← All .science files
pmid:32974187
Matrix Metallopeptidase 14: A Candidate Prognostic Biomarker for Diffuse Large B-Cell Lymphoma.
Chengliang Yin · Junyan Zhang · Ming Shen · Zhenyang Gu · Yan Li · Wanguo Xue · Jinlong Shi · Wenrong Huang
Frontiers in oncology · 2020 doi:10.3389/fonc.2020.01520
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 · 8 items
claims array · 2 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 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 · 420 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 221 items
[3] object · 15 fields
structure object · 15 fields
sample_accessions array · 137 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 24 items
[0] array · 5 items
[1] array · 5 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[10] array · 5 items
[11] array · 1 item
[12] array · 5 items
[13] array · 1 item
[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
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 55 items
[0] array · 3 items
[1] array · 4 items
[2] array · 6 items
[3] array · 6 items
[4] array · 6 items
[5] array · 6 items
[6] array · 6 items
[7] array · 6 items
[8] array · 6 items
[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
[30] array · 6 items
[31] array · 6 items
[32] array · 6 items
[33] array · 6 items
[34] array · 6 items
[35] array · 6 items
[36] array · 6 items
[37] array · 6 items
[38] array · 6 items
[39] array · 6 items
[40] array · 6 items
[41] array · 6 items
[42] array · 6 items
[43] array · 6 items
[44] array · 6 items
[45] array · 6 items
[46] array · 6 items
[47] array · 6 items
[48] array · 6 items
[49] array · 6 items
[50] array · 6 items
[51] array · 6 items
[52] array · 6 items
[53] array · 6 items
[54] array · 6 items
gaps array · 6 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
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 · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 3 items
resolved_accessions array · 3 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 4 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 · 1 item
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 · 11 items
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32974187", "kind": "science-record", "revision": 4, "content_hash": "sha256:69e1c0ee4099f73c212838b6948d9825a3d3f3c841ea2c2cbb9679f1fde07cd2", "created_at": "2026-11-01T15:41:11Z", "updated_at": "2026-11-01T21:23:50Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Matrix Metallopeptidase 14: A Candidate Prognostic Biomarker for Diffuse Large B-Cell Lymphoma.", "doi": "10.3389/fonc.2020.01520", "pmid": "32974187", "authors": ["Chengliang Yin", "Junyan Zhang", "Ming Shen", "Zhenyang Gu", "Yan Li", "Wanguo Xue", "Jinlong Shi", "Wenrong Huang"], "journal": "Frontiers in oncology", "year": 2020, "abstract": "BACKGROUND: Matrix metallopeptidase 14 (MMP14) is an important gene in the regulation of T-cell function. However, the correlation between MMP14 expression, prognosis, and immune cell infiltration in diffuse large B-cell lymphoma (DLBCL) remains unclear.