Identification of Novel lncRNAs Related to Colorectal Cancer Through Bioinformatics Analysis.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39949372", "kind": "science-record", "revision": 2, "content_hash": "sha256:fe539930c366f7b675fb74bd513e180e4478dd0c5cad0b66f55aa06557771f03", "created_at": "2026-11-01T10:25:49Z", "updated_at": "2026-11-01T14:01:34Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Identification of Novel lncRNAs Related to Colorectal Cancer Through Bioinformatics Analysis.", "doi": "10.1155/bmri/5538575", "pmid": "39949372", "authors": null, "journal": "BioMed research international", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "quantitative", "state": "complete", "target": {"value": 6763.0, "unit": "degs", "tolerance": null, "source": "chars 487-670 of source sha256 b1f222b62c24952b360e18202d83259818cd6f1d206bd3a7057965d4b4b9dd58"}, "evidence": [{"asset": "source:pmid:39949372", "locator": "chars 487-670 of source sha256 b1f222b62c24952b360e18202d83259818cd6f1d206bd3a7057965d4b4b9dd58", "quote": "Analysis revealed 6763 DEGs (p < 0.05 and |log fold change (FC)| ≥ 0.5) that include differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA)."}]}], "gaps": ["abstract", "authors"]}, "experiment": {"state": "partial", "objective": "the headline numerical result the paper states for its main finding", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate and its interval from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The number a replication must land on, and the sentence it came from.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:39949372"], "outputs": ["the published estimate, its unit and its interval"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data behind the published result", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:not_downloaded", "description": "The published result cannot be recomputed without the data the paper analysed.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the analysis programme", "kind": "analysis", "state": "blocked", "blocked_on": "no owned computational capability is bound to this experiment", "description": "Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:39949372", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the registered result"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:39949372' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39949372", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/bmri/5538575", "sha256": "sha256:b1f222b62c24952b360e18202d83259818cd6f1d206bd3a7057965d4b4b9dd58", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/bmri/5538575", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:39949372:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:be24a4a45033001db971243d7f5485d8aa7324c6b425a92c30acea33e47fc695", "bytes": 3521, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#tab1", "version": null, "note": "Top upregulated lncRNAs in the analysis of GSE134834 microarray related to CRC. CRC: colorectal cancer, FC: fold change, lncRNA: long noncoding RNA.", "structure": {"pmcid": "PMC11824705", "section_index": 4, "section_title": "2.2. Preprocessing and Analysis of Raw Dataset", "row_count": 23, "column_count": 8}, "table": {"label": "Table 1", "caption": "Top upregulated lncRNAs in the analysis of GSE134834 microarray related to CRC. CRC: colorectal cancer, FC: fold change, lncRNA: long noncoding RNA.", "rows": [["Gene symbol", "lncRNA ID", "Ensemble gene ID", "Official name", "Log (FC)", "p value", "Adjusted p value", "Function in CRC"], ["lncRNA p3467", "ENST00000561864.1", "ENSG00000261650.1", "RP11-474D1.4 (LINC02418)", "4.480166", "2.85e − 06", "0.001741", "High expression of lncRNA p3467 promoted cancer progression in colon cancer cells [21, 22]"], ["lncRNA p15938", "ENST00000500112.1", "ENSG00000247844.1", "RP11-255B23.3", "4.028627", "5.46e − 07", "0.00082", "—"], ["lncRNA p30155", "XR_108886.3", "LOC100507056", "IDLOC100507056", "3.962785", "9.27e − 07", "0.001041", "—"], ["lncRNA p15421", "ENST00000419422.1", "ENSG00000232445.1", "RP11-132A1.4 (LNCPRESS1)", "3.776749", "4.71e − 06", "0.002226", "RP11-132A1.4 is upregulated in tissue from colon cancer [23]"], ["lncRNA p39026_v4", "ENST00000437781.1", "ENSG00000206195.6", "AP000525.9", "3.665108", "1.30e − 05", "0.003626", "High expression in CRC [24]"], ["lncRNA p15430", "ENST00000602761.1", "ENSG00000228742.5", "RP5-884M6.1", "3.471953", "1.41e − 05", "0.003794", "High expression in colon adenocarcinoma [24, 25]"], ["lncRNA p34144_v4", "ENST00000447298.1", "ENSG00000130600.10", "H19-014", "3.388798", "2.04e − 05", "0.004494", "—"], ["LOC340340", "Uncharacterized LOC340340", "—", "—", "3.239423", "8.20e − 05", "0.010084", "—"], ["lncRNA p29027", "ENST00000414790.1", "ENSG00000130600.10", "H19-001", "3.230258", "1.37e − 05", "0.003769", "—"], ["lncRNA p34360_v4", "ENST00000427798.1", "ENSG00000225210.5", "AL589743.1 (DUXAP9/LINC01296)", "3.207409", "4.19e − 05", "0.007123", "LINC01296 knockdown inhibited colon cancer cell proliferation, migration, and invasion in vivo [26]"], ["lncRNA p17009", "ENST00000456532.1", "ENSG00000231566.1", "RP5-1158E12.3", "3.193662", "7.45e − 07", "0.000929", "High expression of LINC02595 promoted tumor progression in CRC [24]"], ["lncRNA p30261", "uc004dgk.1", "AK098783", "", "3.089308", "1.29e − 06", "0.001291", "LncRNA-AK098783 expression level was frequently higher in CRC and RT-PCR [27]"], ["lncRNA p24045", "TCONS_00015168", "XLOC_007214", "linc-FAM84B-8", "3.084878", "1.22e − 06", "0.001291", "—"], ["lncRNA p23831", "TCONS_00014191", "XLOC_006200", "linc-PIK3CG-1", "3.08157", "0.000903", "0.029689", "—"], ["lncRNA p21811", "TCONS_00029614", "XLOC_014268", "linc-PPARA-1", "3.058199", "3.71e − 07", "0.00072", "—"], ["lncRNA p9376", "ENST00000424322.1", "ENSG00000227400.2", "AC012501.2", "3.050053", "0.001343", "0.035616", "—"], ["lncRNA p16370", "ENST00000521586.1", "ENSG00000253929.1", "RP11382A18.2", "2.990761", "2.45e − 05", "0.004912", "Colon cancer risk SNPs [28]"], ["lncRNA p21975", "TCONS_00006729", "XLOC_003364", "linc-BCL6-5", "2.926155", "0.000445", "0.0216", "—"], ["lncRNA p2786", "ENST00000544553.1", "ENSG00000256940.1", "RP11783K16.5 (PPP1R14B-AS1)", "2.904332", "2.08e − 05", "0.004494", "High expression in CRC [24]"], ["lncRNA p35380_v4", "ENST00000521989.2", "ENSG00000253414.2", "RP11150O12.6", "2.900774", "0.000235", "0.01617", "Upregulated in CRC cells [29, 30]"], ["lncRNA p956", "ENST00000432653.1", "ENSG00000234578.1", "RP4-784A16.1", "2.865494", "7.09e − 07", "0.000918", "—"], ["lncRNA p10603", "ENST00000445003.1", "ENSG00000224397.1", "RP11-290F20.3", "2.788621", "0.000184", "0.014888", "High expression of LINC01272, promoted EMT, and metastasis by regulating miR-876/ITGB2 [31]"]], "row_count": 23, "column_count": 8, "numeric_cells": 162, "header_rows": 1, "locator": "section[4]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:39949372:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0ff729c4aaf9457d5c63ef969402365a354b631c0549e11f098d2d3bcbd82ed6", "bytes": 3231, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[2]#tab2", "version": null, "note": "Detail of top downregulated lncRNAs in the analysis of GSE134834 microarray related to CRC. CRC: colorectal cancer, FC: fold change, lncRNA: long noncoding RNA.", "structure": {"pmcid": "PMC11824705", "section_index": 4, "section_title": "2.2. Preprocessing and Analysis of Raw Dataset", "row_count": 22, "column_count": 8}, "table": {"label": "Table 2", "caption": "Detail of top downregulated lncRNAs in the analysis of GSE134834 microarray related to CRC. CRC: colorectal cancer, FC: fold change, lncRNA: long noncoding RNA.", "rows": [["Gene symbol", "lncRNA ID", "Ensemble gene ID", "Official name", "Log (FC)", "p value", "Adjusted p value", "Function in CRC"], ["lncRNA p33911", "uc.217+", "uc.217+", "uc.217+", "−4.93989", "7.23e − 06", "0.002648", "Decreased in