← All .science files
pmid:34225739
Integrative analysis of ceRNA network reveals functional lncRNAs associated with independent recurrent prognosis in colon adenocarcinoma.
Yinling Mao · Jiachen Lv · Li Jiang · Yihui Wang
Cancer cell international · 2021 doi:10.1186/s12935-021-02069-6
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 · 4 items
claims array · 2 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 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 · 585 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 7 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
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 11 items
[0] array · 3 items
[1] array · 4 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[10] array · 5 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 20 items
[0] array · 4 items
[1] array · 3 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[10] array · 5 items
[11] array · 5 items
[12] array · 5 items
[13] array · 5 items
[14] array · 5 items
[15] array · 5 items
[16] array · 5 items
[17] array · 5 items
[18] array · 5 items
[19] array · 5 items
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 9 items
[0] array · 3 items
[1] array · 4 items
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
gaps array · 2 items
analysis object · 4 fields
methods array · 7 items
[0] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[2] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[3] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[4] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[5] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[6] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 1 item
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 3 items
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 3 items
assets array · 6 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 · 7 items
assays array · 3 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 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 · 3 items
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34225739", "kind": "science-record", "revision": 8, "content_hash": "sha256:a5f9c4a582509942d452aed837875f3fdf5800e2409029034557f86e24350426", "created_at": "2026-11-01T15:41:42Z", "updated_at": "2026-11-01T22:47:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrative analysis of ceRNA network reveals functional lncRNAs associated with independent recurrent prognosis in colon adenocarcinoma.", "doi": "10.1186/s12935-021-02069-6", "pmid": "34225739", "authors": ["Yinling Mao", "Jiachen Lv", "Li Jiang", "Yihui Wang"], "journal": "Cancer cell international", "year": 2021, "abstract": "BACKGROUND: Long non-coding RNAs (lncRNAs), acting as competing endogenous RNA (ceRNA) have been reported to regulate the expression of targeted genes by sponging miRNA in colon adenocarcinoma (COAD).\nMETHODS: However, their potential implications for recurrence free survival prognosis and functional roles remains largely unclear in COAD. In this study, we downloaded the TCGA dataset (training dataset) and GSE39582 (validation dataset) of COAD patients with prognostic information.\nRESULTS: A total of 411 differentially expressed genes (DElncRNAs: 12 downregulated and 43 upregulated), 18 DE miRNAs (9 downregulated and 9 upregulated) and 338 DEmRNAs (113 downregulated and 225 upregulated) were identified in recurrence samples compared with non-recurrence samples with the thresholds of FDR < 0.05 and |log2FC|> 0.263. Based on six signature lncRNAs (LINC00899, LINC01503, PRKAG2-AS1, RAD21-AS1, SRRM2-AS1 and USP30-AS1), the risk score (RS) system was constructed. Two prognostic clinical features, including pathologic stage and RS model status were screened for building the nomogram survival model. Moreover, a recurrent-specific ceRNA network was successfully constructed with 2 signature lncRNAs, 4 miRNAs and 113 mRNAs. Furthermore, we further manifested that SRRM2-AS1 predicted a poor prognosis in COAD patients. Furthermore, knockdown of SRRM2-AS1 significantly suppressed cell proliferation, migration, invasion and EMT markers in HT-29 and SW1116 cells.\nCONCLUSION: These identified novel lncRNA signature and ceRNA network associated with recurrence prognosis might provide promising therapeutic targets for COAD patients.", "claims": [{"id": "claim-method", "statement": "Then, differentially expressed DERs, including DElncRNAs, DEmiRNAs and DEmRNAs were screened between recurrence and non-recurrence specimens using the limma package (software version 3.34.7) of R [21].