\nMETHODS: We investigated the influence of MMP14 on clinical prognosis using data obtained from three Gene Expression Omnibus (GEO) database sets (GSE98588, GSE10846, and GSE4475). The expression of MMP14 was analyzed using the Gene Expression Profiling Interactive Analysis (GEPIA). The correlation between MMP14 and immune cell infiltration was investigated using the Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) and Tumor Immune Estimation Resource (TIMER) tools. In addition, the correlation between MMP14 expression and immune gene markers was analyzed by TIMER and GEPIA.\nRESULTS: MMP14 expression positively correlated with favorable progression-free survival (PFS; GSE98588, P = 0.02) and overall survival (OS; GSE98588, P = 0.003; GSE10846, P = 5.517e-05; and GSE4475, P = 9.85e-04). Moreover, MMP14 expression was higher in DLBCL tumors than in normal tissues. Regarding clinical characteristics, high MMP14 expression was found to be correlated with race. MMP14 expression was also correlated with immune cell infiltration and had a remarkable correlation with various immune marker sets. It was found that M0 macrophages were the immune cells most related to survival, decreasing with the increase in Ann Arbor clinical stage. The results especially showed that MMP14 was a prognostic biomarker and related to the macrophages M0.\nCONCLUSION: The results suggest that MMP14 is a novel prognostic molecular marker for DLBCL and is related to the immune cell infiltration, especially related to the macrophages M0. Our study provides insights for understanding the potential roles of MMP14 in tumor immunology and its suitability as a prognosis biomarker in DLBCL.", "claims": [{"id": "claim-method", "statement": "We performed Kaplan–Meier analysis to measure the OS of the 48 patients obtained from TCGA based on the abundance ratio of the 11 identified immune cell types, for which the cut-off level was set at the median value.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32974187", "locator": "sections[7] \"Clinical Relationship With the Immune Cell Most Related to Survival\" paragraph 2", "quote": "We performed Kaplan–Meier analysis to measure the OS of the 48 patients obtained from TCGA based on the abundance ratio of the 11 identified immune cell types, for which the cut-off level was set at the median value."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32974187", "locator": "sections[16] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "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:32974187"], "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:GSE10846"], "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:GSE10846"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32974187", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2020.01520", "sha256": "sha256:f7d6fb41a6cb02b37947deb2eb9f3fab61149795970a7aecb55b9a08fb7cbef7", "bytes": 28620, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2020.01520", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7473157", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE10846", "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=GSE10846", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE10846", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM274895", "GSM274896", "GSM274897", "GSM274898", "GSM274899", "GSM274900", "GSM274901", "GSM274902", "GSM274903", "GSM274904", "GSM274905", "GSM274906", "GSM274907", "GSM274908", "GSM274909", "GSM274910", "GSM274911", "GSM274912", "GSM274913", "GSM274914", "GSM274915", "GSM274916", "GSM274917", "GSM274918", "GSM274919", "GSM274920", "GSM274921", "GSM274922", "