CRC tissue [24]"], ["lncRNA p33840", "uc022axe.1", "FW340046", "auc022axe.1", "−3.893", "0.000264", "0.017247", "Decreased in CRC tissue [24]"], ["lncRNA p4715", "ENST00000497872.2", "ENSG00000253701.1", "AL928768.3", "−3.8548", "0.000469", "0.02198", "Decreased in CRC tissue [32]"], ["lncRNA p12653", "ENST00000506514.1", "ENSG00000249453.1", "RP13-497K6.1", "−3.58082", "5.85e − 05", "0.0087", "Decreased in CRC tissue [24]"], ["lncRNA p16717", "ENST00000422420.1", "ENSG00000240498.2", "CDKN2B-AS1", "−3.52951", "0.000343", "0.019", "Decreased in CRC. CDKN2B-AS induced cell apoptosis and suppressed EMT. CDKN2B-AS1 regulates cell growth and survival by targeting DUSP1 [33]"], ["lncRNA p28599", "ASO1844", "ASO1844", "Accession=AK097806", "−3.49506", "1.67e − 05", "0.004132", "—"], ["lncRNA p22463", "TCONS_00008010", "XLOC_003474", "linc-SOD3-2", "−3.45933", "9.77e − 05", "0.011", "—"], ["lncRNA p20354", "TCONS_00025506", "XLOC_012317", "linc-TNRC6C-3", "−3.37675", "0.000218", "0.015", "—"], ["lncRNA p20353", "TCONS_00025200", "XLOC_012317", "linc-TNRC6C-3", "−3.31869", "0.00018", "0.014", "—"], ["lncRNA p27381", "uc.70-", "uc.70-", "uc.70-", "−3.29996", "2.42e − 05", "0.0041", "—"], ["lncRNA p10205", "ENST00000416200.1", "ENSG00000225953.2", "SATB2-AS1", "−3.26443", "1.23e − 05", "0.003", "Decreased in CRC tissue, suppressed CRC aggressiveness by inhibiting SATB2-dependent snail transcription and EMT [34]"], ["lncRNA p25200", "NR_026542.1", "C21orf88", "C21 orf88(B3GALT5-AS1)", "−3.17449", "0.000467", "0.021", "Decreased in CRC tissue, the suppressive role of B3GALT5-AS1/miR-203/EMT regulation axis was in colon cancer liver metastasis [35, 36]"], ["lncRNA p16220", "ENST00000526382.1", "ENSG00000255130.1", "RP11-396J6.1-001", "−3.12744", "1.03e − 05", "0.003", "—"], ["lncRNA p20355", "TCONS_00025507", "XLOC_012317", "linc-TNRC6C-3", "−3.08187", "0.000289", "0.017", "—"], ["lncRNA p25346", "NR_024418.1", "LOC389332", "LOC389332", "−3.06741", "8.12e − 05", "0.01", "Decreased in CRC tissue. LOC389332 exhibited longer overall survival time than patients with low expression levels of these genes [37]"], ["lncRNA p11319", "ENST00000425296.1", "ENSG00000224822.1", "THRB-IT1", "−2.98159", "2.08e − 05", "0.0044", "—"], ["lncRNA p12499", "ENST00000508106.1", "ENSG00000234828.3", "RP11-526A4.1", "−2.81665", "0.000444", "0.02", "—"], ["lncRNA RNA143457|tRNA_374_71", "RNA143457|tRNA_374_71", "", "", "−2.8047", "7.57e − 05", "0.0097", "—"], ["lncRNA p21571", "TCONS_00028228", "XLOC_013571", "linc-PFDN4-2", "−2.65782", "0.000291", "0.0179", "—"], ["lncRNA p7182", "ENST00000577761.1", "ENSG00000266878.1", "RP11-1090M7.2", "−2.46434", "0.000319", "0.0183", "—"], ["lncRNA p42656_v4", "NR_104064.1", "None", "", "−2.43954", "0.00049", "0.0224", "—"]], "row_count": 22, "column_count": 8, "numeric_cells": 148, "header_rows": 1, "locator": "section[4]/table-wrap[2]#tab2"}}, {"id": "asset:table:pmid:39949372:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:deb0d99142d657872a793bb285178b2eec1861ecb17862fddd755ece48311b74", "bytes": 1482, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#tab3", "version": null, "note": "Top DEmRNA in CRC based on analyses of the GSE134834 dataset. FC: fold change, DEmRNA: differentially expressed mRNA, CRC: colorectal cancer.", "structure": {"pmcid": "PMC11824705", "section_index": 9, "section_title": "3.1. Identification of DEG", "row_count": 11, "column_count": 6}, "table": {"label": "Table 3", "caption": "Top DEmRNA in CRC based on analyses of the GSE134834 dataset. FC: fold change, DEmRNA: differentially expressed mRNA, CRC: colorectal cancer.", "rows": [["Gene symbol", "Log FC", "p value", "Adjusted p value", "Expression and function in CRC in literature", "References"], ["MMP7", "6.941794", "7.06e − 10", "2.38e − 05", "Upregulated: Potential prognostic marker in CRC", "[41, 42]"], ["REG1A", "6.181124", "0.000264", "0.017247", "Upregulated: Potential prognostic marker in CRC", "[43, 