINs) are reported to play crucial role in various cancers. In this study, we used CIBERSORTx, a digital cytometry tool to evaluate the neutrophils infiltration in CRC based on gene expression data of CRC tissues from GSE39582 data set and The Cancer Genome Atlas data set (TCGA-COAD and TCGA-READ). Weighted gene co-expression network analysis (WGCNA) was conducted in GSE39582 data set to identify hub genes associated with neutrophil infiltration. The association of hub gene and neutrophils was then validated in TCGA cohorts and an independent RJ cohort. Functional analysis was performed to investigate the molecular mechanisms of the interested hub gene. We found that neutrophil infiltration is elevated in CRC tissues, and it is related to a poorer prognosis. A total of 18 gene modules are identified by WGCNA in GSE39582 data set, among which lightcyan module is significantly correlated with neutrophils infiltration. Furthermore, Superoxide Dismutase 2 (SOD2) in lightcyan module was proved to correlated with neutrophils infiltration in various cancer types. In addition, SOD2 expression is highly associated with several chemokines, including CXCL8, a neutrophils-related attractant, and functional analysis revealed that SOD2 is involved in neutrophils recruitment biological process. These results indicate that an 'SOD2-CXCL8-neutrophil recruitment' axis plays a potential role in colorectal cancer progression.", "claims": [{"id": "claim-method", "statement": "Wilcoxon test was used to compare the neutrophil scores/counts in different sample groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33666342", "locator": "sections[9] \"Statistics and data visualization\" paragraph 2", "quote": "Wilcoxon test was used to compare the neutrophil scores/counts in different sample groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The RNA sequencing data of CRC patients were downloaded from Xena (http://xena.ucsc.edu/). GSE39582 and GSE36133 were obtained from GEO database (https://www.ncbi.nlm.nih.gov/gds/). Other data analysed during this study are included in this published article and the supplementary material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33666342", "locator": "sections[23] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The RNA sequencing data of CRC patients were downloaded from Xena (http://xena.ucsc.edu/). GSE39582 and GSE36133 were obtained from GEO database (https://www.ncbi.nlm.nih.gov/gds/). Other data analysed during this study are included in this published article and the supplementary material."}], "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:33666342"], "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:GSE36133"], "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:group_comparison_wilcoxon", "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:GSE36133"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33666342", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1111/jcmm.16414", "sha256": "sha256:ca2283f1042cbf2bb66a4e3390ab05f575c74e6e8c80bc3e838550b088bdd9a9", "bytes": 29268, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1111/jcmm.16414", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8034475", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE36133", "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=GSE36133", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE36133", "version": null, "note": "The RNA sequencing data of CRC patients were downloaded from Xena (http://xena.ucsc.edu/). GSE39582 