GSM274923", "GSM274924", "GSM274925", "GSM274926", "GSM274927", "GSM274928", "GSM274929", "GSM274930", "GSM274931", "GSM274932", "GSM274933", "GSM274934", "GSM274935", "GSM274936", "GSM274937", "GSM274938", "GSM274939", "GSM274940", "GSM274941", "GSM274942", "GSM274943", "GSM274944", "GSM274945", "GSM274946", "GSM274947", "GSM274948", "GSM274949", "GSM274950", "GSM274951", "GSM274952", "GSM274953", "GSM274954", "GSM274955", "GSM274956", "GSM274957", "GSM274958", "GSM274959", "GSM274960", "GSM274961", "GSM274962", "GSM274963", "GSM274964", "GSM274965", "GSM274966", "GSM274967", "GSM274968", "GSM274969", "GSM274970", "GSM274971", "GSM274972", "GSM274973", "GSM274974", "GSM274975", "GSM274976", "GSM274977", "GSM274978", "GSM274979", "GSM274980", "GSM274981", "GSM274982", "GSM274983", "GSM274984", "GSM274985", "GSM274986", "GSM274987", "GSM274988", "GSM274989", "GSM274990", "GSM274991", "GSM274992", "GSM274993", "GSM274994", "GSM274995", "GSM274996", "GSM274997", "GSM274998", "GSM274999", "GSM275000", "GSM275001", "GSM275002", "GSM275003", "GSM275004", "GSM275005", "GSM275006", "GSM275007", "GSM275008", "GSM275009", "GSM275010", "GSM275011", "GSM275012", "GSM275013", "GSM275014", "GSM275015", "GSM275016", "GSM275017", "GSM275018", "GSM275019", "GSM275020", "GSM275021", "GSM275022", "GSM275023", "GSM275024", "GSM275025", "GSM275026", "GSM275027", "GSM275028", "GSM275029", "GSM275030", "GSM275031", "GSM275032", "GSM275033", "GSM275034", "GSM275035", "GSM275036", "GSM275037", "GSM275038", "GSM275039", "GSM275040", "GSM275041", "GSM275042", "GSM275043", "GSM275044", "GSM275045", "GSM275046", "GSM275047", "GSM275048", "GSM275049", "GSM275050", "GSM275051", "GSM275052", "GSM275053", "GSM275054", "GSM275055", "GSM275056", "GSM275057", "GSM275058", "GSM275059", "GSM275060", "GSM275061", "GSM275062", "GSM275063", "GSM275064", "GSM275065", "GSM275066", "GSM275067", "GSM275068", "GSM275069", "GSM275070", "GSM275071", "GSM275072", "GSM275073", "GSM275074", "GSM275075", "GSM275076", "GSM275077", "GSM275078", "GSM275079", "GSM275080", "GSM275081", "GSM275082", "GSM275083", "GSM275084", "GSM275085", "GSM275086", "GSM275087", "GSM275088", "GSM275089", "GSM275090", "GSM275091", "GSM275092", "GSM275093", "GSM275094", "GSM275095", "GSM275096", "GSM275097", "GSM275098", "GSM275099", "GSM275100", "GSM275101", "GSM275102", "GSM275103", "GSM275104", "GSM275105", "GSM275106", "GSM275107", "GSM275108", "GSM275109", "GSM275110", "GSM275111", "GSM275112", "GSM275113", "GSM275114", "GSM275115", "GSM275116", "GSM275117", "GSM275118", "GSM275119", "GSM275120", "GSM275121", "GSM275122", "GSM275123", "GSM275124", "GSM275125", "GSM275126", "GSM275127", "GSM275128", "GSM275129", "GSM275130", "GSM275131", "GSM275132", "GSM275133", "GSM275134", "GSM275135", "GSM275136", "GSM275137", "GSM275138", "GSM275139", "GSM275140", "GSM275141", "GSM275142", "GSM275143", "GSM275144", "GSM275145", "GSM275146", "GSM275147", "GSM275148", "GSM275149", "GSM275150", "GSM275151", "GSM275152", "GSM275153", "GSM275154", "GSM275155", "GSM275156", "GSM275157", "GSM275158", "GSM275159", "GSM275160", "GSM275161", "GSM275162", "GSM275163", "GSM275164", "GSM275165", "GSM275166", "GSM275167", "GSM275168", "GSM275169", "GSM275170", "GSM275171", "GSM275172", "GSM275173", "GSM275174", "GSM275175", "GSM275176", "GSM275177", "GSM275178", "GSM275179", "GSM275180", "GSM275