44]"], ["THBS2", "6.164384", "3.78e − 09", "4.66e − 05", "Upregulated: Potential prognostic marker in CRC", "[45]"], ["CST2", "5.719364", "3.17e − 07", "0.000667", "Upregulated: Potential prognostic marker in CRC", "[46]"], ["CST1", "5.669326", "1.20e − 07", "0.000367", "Upregulated in CRC tissues", "[47–49]"], ["FOXQ1", "5.266674", "3.85e − 07", "0.00072", "Upregulated: Potential prognostic biomarker", "[50–52]"], ["CA1", "−6.90487", "0.000302", "0.018054", "Downregulated: Patients with lower CA1 expression levels had a worse prognosis", "[53]"], ["GCG", "−6.34476", "1.13e − 05", "0.003345", "Downregulated: Had a major role in suppressing the development of CRC", "[52, 54]"], ["SST", "−5.74713", "2.93e − 07", "0.000659", "Downregulated in CRC: Promising prognostic biomarkers", "[52, 55]"], ["CD177", "−5.57313", "0.00013", "0.012561", "Downregulated in CRC tissue", "[56, 57]"]], "row_count": 11, "column_count": 6, "numeric_cells": 41, "header_rows": 1, "locator": "section[9]/table-wrap[1]#tab3"}}, {"id": "asset:table:pmid:39949372:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5baeedcda5a35573601e4099ac12c17d06332f1af8c0fa1ed5b6ae42b7932156", "bytes": 2282, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#tab4", "version": null, "note": "Lightpink4 and pink modules enrichment results of analysis of GSE134834 microarray for CRC.", "structure": {"pmcid": "PMC11824705", "section_index": 11, "section_title": "3.3. Module Pathway Enrichment", "row_count": 29, "column_count": 4}, "table": {"label": "Table 4", "caption": "Lightpink4 and pink modules enrichment results of analysis of GSE134834 microarray for CRC.", "rows": [["Lightpink4 module gene ontology", "Pink module gene ontology"], ["Biological pathway", "p value", "Biological pathway", "p value"], ["Cell cycle, mitotic", "1.51e − 33", "β1 integrin cell surface interactions", "7.32e − 05"], ["DNA replication", "5.9e − 28", "Endothelin", "0.000101"], ["Mitotic M-M/G1 phases", "6.92e − 25", "Signaling events mediated by VEGFR1 and VEGFR2", "0.000148"], ["Cell cycle checkpoints", "1.01e − 18", "LKB1 signaling events", "0.000157"], ["S phase", "2.63e − 17", "Glypican 1 network", "0.000166"], ["Mitotic G1-G1/S phases", "6.9e − 17", "ErbB receptor signaling network", "0.000176"], ["Molecular function", "p value", "Molecular function", "p value"], ["Protein binding", "1.68e − 05", "Transmembrane receptor protein tyrosine kinase activity", "0.000171"], ["DNA binding", "7.16e − 05", "Ligase activity", "0.003422"], ["DNA-directed RNA polymerase activity", "8.2e − 05", "Catalytic activity", "0.010486"], ["Chaperone activity", "0.000109", "Transferase activity", "0.010898"], ["RNA binding", "0.000333", "Ligand-dependent nuclear receptor activity", "0.01265"], ["Complement activity", "0.001271", "Acyltransferase activity", "0.013939"], ["Cellular component", "p value", "Cellular component", "p value"], ["Nucleolus", "6.77e − 36", "Extracellular matrix", "5.92e − 06"], ["Centrosome", "4e − 22", "Membrane fraction", "0.001116"], ["Nucleoplasm", "3.55e − 19", "Nucleoplasm", "0.00122"], ["Nucleus", "2.99e − 16", "Cytosol", "0.001908"], ["Cytoplasm", "1.03e − 11", "Soluble fraction", "0.001939"], ["Kinetochore", "3.88e − 10", "Exosomes", "0.002625"], ["Biological process", "p value", "Biological process", "p value"], ["Regulation of nucleobase, nucleoside, nucleotide, and nucleic acid metabolism", "6.24e − 05", "Energy pathways", "0.000194"], ["Regulation of cell cycle", "0.000108", "Metabolism", "0.000205"], ["Protein metabolism", "0.000325", "DNA repair", "0.003073"], ["Cell proliferation", "0.000533", "Electron transport", "0.006762"], ["DNA replication", "0.002767", "Meiosis", "0.015513"], ["Peptide metabolism", "0.0068", "Cell proliferation", "0.022418"]], "row_count": 29, "column_count": 4, "numeric_cells": 50, "header_rows": 1, "locator": "section[11]/table-wrap[1]#tab4"}}, {"id": "asset:table:pmid:39949372:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:baddf27d0409a27e1f81da38301002d0f64da36a268731c65714c3567feae35e", "bytes": 