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34225739", "locator": "sections[4] \"Analysis of differential expressed RNAs (DERs)\" paragraph 2", "quote": "Then, differentially expressed DERs, including DElncRNAs, DEmiRNAs and DEmRNAs were screened between recurrence and non-recurrence specimens using the limma package (software version 3.34.7) of R [21]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34225739", "locator": "sections[33] \"Availability of data and materials\" paragraph 2", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:34225739"], "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:GSE39582"], "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:GSE39582"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34225739", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12935-021-02069-6", "sha256": "sha256:3978eaa6712471f15a596f41f21c55c583a85b85a9dbec44c190d6df62dac361", "bytes": 49164, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12935-021-02069-6", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8259330", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"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 datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "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}}, {"id": "asset:table:pmid:34225739:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e95ee5fc29a18e7cef871bae59c936cab378b8f322e599cd64900b8c82857f5c", "bytes": 654, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#Tab1", "version": null, "note": "A 6-lncRNA signature significantly and independently correlated to prognosis", "structure": {"pmcid": "PMC8259330", "section_index": 18, "section_title": "Construction and validation of 6 lncRNA-based prognostic signature", "row_count": 7, "column_count": 5}, "table": {"label": "Table 1", "caption": "A 6-lncRNA signature significantly and independently correlated to prognosis", "rows": [["Symbol", "coef", "Pr ( >|z|)", "Hazard Ratio", "95%CI"], ["LINC00899", "1.0109537", "0.041095", "2.852", "1.875–4.298"], ["LINC01503", "0.6383124", "0.003025", "2.150", "1.245–3.712"], ["PRKAG2-AS1", "− 0.499666", "0.000635", "0.483", "0.310–0.752"], ["RAD21-AS1", "− 1.977238", "0.002405", "0.040", "0.018–0.186"], ["SRRM2-AS1", "2.0163898", "0.01163", "3.511", "1.624–7.592"], ["USP30-AS1", "− 0.386197", "0.04873", "0.694", "0.450–0.969"]], "row_count": 7, "column_count": 5, "numeric_cells": 29, "header_rows": 1, "locator": "section[18]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:34225739:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2205e3466cebbab5e86accf2c12c9174f680a88bd04f1fb14859c70137a7640e", "bytes": 1118, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[19]/table-wrap[1]#Tab2", "version": null, "note": "Determination of prognostic clinical factors", "structure": {"pmcid": "PMC8259330", "section_index": 19, "section_title": "Building nomogram based on prognostic clinical factors and the six-lncRNA signature", "row_count": 11, "column_count": 5}, "table": {"label": "Table 2", "caption": "Determination of prognostic clinical factors", "rows": [["Variables", "Univariate analysis", "Multivariate analysis"], ["HR (95% CI)", "P value", "HR (95% CI)", "P value"], ["Age (years, mean ± SD)", "0.989 (0.971–1.006)", "1.937E−01", "NA", "NA"], ["Gender (Male/Female)", "1.630 (1.030–2.579)", "3.521E−02*", "1.567 (0.984–2.495)", "5.872E−02"], ["Pathologic M (M0/M1/−)", "3.498 (2.015–6.072)", "2.162E−06*", "2.358 (0.870–6.391)", "9.165E−02"], ["Pathologic N (N0/N1/N2)", "0.909 (0.537–1.540)", "7.226E−01", "NA", "NA"], ["Pathologic T (T1/T2/T3/T4)", "2.310 (1.484–3.597)", "3.167E−04*", "1.552 (0.909–2.649)", "1.070E−01"], ["Pathologic stage (I/II/III/IV/−)", "1.849 (1.423–2.402)", "2.874E−06*", "1.482 (1.105–1.986)", "8.541E−03*"], ["lncRNA RS model (High/Low)", "2.925 (1.773–4.825)", "1.062E−05*", "2.438 (1.443–4.118)", "8.610E−04*"], ["Recurrence (Yes/No)", "NA", "NA", "NA", "NA"], ["Recurrence free survival time (months, mean ± SD)", "NA", "NA", "NA", "NA"]], "row_count": 11, "column_count": 5, "numeric_cells": 26, "header_rows": 2, "locator": "section[19]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:34225739:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:cb91323ad96b68f463d00224524fb86d8f6d4a7a7cc99c922ae899817dd7f178", "bytes": 925, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[22]/table-wrap[1]#Tab3", "version": null, "note": "Association between SRRM2-AS1 expression and clinicopathological characteristics of COAD patients", "structure": {"pmcid": "PMC8259330", "section_index": 22, "section_title": "SRRM2-AS1 was upregulated in COAD and high SRRM2-AS1 level predicted worse prognosis", "row_count": 20, "column_count": 5}, "table": {"label": "Table 3", "caption": "Association between SRRM2-AS1 expression and clinicopathological characteristics of COAD patients", "rows": [["Characteristics", "Cases (n = 60)", "SRRM2-AS1 expression", "P value"], ["Low (n = 22)", "High (n = 38)", "(chi-square test)"], ["Age", "", "", "", "0.310"], ["< 55", "26", "10", "16", ""], ["≥ 55", "34", "12", "22", ""], ["Gender", "", "", "", "0.746"], ["Male", "32", "9", "23", ""], ["Female", "28", "13", "15", ""], ["Tumor size (cm)", "", "", "", "0.031*"], ["< 5", "38", "16", "22", ""], ["≥ 5", "22", "6", "16", ""], ["Lymph node metastasis", "", "", "", "0.023*"], ["Negative", "35", "15", "20", ""], ["Positive", "25", "7", "18", ""], ["TNM stage", "", "", "", "0.009*"], ["I–II", "33", "15", "18", ""], ["III–IV", "27", "7", "20", ""], ["Differentiation", "", "", "", "0.295"], ["Well/moderately", "42", "15", "27", ""], ["Poorly", "18", "7", "11", ""]], "row_count": 20, "column_count": 5, "numeric_cells": 49, "header_rows": 