and GSE36133 were obtained from GEO database (https://www.ncbi.nlm.nih.gov/gds/). Other data analysed during this study are included in this published article and the supplementary material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The RNA sequencing data of CRC patients were downloaded from Xena (http://xena.ucsc.edu/). GSE39582 and GSE36133 were obtained from GEO database (https://www.ncbi.nlm.nih.gov/gds/). Other data analysed during this study are included in this published article and the supplementary material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM886835", "GSM886836", "GSM886837", "GSM886838", "GSM886839", "GSM886840", "GSM886841", "GSM886842", "GSM886843", "GSM886844", "GSM886845", "GSM886846", "GSM886847", "GSM886848", "GSM886849", "GSM886850", "GSM886851", "GSM886852", "GSM886853", "GSM886854", "GSM886855", "GSM886856", "GSM886857", "GSM886858", "GSM886859", "GSM886860", "GSM886861", "GSM886862", "GSM886863", "GSM886864", "GSM886865", "GSM886866", "GSM886867", "GSM886868", "GSM886869", "GSM886870", "GSM886871", "GSM886872", "GSM886873", "GSM886874", "GSM886875", "GSM886876", "GSM886877", "GSM886878", "GSM886879", "GSM886880", "GSM886881", "GSM886882", "GSM886883", "GSM886884", "GSM886885", "GSM886886", "GSM886887", "GSM886888", "GSM886889", "GSM886890", "GSM886891", "GSM886892", "GSM886893", "GSM886894", "GSM886895", "GSM886896", "GSM886897", "GSM886898", "GSM886899", "GSM886900", "GSM886901", "GSM886902", "GSM886903", "GSM886904", "GSM886905", "GSM886906", "GSM886907", "GSM886908", "GSM886909", "GSM886910", "GSM886911", "GSM886912", "GSM886913", "GSM886914", "GSM886915", "GSM886916", "GSM886917", "GSM886918", "GSM886919", "GSM886920", "GSM886921", "GSM886922", "GSM886923", "GSM886924", "GSM886925", "GSM886926", "GSM886927", "GSM886928", "GSM886929", "GSM886930", "GSM886931", "GSM886932", "GSM886933", "GSM886934", "GSM886935", "GSM886936", "GSM886937", "GSM886938", "GSM886939", "GSM886940", "GSM886941", "GSM886942", "GSM886943", "GSM886944", "GSM886945", "GSM886946", "GSM886947", "GSM886948", "GSM886949", "GSM886950", "GSM886951", "GSM886952", "GSM886953", "GSM886954", "GSM886955", "GSM886956", "GSM886957", "GSM886958", "GSM886959", "GSM886960", "GSM886961", "GSM886962", "GSM886963", "GSM886964", "GSM886965", "GSM886966", "GSM886967", "GSM886968", "GSM886969", "GSM886970", "GSM886971", "GSM886972", "GSM886973", "GSM886974", "GSM886975", "GSM886976", "GSM886977", "GSM886978", "GSM886979", "GSM886980", "GSM886981", "GSM886982", "GSM886983", "GSM886984", "GSM886985", "GSM886986", "GSM886987", "GSM886988", "GSM886989", "GSM886990", "GSM886991", "GSM886992", "GSM886993", "GSM886994", "GSM886995", "GSM886996", "GSM886997", "GSM886998", "GSM886999", "GSM887000", "GSM887001", "GSM887002", "GSM887003", "GSM887004", "GSM887005", "GSM887006", "GSM887007", "GSM887008", "GSM887009", "GSM887010", "GSM887011", "GSM887012", "GSM887013", "GSM887014", "GSM887015", "GSM887016", "GSM887017", "GSM887018", "GSM887019", "GSM887020", "GSM887021", "GSM887022", "GSM887023", "GSM887024", "GSM887025", "GSM887026", "GSM887027", "GSM887028", "GSM887029", "GSM887030", "GSM887031", "GSM887032", "GSM887033", "GSM887034", "GSM887035", "GSM887036", "GSM887037", "GSM887038", "GSM887039", "GSM887040", "GSM887041", "GSM887042", "GSM887043", "GSM887044", "GSM887045", "GSM887046", "GSM887047", "GSM887048", "GSM887049", "GSM887050", "GSM887051", "GSM887052", "GSM887053", "GSM887054", "GSM887055", "GSM887056", "GSM887057", "GSM887058", "GSM887059", "GSM887060", "GSM887061", "GSM887062", "GSM887063", "GSM887064", "GSM887065", "GSM887066", "GSM887067", "GSM887068", "GSM887069", "GSM887070", "GSM887071", "GSM887072", "GSM887073", "GSM887074", "GSM887075", "GSM887076", "GSM887077", "GSM887078", "GSM887079", "GSM887080", "GSM887081", "GSM887082", "GSM887083", "GSM887084", "GSM887085", "GSM887086", "GSM887087", "GSM887088", "GSM887089", "GSM887090", "GSM887091", "GSM887092", "GSM887093", "GSM887094", "GSM887095", "GSM887096", "GSM887097", "GSM887098", "GSM887099", "GSM887100", "GSM887101", "GSM887102", "GSM887103", "GSM887104", "GSM887105", "GSM887106", "GSM887107", "GSM887108", "GSM887109", "GSM887110", "GSM887111", "GSM887112", "GSM887113", "GSM887114", "GSM887115", "GSM887116", "GSM887117", "GSM887118", "GSM887119", "GSM887120", "GSM887121", "GSM887122", "GSM887123", "GSM887124", "GSM887125", "GSM887126", "GSM887127", "GSM887128", "GSM887129", "GSM887130", "GSM887131", "GSM887132", "GSM887133", "GSM887134", "GSM887135", "GSM887136", "GSM887137", "GSM887138", "GSM887139", "GSM887140", "GSM887141", "GSM887142", "GSM887143", "GSM887144", "GSM887145", "GSM887146", "GSM887147", "GSM887148", "GSM887149", "GSM887150", "GSM887151", "GSM887152", "GSM887153", "GSM887154", "GSM887155", "GSM887156", "GSM887157", "GSM887158", "GSM887159", "GSM887160", "GSM887161", "GSM887162", "GSM887163", "GSM887164", "GSM887165", "GSM887166", "GSM887167", "GSM887168", "GSM887169", "GSM887170", "GSM887171", "GSM887172", "GSM887173", "GSM887174", "GSM887175", "GSM887176", "GSM887177", "GSM887178", "GSM887179", "GSM887180", "GSM887181", "GSM887182", "GSM887183", "GSM887184", "GSM887185", "GSM887186", "GSM887187", "GSM887188", "GSM887189", "GSM887190", "GSM887191", "GSM887192", "GSM887193", "GSM887194", "GSM887195", "GSM887196", "GSM887197", "GSM887198", "GSM887199", "GSM887200", "GSM887201", "GSM887202", "GSM887203", "GSM887204", "GSM887205", "GSM887206", "GSM887207", "GSM887208", "GSM887209", "GSM887210", "GSM887211", "GSM887212", "GSM887213", "GSM887214", "GSM887215", "GSM887216", "GSM887217", "GSM887218", "GSM887219", "GSM887220", "GSM887221", "GSM887222", "GSM887223", "GSM887224", "GSM887225", "GSM887226", "GSM887227", "GSM887228", "GSM887229", "GSM887230", "GSM887231", "GSM887232", "GSM887233", "GSM887234", "GSM887235", "GSM887236", "GSM887237", "GSM887238", "GSM887239", "GSM887240", "GSM887241", "GSM887242", "GSM887243", "GSM887244", "GSM887245", "GSM887246", "GSM887247", "GSM887248", "GSM887249", "GSM887250", "GSM887251", "GSM887252", "GSM887253", "GSM887254", "GSM887255", "GSM887256", "GSM887257", "GSM887258", "GSM887259", "GSM887260", "GSM887261", "GSM887262", "GSM887263", "GSM887264", "GSM887265", "GSM887266", "GSM887267", "GSM887268", "GSM887269", "GSM887270", "GSM887271", "GSM887272", "GSM887273", "GSM887274", "GSM887275", "GSM887276", "GSM887277", "GSM887278", "GSM887279", "GSM887280", "GSM887281", "GSM887282", "GSM887283", "GSM887284", "GSM887285", "GSM887286", "GSM887287", "GSM887288", "GSM887289", "GSM887290", "GSM887291", "GSM887292", "GSM887293", "GSM887294", "GSM887295", "GSM887296", "GSM887297", "GSM887298", "GSM887299", "GSM887300", "GSM887301", "GSM887302", "GSM887303", "GSM887304", "GSM887305", "GSM887306", "GSM887307", "GSM887308", "GSM887309", "GSM887310", "GSM887311", "GSM887312", "GSM887313", "GSM887314", "GSM887315", "GSM887316", "GSM887317", "GSM887318", "GSM887319", "GSM887320", "GSM887321", "GSM887322", "GSM887323", "GSM887324", "GSM887325", "GSM887326", "GSM887327", "GSM887328", "GSM887329", "GSM887330", "GSM887331", "GSM887332", "GSM887333", "GSM887334", "GSM887335", "GSM887336", "GSM887337", "GSM887338", "GSM887339", "GSM887340", "GSM887341", "GSM887342", "GSM887343", "GSM887344", "GSM887345", "GSM887346", "GSM887347", "GSM887348", "GSM887349", "GSM887350", "GSM887351", "GSM887352", "GSM887353", "GSM887354", "GSM887355", "GSM887356", "GSM887357", "GSM887358", "GSM887359", "GSM887360", "GSM887361", "GSM887362", "GSM887363", "GSM887364", "GSM887365", "GSM887366", "GSM887367", "GSM887368", "GSM887369", "GSM887370", "GSM887371", "GSM887372", "GSM887373", "GSM887374", "GSM887375", "GSM887376", "GSM887377", "GSM887378", "GSM887379", "GSM887380", "GSM887381", "GSM887382", "GSM887383", "GSM887384", "GSM887385", "GSM887386", "GSM887387", "GSM887388", "GSM887389", "GSM887390", "GSM887391", "GSM887392", "GSM887393", "GSM887394", "GSM887395", "GSM887396", "GSM887397", "GSM887398", "GSM887399", "GSM887400", "GSM887401", "GSM887402", "GSM887403", "GSM887404", "GSM887405", "GSM887406", "GSM887407", "GSM887408", "GSM887409", "GSM887410", "GSM887411", "GSM887412", "GSM887413", "GSM887414", "GSM887415", "GSM887416", "GSM887417", "GSM887418", "GSM887419", "GSM887420", "GSM887421", "GSM887422", "GSM887423", "GSM887424", "GSM887425", "GSM887426", "GSM887427", "GSM887428", "GSM887429", "GSM887430", "GSM887431", "GSM887432", "GSM887433", "GSM887434", "GSM887435", "GSM887436", "GSM887437", "GSM887438", "GSM887439", "GSM887440", "GSM887441", "GSM887442", "GSM887443", "GSM887444", "GSM887445", "GSM887446", "GSM887447", "GSM887448", "GSM887449", "GSM887450", "GSM887451", "GSM887452", "GSM887453", "GSM887454", "GSM887455", "GSM887456", "GSM887457", "GSM887458", "GSM887459", "GSM887460", "GSM887461", "GSM887462", "GSM887463", "GSM887464", "GSM887465", "GSM887466", "GSM887467", "GSM887468", "GSM887469", "GSM887470", "GSM887471", "GSM887472", "GSM887473", "GSM887474", "GSM887475", "GSM887476", "GSM887477", "GSM887478", "GSM887479", "GSM887480", "GSM887481", "GSM887482", "GSM887483", "GSM887484", "GSM887485", "GSM887486", "GSM887487", "GSM887488", "GSM887489", "GSM887490", "GSM887491", "GSM887492", "GSM887493", "GSM887494", "GSM887495", "GSM887496", "GSM887497", "GSM887498", "GSM887499", "GSM887500", "GSM887501", "GSM887502", "GSM887503", "GSM887504", "GSM887505", "GSM887506", "GSM887507", "GSM887508", "GSM887509", "GSM887510", "GSM887511", "GSM887512", "GSM887513", "GSM887514", "GSM887515", "GSM887516", "GSM887517", "GSM887518", "GSM887519", "GSM887520", "GSM887521", "GSM887522", "GSM887523", "GSM887524", "GSM887525", "GSM887526", "GSM887527", "GSM887528", "GSM887529", "GSM887530", "GSM887531", "GSM887532", "GSM887533", "GSM887534", "GSM887535", "GSM887536", "GSM887537", "GSM887538", "GSM887539", "GSM887540", "GSM887541", "GSM887542", "GSM887543", "GSM887544", "GSM887545", "GSM887546", "GSM887547", "GSM887548", "GSM887549", "GSM887550", "GSM887551", "GSM887552", "GSM887553", "GSM887554", "GSM887555", "GSM887556", "GSM887557", "GSM887558", "GSM887559", "GSM887560", "GSM887561", "GSM887562", "GSM887563", "GSM887564", "GSM887565", "GSM887566", "GSM887567", "GSM887568", "GSM887569", "GSM887570", "GSM887571", "GSM887572", "GSM887573", "GSM887574", "GSM887575", "GSM887576", "GSM887577", "GSM887578", "GSM887579", "GSM887580", "GSM887581", "GSM887582", "GSM887583", "GSM887584", "GSM887585", "GSM887586", "GSM887587", "GSM887588", "GSM887589", "GSM887590", "GSM887591", "GSM887592", "GSM887593", "GSM887594", "GSM887595", "GSM887596", "GSM887597", "GSM887598", "GSM887599", "GSM887600", "GSM887601", "GSM887602", "GSM887603", "GSM887604", "GSM887605", "GSM887606", "GSM887607", "GSM887608", "GSM887609", "GSM887610", "GSM887611", "GSM887612", "GSM887613", "GSM887614", "GSM887615", "GSM887616", "GSM887617", "GSM887618", "GSM887619", "GSM887620", "GSM887621", "GSM887622", "GSM887623", "GSM887624", "GSM887625", "GSM887626", "GSM887627", "GSM887628", "GSM887629", "GSM887630", "GSM887631", "GSM887632", "GSM887633", "GSM887634", "GSM887635", "GSM887636", "GSM887637", "GSM887638", "GSM887639", "GSM887640", "GSM887641", "GSM887642", "GSM887643", "GSM887644", "GSM887645", "GSM887646", "GSM887647", "GSM887648", "GSM887649", "GSM887650", "GSM887651", "GSM887652", "GSM887653", "GSM887654", "GSM887655", "GSM887656", "GSM887657", "GSM887658", "GSM887659", "GSM887660", "GSM887661", "GSM887662", "GSM887663", "GSM887664", "GSM887665", "GSM887666", "GSM887667", "GSM887668", "GSM887669", "GSM887670", "GSM887671", "GSM887672", "GSM887673", "GSM887674", "GSM887675", "GSM887676", "GSM887677", "GSM887678", "GSM887679", "GSM887680", "GSM887681", "GSM887682", "GSM887683", "GSM887684", "GSM887685", "GSM887686", "GSM887687", "GSM887688", "GSM887689", "GSM887690", "GSM887691", "GSM887692", "GSM887693", "GSM887694", "GSM887695", "GSM887696", "GSM887697", "GSM887698", "GSM887699", "GSM887700", "GSM887701", "GSM887702", "GSM887703", "GSM887704", "GSM887705", "GSM887706", "GSM887707", "GSM887708", "GSM887709", "GSM887710", "GSM887711", "GSM887712", "GSM887713", "GSM887714", "GSM887715", "GSM887716", "GSM887717", "GSM887718", "GSM887719", "GSM887720", "GSM887721", "GSM887722", "GSM887723", "GSM887724", "GSM887725", "GSM887726", "GSM887727", "GSM887728", "GSM887729", "GSM887730", "GSM887731", "GSM887732", "GSM887733", "GSM887734", "GSM887735", "GSM887736", "GSM887737", "GSM887738", "GSM887739", "GSM887740", "GSM887741", "GSM887742", "GSM887743", "GSM887744", "GSM887745", "GSM887746", "GSM887747", "GSM887748", "GSM887749", "GSM887750", "GSM887751"], "sample_count": 917, "group_sizes": null, "group_sizes_basis": null, "platform": "15308", "taxon": "Homo sapiens", "title": "Expression data from the Cancer Cell Line Encyclopedia (CCLE)", "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:GSE39582", "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=GSE39582", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39582", "version": null, "note": "The RNA sequencing data of CRC patients were downloaded from Xena (http://xena.ucsc.edu/). GSE39582 and GSE36133 were obtained from GEO database (https://www.ncbi.nlm.nih.gov/gds/). Other data analysed during this study are included in this published article and the supplementary material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The RNA sequencing data of CRC patients were downloaded from Xena (http://xena.ucsc.edu/). GSE39582 and GSE36133 were obtained from GEO database (https://www.ncbi.nlm.nih.gov/gds/). Other data analysed during this study are included in this published article and the supplementary material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1681353", "GSM1681354", "GSM1681355", "GSM1681356", "GSM1681357", "GSM1681358", "GSM1681359", "GSM1681360", "GSM1681361", "GSM1681362", "GSM1681363", "GSM1681364", "GSM1681365", "GSM1681366", "GSM1681367", "GSM1681368", "GSM1681369", "GSM1681370", "GSM1681371", "GSM971957", "GSM971958", "GSM971959", "GSM971960", "GSM971961", "GSM971962", "GSM971963", "GSM971964", "GSM971965", "GSM971966", "GSM971967", "GSM971968", "GSM971969", "GSM971970", "GSM971971", "GSM971972", "GSM971973", "GSM971974", "GSM971975", "GSM971976", "GSM971977", "GSM971978", "GSM971979", "GSM971980", "GSM971981", "GSM971982", "GSM971983", "GSM971984", "GSM971985", "GSM971986", "GSM971987", "GSM971988", "GSM971989", "GSM971990", "GSM971991", "GSM971992", "GSM971993", "GSM971994", "GSM971995", "GSM971996", "GSM971997", "GSM971998", "GSM971999", "GSM972000", "GSM972001", "GSM972002", "GSM972003", "GSM972004", "GSM972005", "GSM972006", "GSM972007", "GSM972008", "GSM972009", "GSM972010", "GSM972011", "GSM972012", "GSM972013", "GSM972014", "GSM972015", "GSM972016", "GSM972017", "GSM972018", "GSM972019", "GSM972020", "GSM972021", "GSM972022", "GSM972023", "GSM972024", "GSM972025", "GSM972026", "GSM972027", "GSM972028", "GSM972029", "GSM972030", "GSM972031", "GSM972032", "GSM972033", "GSM972034", "GSM972035", "GSM972036", "GSM972037", "GSM972038", "GSM972039", "GSM972040", "GSM972041", "GSM972042", "GSM972043", "GSM972044", "GSM972045", "GSM972046", "GSM972047", "GSM972048", "GSM972049", "GSM972050", "GSM972051", "GSM972052", "GSM972053", "GSM972054", "GSM972055", "GSM972056", "GSM972057", "GSM972058", "GSM972059", "GSM972060", "GSM972061", "GSM972062", "GSM972063", "GSM972064", "GSM972065", "GSM972066", "GSM972067", "GSM972068", "GSM972069", "GSM972070", "GSM972071", "GSM972072", "GSM972073", "GSM972074", "GSM972075", "GSM972076", "GSM972077", "GSM972078", "GSM972079", "GSM972080", "GSM972081", "GSM972082", "GSM972083", "GSM972084", "GSM972085", "GSM972086", "GSM972087", "GSM972088", "GSM972089", "GSM972090", "GSM972091", "GSM972092", "GSM972093", "GSM972094", "GSM972095", "GSM972096", "GSM972097", "GSM972098", "GSM972099", "GSM972100", "GSM972101", "GSM972102", "GSM972103", "GSM972104", "GSM972105", "GSM972106", "GSM972107", "GSM972108", "GSM972109", "GSM972110", "GSM972111", "GSM972112", "GSM972113", "GSM972114", "GSM972115", "GSM972116", "GSM972117", "GSM972118", "GSM972119", "GSM972120", "GSM972121", "GSM972122", "GSM972123", "GSM972124", "GSM972125", "GSM972126", "GSM972127", "GSM972128", "GSM972129", "GSM972130", "GSM972131", "GSM972132", "GSM972133", "GSM972134", "GSM972135", "GSM972136", "GSM972137", "GSM972138", "GSM972139", "GSM972140", "GSM972141", "GSM972142", "GSM972143", "GSM972144", "GSM972145", "GSM972146", "GSM972147", "GSM972148", "GSM972149", "GSM972150", "GSM972151", "GSM972152", "GSM972153", "GSM972154", "GSM972155", "GSM972156", "GSM972157", "GSM972158", "GSM972159", "GSM972160", "GSM972161", "GSM972162", "GSM972163", "GSM972164", "GSM972165", "GSM972166", "GSM972167", "GSM972168", "GSM972169", "GSM972170", "GSM972171", "GSM972172", "GSM972173", "GSM972174", "GSM972175", "GSM972176", "GSM972177", "GSM972178", "GSM972179", "GSM972180", "GSM972181", "GSM972182", "GSM972183", "GSM972184", "GSM972185", "GSM972186", "GSM972187", "GSM972188", "GSM972189", "GSM972190", "GSM972191", "GSM972192", "GSM972193", "GSM972194", "GSM972195", "GSM972196", "GSM972197", "GSM972198", "GSM972199", "GSM972200", "GSM972201", "GSM972202", "GSM972203", "GSM972204", "GSM972205", "GSM972206", "GSM972207", "GSM972208", "GSM972209", "GSM972210", "GSM972211", "GSM972212", "GSM972213", "GSM972214", "GSM972215", "GSM972216", "GSM972217", "GSM972218", "GSM972219", "GSM972220", "GSM972221", "GSM972222", "GSM972223", "GSM972224", "GSM972225", "GSM972226", "GSM972227", "GSM972228", "GSM972229", "GSM972230", "GSM972231", "GSM972232", "GSM972233", "GSM972234", "GSM972235", "GSM972236", "GSM972237", "GSM972238", "GSM972239", "GSM972240", "GSM972241", "GSM972242", "GSM972243", "GSM972244", "GSM972245", "GSM972246", "GSM972247", "GSM972248", "GSM972249", "GSM972250", "GSM972251", "GSM972252", "GSM972253", "GSM972254", "GSM972255", "GSM972256", "GSM972257", "GSM972258", "GSM972259", "GSM972260", "GSM972261", "GSM972262", "GSM972263", "GSM972264", "GSM972265", "GSM972266", "GSM972267", "GSM972268", "GSM972269", "GSM972270", "GSM972271", "GSM972272", "GSM972273", "GSM972274", "GSM972275", "GSM972276", "GSM972277", "GSM972278", "GSM972279", "GSM972280", "GSM972281", "GSM972282", "GSM972283", "GSM972284", "GSM972285", "GSM972286", "GSM972287", "GSM972288", "GSM972289", "GSM972290", "GSM972291", "GSM972292", "GSM972293", "GSM972294", "GSM972295", "GSM972296", "GSM972297", "GSM972298", "GSM972299", "GSM972300", "GSM972301", "GSM972302", "GSM972303", "GSM972304", "GSM972305", "GSM972306", "GSM972307", "GSM972308", "GSM972309", "GSM972310", "GSM972311", "GSM972312", "GSM972313", "GSM972314", "GSM972315", "GSM972316", "GSM972317", "GSM972318", "GSM972319", "GSM972320", "GSM972321", "GSM972322", "GSM972323", "GSM972324", "GSM972325", "GSM972326", "GSM972327", "GSM972328", "GSM972329", "GSM972330", "GSM972331", "GSM972332", "GSM972333", "GSM972334", "GSM972335", "GSM972336", "GSM972337", "GSM972338", "GSM972339", "GSM972340", "GSM972341", "GSM972342", "GSM972343", "GSM972344", "GSM972345", "GSM972346", "GSM972347", "GSM972348", "GSM972349", "GSM972350", "GSM972351", "GSM972352", "GSM972353", "GSM972354", "GSM972355", "GSM972356", "GSM972357", "GSM972358", "GSM972359", "GSM972360", "GSM972361", "GSM972362", "GSM972363", "GSM972364", "GSM972365", "GSM972366", "GSM972367", "GSM972368", "GSM972369", "GSM972370", "GSM972371", "GSM972372", "GSM972373", "GSM972374", "GSM972375", "GSM972376", "GSM972377", "GSM972378", "GSM972379", "GSM972380", "GSM972381", "GSM972382", "GSM972383", "GSM972384", "GSM972385", "GSM972386", "GSM972387", "GSM972388", "GSM972389", "GSM972390", "GSM972391", "GSM972392", "GSM972393", "GSM972394", "GSM972395", "GSM972396", "GSM972397", "GSM972398", "GSM972399", "GSM972400", "GSM972401", "GSM972402", "GSM972403", "GSM972404", "GSM972405", "GSM972406", "GSM972407", "GSM972408", "GSM972409", "GSM972410", "GSM972411", "GSM972412", "GSM972413", "GSM972414", "GSM972415", "GSM972416", "GSM972417", "GSM972418", "GSM972419", "GSM972420", "GSM972421", "GSM972422", "GSM972423", "GSM972424", "GSM972425", "GSM972426", "GSM972427", "GSM972428", "GSM972429", "GSM972430", "GSM972431", "GSM972432", "GSM972433", "GSM972434", "GSM972435", "GSM972436", "GSM972437", "GSM972438", "GSM972439", "GSM972440", "GSM972441", "GSM972442", "GSM972443", "GSM972444", "GSM972445", "GSM972446", "GSM972447", "GSM972448", "GSM972449", "GSM972450", "GSM972451", "GSM972452", "GSM972453", "GSM972454", "GSM972455", "GSM972456", "GSM972457", "GSM972458", "GSM972459", "GSM972460", "GSM972461", "GSM972462", "GSM972463", "GSM972464", "GSM972465", "GSM972466", "GSM972467", "GSM972468", "GSM972469", "GSM972470", "GSM972471", "GSM972472", "GSM972473", "GSM972474", "GSM972475", "GSM972476", "GSM972477", "GSM972478", "GSM972479", "GSM972480", "GSM972481", "GSM972482", "GSM972483", "GSM972484", "GSM972485", "GSM972486", "GSM972487", "GSM972488", "GSM972489", "GSM972490", "GSM972491", "GSM972492", "GSM972493", "GSM972494", "GSM972495", "GSM972496", "GSM972497", "GSM972498", "GSM972499", "GSM972500", "GSM972501", "GSM972502", "GSM972503", "GSM972504", "GSM972505", "GSM972506", "GSM972507", "GSM972508", "GSM972509", "GSM972510", "GSM972511", "GSM972512", "GSM972513", "GSM972514", "GSM972515", "GSM972516", "GSM972517", "GSM972518", "GSM972519", "GSM972520", "GSM972521", "GSM972522"], "sample_count": 585, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics [Expression]", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE36133 not downloaded", "asset:data:geo:GSE36133 licence not read", "asset:data:geo:GSE39582 not downloaded", "asset:data:geo:GSE39582 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Wilcoxon test was used to compare the neutrophil scores/counts in different sample groups."