181", "GSM275182", "GSM275183", "GSM275184", "GSM275185", "GSM275186", "GSM275187", "GSM275188", "GSM275189", "GSM275190", "GSM275191", "GSM275192", "GSM275193", "GSM275194", "GSM275195", "GSM275196", "GSM275197", "GSM275198", "GSM275199", "GSM275200", "GSM275201", "GSM275202", "GSM275203", "GSM275204", "GSM275205", "GSM275206", "GSM275207", "GSM275208", "GSM275209", "GSM275210", "GSM275211", "GSM275212", "GSM275213", "GSM275214", "GSM275215", "GSM275216", "GSM275217", "GSM275218", "GSM275219", "GSM275220", "GSM275221", "GSM275222", "GSM275223", "GSM275224", "GSM275225", "GSM275226", "GSM275227", "GSM275228", "GSM275229", "GSM275230", "GSM275231", "GSM275232", "GSM275233", "GSM275234", "GSM275235", "GSM275236", "GSM275237", "GSM275238", "GSM275239", "GSM275240", "GSM275241", "GSM275242", "GSM275243", "GSM275244", "GSM275245", "GSM275246", "GSM275247", "GSM275248", "GSM275249", "GSM275250", "GSM275251", "GSM275252", "GSM275253", "GSM275254", "GSM275255", "GSM275256", "GSM275257", "GSM275258", "GSM275259", "GSM275260", "GSM275261", "GSM275262", "GSM275263", "GSM275264", "GSM275265", "GSM275266", "GSM275267", "GSM275268", "GSM275269", "GSM275270", "GSM275271", "GSM275272", "GSM275273", "GSM275274", "GSM275275", "GSM275276", "GSM275277", "GSM275278", "GSM275279", "GSM275280", "GSM275281", "GSM275282", "GSM275283", "GSM275284", "GSM275285", "GSM275286", "GSM275287", "GSM275288", "GSM275289", "GSM275290", "GSM275291", "GSM275292", "GSM275293", "GSM275294", "GSM275295", "GSM275296", "GSM275297", "GSM275298", "GSM275299", "GSM275300", "GSM275301", "GSM275302", "GSM275303", "GSM275304", "GSM275305", "GSM275306", "GSM275307", "GSM275308", "GSM361239", "GSM361240", "GSM361241", "GSM361242", "GSM361243", "GSM361244"], "sample_count": 420, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Prediction of survival in diffuse large B cell lymphoma treated with chemotherapy plus Rituximab", "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:GSE4475", "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=GSE4475", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE4475", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM100454", "GSM100455", "GSM100456", "GSM100457", "GSM100458", "GSM100459", "GSM100460", "GSM100461", "GSM100462", "GSM100463", "GSM100464", "GSM100465", "GSM100466", "GSM100467", "GSM100468", "GSM100469", "GSM100470", "GSM100471", "GSM100472", "GSM100473", "GSM100474", "GSM100475", "GSM100476", "GSM100477", "GSM100478", "GSM100479", "GSM100480", "GSM100481", "GSM100482", "GSM100483", "GSM100484", "GSM100485", "GSM100486", "GSM100487", "GSM100488", "GSM100489", "GSM100490", "GSM100491", "GSM100492", "GSM100493", "GSM100494", "GSM100495", "GSM100496", "GSM100497", "GSM100498", "GSM100499", "GSM100500", "GSM100501", "GSM100502", "GSM100503", "GSM100504", "GSM100505", "GSM100506", "GSM100507", "GSM100508", "GSM100509", "GSM100510", "GSM100511", "GSM100512", "GSM100513", "GSM100514", "GSM100515", "GSM100516", "GSM100517", "GSM100518", "GSM100519", "GSM100520", "GSM100521", "GSM100522", "GSM100523", "GSM100524", "GSM100525", "GSM100526", "GSM100527", "GSM100528", "GSM100529", "GSM100530", "GSM100531", "GSM100532", "GSM100533", "GSM100534", "GSM100535", "GSM100536", "GSM100537", "GSM100538", "GSM100539", "GSM100540", "GSM100541", "GSM100542", "GSM100543", "GSM100544", "GSM100545", "GSM100546", "GSM100547", "GSM100548", "GSM100549", "GSM100550", "GSM100551", "GSM100552", "GSM100553", "GSM100554", "GSM100555", "GSM100556", "GSM100557", "GSM100558", "GSM100559", "GSM100560", "GSM100561", "GSM100562", "GSM100563", "GSM100564", "GSM100565", "GSM100566", "GSM100567", "GSM100568", "GSM100569", "GSM100570", "GSM100571", "GSM100572", "GSM100573", "GSM100574", "GSM100575", "GSM100576", "GSM100577", "GSM100578", "GSM100579", "GSM100580", "GSM100581", "GSM100582", "GSM100583", "GSM100584", "GSM100585", "GSM100586", "GSM100587", "GSM100588", "GSM100589", "GSM100590", "GSM100591", "GSM100592", "GSM100593", "GSM100594", "GSM100595", "GSM100596", "GSM100597", "GSM100598", "GSM100599", "GSM100600", "GSM100601", "GSM100602", "GSM100603", "GSM100604", "GSM100605", "GSM100606", "GSM100607", "GSM100608", "GSM100609", "GSM100610", "GSM100611", "GSM100612", "GSM100613", "GSM100614", "GSM100615", "GSM100616", "GSM100617", "GSM100618", "GSM100619", "GSM100620", "GSM100621", "GSM100622", "GSM100623", "GSM100624", "GSM100625", "GSM100626", "GSM100627", "GSM100628", "GSM100629", "GSM100630", "GSM100631", "GSM100632", "GSM100633", "GSM100634", "GSM100635", "GSM100636", "GSM100637", "GSM100638", "GSM100639", "GSM100640", "GSM100641", "GSM100642", "GSM100643", "GSM100644", "GSM100645", "GSM100646", "GSM100647", "GSM100648", "GSM100649", "GSM100650", "GSM100651", "GSM100652", "GSM100653", "GSM100654", "GSM100655", "GSM100656", "GSM100657", "GSM100658", "GSM100659", "GSM100660", "GSM100661", "GSM100662", "GSM100663", "GSM100664", "GSM100665", "GSM100666", "GSM100667", "GSM100668", "GSM100669", "GSM100670", "GSM100671", "GSM100672", "GSM100673", "GSM100674"], "sample_count": 221, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "A Biologic Definition of Burkitt's Lymphoma from Transcriptional and Genomic Profiling", "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:GSE98588", "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=GSE98588", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE98588", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2601334", "GSM2601335", "GSM2601336", "GSM2601337", "GSM2601338", "GSM2601339", "GSM2601340", "GSM2601341", "GSM2601342", "GSM2601343", "GSM2601344", "GSM2601345", "GSM2601346", "GSM2601347", "GSM2601348", "GSM2601349", "GSM2601350", "GSM2601351", "GSM2601352", "GSM2601353", "GSM2601354", "GSM2601355", "GSM2601356", "GSM2601357", "GSM2601358", "GSM2601359", "GSM2601360", "GSM2601361", "GSM2601362", "GSM2601363", "GSM2601364", "GSM2601365", "GSM2601366", "GSM2601367", "GSM2601368", "GSM2601369", "GSM2601370", "GSM2601371", "GSM2601372", "GSM2601373", "GSM2601374", "GSM2601375", "GSM2601376", "GSM2601377", "GSM2601378", "GSM2601379", "GSM2601380", "GSM2601381", "GSM2601382", "GSM2601383", "GSM2601384", "GSM2601385", "GSM2601386", "GSM2601387", "GSM2601388", "GSM2601389", "GSM2601390", "GSM2601391", "GSM2601392", "GSM2601393", "GSM2601394", "GSM2601395", "GSM2601396", "GSM2601397", "GSM2601398", "GSM2601399", "GSM2601400", "GSM2601401", "GSM2601402", "GSM2601403", "GSM2601404", "GSM2601405", "GSM2601406", "GSM2601407", "GSM2601408", "GSM2601409", "GSM2601410", "GSM2601411", "GSM2601412", "GSM2601413", "GSM2601414", "GSM2601415", "GSM2601416", "GSM2601417", "GSM2601418", "GSM2601419", "GSM2601420", "GSM2601421", "GSM2601422", "GSM2601423", "GSM2601424", "GSM2601425", "GSM2