2, "locator": "section[22]/table-wrap[1]#Tab3"}}, {"id": "asset:table:pmid:34225739:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:ec106a7c69b177fa6ea81d48930dbb0c8c704c515517cf50f24dbbd0261a18fb", "bytes": 871, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[22]/table-wrap[2]#Tab4", "version": null, "note": "Cox regression analysis of prognostic predictors affecting overall survival in COAD patients", "structure": {"pmcid": "PMC8259330", "section_index": 22, "section_title": "SRRM2-AS1 was upregulated in COAD and high SRRM2-AS1 level predicted worse prognosis", "row_count": 9, "column_count": 5}, "table": {"label": "Table 4", "caption": "Cox regression analysis of prognostic predictors affecting overall survival in COAD patients", "rows": [["Characteristics", "Univariate analysis", "Multivariate analysis"], ["HR (95% CI)", "P value", "HR (95% CI)", "P value"], ["Age", "1.102 (0.835–1.998)", "0.375", "NA", "NA"], ["Gender", "0.895 (0.486–1.278)", "0.812", "NA", "NA"], ["Tumor size (cm)", "3.214 (2.278–4.325)", "0.023*", "2.845 (1.696–3.142)", "0.018*"], ["Lymph node metastasis", "2.013 (1.843–3.204)", "0.028*", "1.734 (0.996–2.512)", "0.042*"], ["TNM stage", "1.421 (1.046–2.417)", "0.013*", "1.989 (1.296–2.751)", "0.051"], ["Differentiation", "1.204 (0.712–2.048)", "0.475", "NA", "NA"], ["SRRM2-AS1 expression", "0.998 (0.546–1.312)", "0.013*", "0.853 (0.496–1.143)", "0.024*"]], "row_count": 9, "column_count": 5, "numeric_cells": 24, "header_rows": 2, "locator": "section[22]/table-wrap[2]#Tab4"}}], "gaps": ["asset:data:geo:GSE39582 not downloaded", "asset:data:geo:GSE39582 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Then, differentially expressed DERs, including DElncRNAs, DEmiRNAs and DEmRNAs were screened between recurrence and non-recurrence specimens using the limma package (software version 3.34.7) of R [21]."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox regression"}}, {"id": "method-4", "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": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-5", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson Correlation"}}, {"id": "method-6", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "hierarchical clustering"}}, {"id": "method-7", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "chi-square"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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"], "resolved_accessions": ["GSE39582"], "statements": ["The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE39582 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:34225739", "data:geo:GSE39582", "asset:table:pmid:34225739:1", "asset:table:pmid:34225739:2", "asset:table:pmid:34225739:3", "asset:table:pmid:34225739:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE39582"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:31:54Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 41204, "completion_tokens": 1507, "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:34225739", "type": "paper", "label": "pmid:34225739"}, {"id": "source:pmid:34225739", "type": "manuscript", "label": "PMID 34225739 full text"}, {"id": "data:geo:GSE39582", "type": "dataset", "label": "GEO GSE39582"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34225739", "type": "paper", "label": "pmid:34225739"}, {"id": "source:pmid:34225739", "type": "manuscript", "label": "PMID 34225739 full text"}, {"id": "data:geo:GSE39582", "type": "dataset", "label": "GEO GSE39582"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34225739", "type": "extraction", "used": ["source:pmid:34225739"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE39582", "type": "accession_resolution", "used": ["data:geo:GSE39582"], "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:34225739", "parent_hash": "sha256:a7f0371e323c945e25a6bdcf9f4567619491d5afa9d54b56d15d031f9f538430", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE39582 licence not read", "asset:data:geo:GSE39582 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["oor prognosis in COAD patients. Furthermore, knockdown of SRRM2-AS1 significantly suppressed cell p", ".8 in R3.4.1 language [23]. Cell culture and transfection Four COAD cell lines (HT-29, DLD-1, SW1116 a", "of SRRM2-AS1 in HT-29 and SW1116 cells. Cell transfection was achieved using Lipofectamine 3000 (Invit", "d, CA). Samples were harvested after 48 h of transfection. Statistical analysis The statistical analys"], "order_basis": "paper_text_order:1435", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["re Collection (ATCC, Manassas, VA, USA). All cell lines were cultured in DMEM medium (Gibco, Carlsbad, CA) with 10", "TCC, Manassas, VA, USA). All cell lines were cultured in DMEM medium (Gibco, Carlsbad, CA) with 10% f"], "order_basis": "paper_text_order:2833", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Then, differentially expressed DERs, including DElncRNAs, DEmiRNAs and DEmRNAs were screened between recurrence and non-recurrence specimens using the limma package (software version 3.34.7) of R [21]."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}