}}], "targets": [], "gaps": ["method.group_comparison_wilcoxon"]}, "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": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "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": ["GSE39582", "GSE36133"], "resolved_accessions": ["GSE39582", "GSE36133"], "statements": ["The RNA sequencing data of CRC patients were downloaded from Xena (http://xena.ucsc.edu/). GSE39582 and GSE36133 were obtained from GEO database (https://www.ncbi.nlm.nih.gov/gds/). Other data analysed during this study are included in this published article and the supplementary material."], "basis": "The paper names GSE39582, GSE36133 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:33666342", "data:geo:GSE36133"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE36133"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:27:34Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 21321, "completion_tokens": 2462, "cached_tokens": 793}}, "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:33666342", "type": "paper", "label": "pmid:33666342"}, {"id": "source:pmid:33666342", "type": "manuscript", "label": "PMID 33666342 full text"}, {"id": "data:geo:GSE36133", "type": "dataset", "label": "GEO GSE36133"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33666342", "type": "paper", "label": "pmid:33666342"}, {"id": "source:pmid:33666342", "type": "manuscript", "label": "PMID 33666342 full text"}, {"id": "data:geo:GSE36133", "type": "dataset", "label": "GEO GSE36133"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33666342", "type": "extraction", "used": ["source:pmid:33666342"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE36133", "type": "accession_resolution", "used": ["data:geo:GSE36133"], "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:33666342", "parent_hash": "sha256:570594ff2f0c312014d509f3fc8b60b9729827e41b5e8200fd49f06b6f4cc953", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE36133 licence not read", "asset:data:geo:GSE36133 not downloaded", "asset:data:geo:GSE39582 licence not read", "asset:data:geo:GSE39582 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "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": 0.99, "evidence": ["oaded from Gene Expression Omnibus (GEO). 11 RNA sequencing data of 17 382 samples of 30 different types", "m Xena (https://xenabrowser.net/datapages/). Transcriptome data of 566 colorectal cancer (CRC) samples", "ype‐Tissue Expression (GTEx) project, 12 and transcriptome of 917 cancer cell line derived from tumour"], "order_basis": "paper_text_order:1944", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["of RJ Cohort from our hospital were used for immunohistochemical validation. In RJ cohort, a total of 79 pati", "ther validation. RJ cohort were utilized for immunohistochemistry Higher TIN levels indicating poorer prognosi"], "order_basis": "paper_text_order:3344", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Wilcoxon test was used to compare the neutrophil scores/counts in different sample groups."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}