601426", "GSM2601427", "GSM2601428", "GSM2601429", "GSM2601430", "GSM2601431", "GSM2601432", "GSM2601433", "GSM2601434", "GSM2601435", "GSM2601436", "GSM2601437", "GSM2601438", "GSM2601439", "GSM2601440", "GSM2601441", "GSM2601442", "GSM2601443", "GSM2601444", "GSM2601445", "GSM2601446", "GSM2601447", "GSM2601448", "GSM2601449", "GSM2601450", "GSM2601451", "GSM2601452", "GSM2601453", "GSM2601454", "GSM2601455", "GSM2601456", "GSM2601457", "GSM2601458", "GSM2601459", "GSM2601460", "GSM2601461", "GSM2601462", "GSM2601463", "GSM2601464", "GSM2601465", "GSM2601466", "GSM2601467", "GSM2601468", "GSM2601469", "GSM2601470"], "sample_count": 137, "group_sizes": null, "group_sizes_basis": null, "platform": "23432", "taxon": "Homo sapiens", "title": "Genetically-defined Diffuse Large B-cell Lymphoma Subsets Arise by Distinct Pathogenetic Mechanisms and Predicts Outcome", "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:32974187:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b5e309f083a846f9b1bb43392332abf2c436b7eeb16bbf35a90d92f3701c10b9", "bytes": 1622, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T1", "version": null, "note": "Most significantly correlated signaling pathways with matrix metallopeptidase 14 (MMP14) expression, based on their normalized enrichment score (NES) and P-value (top five modules).", "structure": {"pmcid": "PMC7473157", "section_index": 11, "section_title": "Matrix Metallopeptidase 14 Expression Correlation With Clinical Characteristics and Predicted Biological Functions", "row_count": 24, "column_count": 5}, "table": {"label": "TABLE 1", "caption": "Most significantly correlated signaling pathways with matrix metallopeptidase 14 (MMP14) expression, based on their normalized enrichment score (NES) and P-value (top five modules).", "rows": [["", "GO name", "NES", "NOM p-value", "FDR q-value"], ["Positive", "Regulation of macrophage migration", "2.248", "0", "9.46e-04"], ["", "2.246", "0", "", "4.73e-04"], ["", "2.246", "0", "", "3.15e-04"], ["", "Iron ion homeostasis", "2.202", "0", "4.78e-04"], ["", "Collagen catabolic process", "2.199", "0", "3.82e-04"], ["Negative", "Nuclear-transcribed mRNA catabolic process", "−2.112", "0", "5.89e-023"], ["", "Viral gene expression", "-2.031", "0", "1.19e-02"], ["", "Nuclear-transcribed mRNA catabolic process nonsense-mediated decay", "−2.005", "2.08e-03", "1.39e-02"], ["", "rRNA methylation", "−1.993", "2.07e-03", "1.48e-02"], ["", "Translational initiation", "−1.993", "4.23e-03", "1.19e-02"], [""], ["", "KEGG name", "NES", "NOM p-value", "FDR q-value"], [""], ["Positive", "Lysosome", "2.246", "0", "0"], ["", "Glycosaminoglycan degradation", "2.012", "0", "2.11e-02"], ["", "Ecm receptor interaction", "1.990", "0", "2.00e-02"], ["", "Other glycan degradation", "1.986", "0", "1.76e-02"], ["", "Complement and coagulation cascades", "1.917", "0", "3.47e-02"], ["Negative", "RNA polymerase", "−1.729", "2.35e-02", "2.00e-01"], ["", "Ribosome", "−1.644", "4.55e-02", "2.27 e-01"], ["", "Nucleotide excision repair", "−1.636", "4.58e-02", "1.63 e-01"], ["", "Spliceosome", "−1.633", "5.54e-02", "1.24 e-01"], ["", "Base excision repair", "−1.584", "6.11e-02", "1.46 e-01"]], "row_count": 24, "column_count": 5, "numeric_cells": 60, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:32974187:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:52bf77de626b784a7896676d691bf1356ff4d2baa42012965d0e5c764a1026f1", "bytes": 3304, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T2", "version": null, "note": "Correlation analysis between MMP14 and immune cell-related genes and markers, as assessed with Tumor Immune Estimation Resource (TIMER).", "structure": {"pmcid": "PMC7473157", "section_index": 12, "section_title": "Matrix Metallopeptidase 14 Expression Is Correlated With Immune Cell Infiltration in Diffuse Large B-Cell Lymphoma", "row_count": 55, "column_count": 6}, "table": {"label": "TABLE 2", "caption": "Correlation analysis between MMP14 and immune cell-related genes and markers, as assessed with Tumor Immune Estimation Resource (TIMER).", "rows": [["Description", "Gene markers", "DLBCL"], ["", "", "No adjustment", "Purity adjusted"], ["", "", "Cor", "P", "Cor", "P"], ["B cell", "CD19", "-0.254", "8.19e-02", "−0.259", "1.02e-01"], ["", "CD79A", "−0.147", "3.18e-01", "−0.161", "3.15e-01"], ["Monocyte", "CD86", "0.253", "8.24e-02", "0.319", "4.20e-02"], ["", "CD115 (CSF1R)", "0.636", "2.2e-06", "0.589", "5.07e-05"], ["TAM", "CCL2", "0.281", "5.32e-02", "0.265", "9.43e-02"], ["", "CD68", "0.782", "0e-00", "0.786", "1.18e-09"], ["", "IL10", "0.359", "1.26e-02", "0.276", "8.05e-02"], ["Macrophage M0", "MMP9", "0.716", "5.92e-08", "0.66", "2.73e-06"], ["", "NCF2", "0.601", "9.70e-08", "0.556", "1.59e-04"], ["", "ACP5", "0.633", "2.50e-06", "0.558", "1.49e-04"], ["", "PLA2G7", "0.687", "2.27e-07", "0.668", "1.85e-06"], ["Macrophage M1", "INOS (NOS2)", "0.292", "4.44e-02", "0.181", "2.57e-01"], ["", "IRF5", "0.197", "1.79e-01", "0.037", "8.16e-01"], ["", "COX2(PTGS2)", "0.246", "9.2e-02", "0.061", "3.14e-01"], ["Macrophage M2", "CD163", "0.465", "9.84e-04", "0.488", "1.21e-03"], ["", "VSIG4", "0.502", "8.36e-04", "0.532", "3.48e-04"], ["", "MS4A4A", "0.281", "5.3e-02", "0.253", "1.10e-01"], ["Neutrophils", "CD66b (CEACAM8)", "0.252", "8.35e-02", "0.223", "1.61e-01"], ["", "CD11b (ITGAM)", "0.765", "0e-00", "0.765", "5.55e-09"], ["", "CCR7", "0.018", "9.05e-01", "−0.141", "3.79e-01"], ["Dendritic cells", "HLA-DPB1", "0.047", "7.48e-01", "0.058", "7.16e-01"], ["", "HLA-DQB1", "−0.038", "7.95e-01", "0.055", "7.33e-01"], ["", "HLA-DRA", "0.117", "4.25e-01", "0.072", "6.55e-01"], ["", "HLA-DPA1", "0.132", "3.72e-01", "0.101", "5.30e-01"], ["", "BDCA-1(CD1C)", "−0.153", "2.97e-01", "−0.203", "2.03e-01"], ["", "BDCA-4(NRP1)", "0.536", "1.13e-04", "0.421", "6.15e-03"], ["", "CD11c (ITGAX)", "0.443", "1.79e-03", "0.345", "2.72e-02"], ["CD8 + T cell", "CD8A", "0.205", "1.62e-01", "0.061", "7.05e-01"], ["", "CD8B", "0.125", "3.95e-01", "0.021", "8.94e-01"], ["T cell (general)", "CD3D", "−0.022", "8.8e-01", "0.282", "7.37e-02"], ["", "CD3E", "0.115", "4.36e-01", "−0.065", "6.85e-01"], ["", "CD2", "0.166", "2.58e-01", "0.031", "8.48e-01"], ["Natural killer cell", "KIR2DL1", "0.048", "7.48e-01", "−0.1", "5.33e-01"], ["", "KIR2DL3", "0.15", "3.08e-01", "0.063", "6.96e-01"], ["", "KIR2DL4", "0.324", "2.48e-02", "0.204", "2.02e-01"], ["", "KIR3DL1", "0.087", "5.58e-01", "0.056", "7028e-01"], ["", "KIR3DL2", "0.047", "7.49e-01", "−0.062", "7.00e-01"], ["", "KIR3DL3", "-0.117", "4.27e-01", "−0.112", "4.87e-01"], ["", "KIR2DS4", "0.09", "5.44e-01", "0.013", "9.37e-01"], ["Th1", "T-bet (TBX21)", "0.233", "1.11e-01", "0.14", "3.81e-01"], ["", "STAT4", "0.16", "2.76e-01", "-0.052", "7.45e-01"], ["", "STAT1", "0.472", "8.19e-04", "0.442", "3.85e-03"], ["", "IFN-γ (IFNG)", "0.532", "2.15e-02", "0.291", "6.52e-02"], ["", "TNF-α (TNF)", "0.338", "1.92e-02", "0.265", "9.38e-02"], ["", "GATA3", "0.183", "2.13e-01", "0.035", "8.27e-01"], ["", "STAT6", "0.146", "3.2e-01", "0.076", "6.39e-01"], ["", "STAT5A", "0.224", "1.26e-01", "0.225", "1.58e-01"], ["", "IL13", "0.067", "9.63e-01", "−0.026", "8.58e-01"], ["Tfh", "BCL6", "-0.134", "3.61e-01", "-0.033", "8.38e-01"], ["", "IL21", "0.167", "2.58e-01", "0.072", "6.57e-01"], ["Th17", "STAT3", "0.402", "4.89e-03", "0.315", "4.48e-02"], ["", "IL17A", "0.081", "5.83e-01", "0.024", "8.82e-01"]], "row_count": 55, "column_count": 6, "numeric_cells": 225, "header_rows": 3, "locator": "section[12]/table-wrap[1]#T2"}}], "gaps": ["asset:data:geo:GSE10846 not downloaded", "asset:data:geo:GSE10846 licence not read", "asset:data:geo:GSE4475 not downloaded", "asset:data:geo:GSE4475 licence not read", "asset:data:geo:GSE98588 not downloaded", "asset:data:geo:GSE98588 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Kaplan–Meier survival analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We performed Kaplan–Meier analysis to measure the OS of the 48 patients obtained from TCGA based on the abundance ratio of the 11 identified immune cell types, for which the cut-off level was set at the median value."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Kaplan–Meier survival analysis), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE98588", "GSE10846", "GSE4475"], "resolved_accessions": ["GSE98588", "GSE10846", "GSE4475"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."], "basis": "The paper names GSE98588, GSE10846, GSE4475 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:32974187", "data:geo:GSE10846", "asset:table:pmid:32974187:1", "asset:table:pmid:32974187:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE10846"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:22:45Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 20354, "completion_tokens": 2049, "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:32974187", "type": "paper", "label": "pmid:32974187"}, {"id": "source:pmid:32974187", "type": "manuscript", "label": "PMID 32974187 full text"}, {"id": "data:geo:GSE10846", "type": "dataset", "label": "GEO GSE10846"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32974187", "type": "paper", "label": "pmid:32974187"}, {"id": "source:pmid:32974187", "type": "manuscript", "label": "PMID 32974187 full text"}, {"id": "data:geo:GSE10846", "type": "dataset", "label": "GEO GSE10846"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32974187", "type": "extraction", "used": ["source:pmid:32974187"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE10846", "type": "accession_resolution", "used": ["data:geo:GSE10846"], "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:32974187", "parent_hash": "sha256:9f570cdbb526c4e8bd08f52b1dd09d8356952ae1ead5c5cf76afb1881ab58319", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE10846 licence not read", "asset:data:geo:GSE10846 not downloaded", "asset:data:geo:GSE4475 licence not read", "asset:data:geo:GSE4475 not downloaded", "asset:data:geo:GSE98588 licence not read", "asset:data:geo:GSE98588 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"]}