1176, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#tab5", "version": null, "note": "Top dysregulated lncRNA coexpression modules and module hub genes in the analysis of GSE134834 microarray related to CRC.", "structure": {"pmcid": "PMC11824705", "section_index": 12, "section_title": "3.4. PPI Network and Hub Genes", "row_count": 4, "column_count": 5}, "table": {"label": "Table 5", "caption": "Top dysregulated lncRNA coexpression modules and module hub genes in the analysis of GSE134834 microarray related to CRC.", "rows": [["Modules", "DElnc", "PPI networks", "Hub genes"], ["Upregulated lncRNAs", "Downregulated lncRNAs"], ["Lightpink4", "p3467, p15938, p30155, p15421, p39026_v4, p34144_v4, p29027, p34360_v4, p17009, p30261, p24045, p21811, p9376, p16370, p21975, p2786, p10603, p44527_v4, p28920, LOC100653147, p2227, p18281, p10499, p14903, p21076, p21710, and p30340", "17436, p42655_v4, p26713, p40499_v4, p42344_v4, p4428, p4443, p33911, RNA143457|tRNA_374_71, p42656_v4, p42366_v4, and p2983", "805 nodes and 4651 edges", "MRTO4, CDK1, CDC20, RPF2, NOP58, NIFK, GTPBP4, BUB1, BUB1B, and BOP1"], ["Pink", "p15430, p35380_v4, p956, p16534, p23831, and LOC340340", "p33840, p4715, p12653, p16717, p28599, p22463, p20354, p20353, p27381, p10205, p25200, p16220, p20355, p25346, p11319, p12499, p21571, p7182, p9438, p12621, and p12806", "713 nodes and 1656 edges", "BYSL, RPS23, RSL1D1, NAT10, NOP14, GNL2, MRPS12, NOL6, IMP4, and RRP12"]], "row_count": 4, "column_count": 5, "numeric_cells": 8, "header_rows": 2, "locator": "section[12]/table-wrap[1]#tab5"}}], "gaps": ["asset:source:pmid:39949372 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", "tier": null, "blocking_axis": null, "blocked_on": null, "axes": {}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:39949372", "asset:table:pmid:39949372:1", "asset:table:pmid:39949372:2", "asset:table:pmid:39949372:3", "asset:table:pmid:39949372:4", "asset:table:pmid:39949372:5"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:39949372"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "f7cb0f9c793d0e45986a8dffff8be116d10abdb2ca5aa56cc00748fe7f287892", "source_hash": "b1f222b62c24952b360e18202d83259818cd6f1d206bd3a7057965d4b4b9dd58", "raw_response_sha256": "sha256:cb0e58d6b7f85d272dc74dcacffbc9f022a660290626cc334186c342b637f375", "raw_response_chars": 4016}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "60c0c6a1df828c7cd92d3c2641e79f6f7220323cc6d18f721159c216ee83967d", "source_hash": "b1f222b62c24952b360e18202d83259818cd6f1d206bd3a7057965d4b4b9dd58", "raw_response_sha256": "sha256:a0dac3cfc6dbe71959b66764df082aa56f0be1bd597eb508a1cc7aa85023ecb3", "raw_response_chars": 39684}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "f73ee1730f11704919577aae37c48bdd44eacdf5160ea5a84d43a4729e59e5df", "source_hash": "b1f222b62c24952b360e18202d83259818cd6f1d206bd3a7057965d4b4b9dd58", "raw_response": "{\"parent_value\":6763,\"unit\":\"DEGs\",\"evidence\":\"Analysis revealed 6763 DEGs (p < 0.05 and |log fold change (FC)| ≥ 0.5) that include differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA).\",\"target_result\":\"The paper reports 6763 differentially expressed genes in colorectal cancer samples compared with normal samples.\",\"number_stated\":true}", "reading": {"parent_value": 6763, "unit": "DEGs", "evidence": "Analysis revealed 6763 DEGs (p < 0.05 and |log fold change (FC)| ≥ 0.5) that include differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA).", "target_result": "The paper reports 6763 differentially expressed genes in colorectal cancer samples compared with normal samples.", "number_stated": true, "source_locator": "chars 487-670 of source sha256 b1f222b62c24952b360e18202d83259818cd6f1d206bd3a7057965d4b4b9dd58"}, "recorded_at": "2026-10-31T15:24:15.366041+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "d50ddacde4f8afde9f9c86ed98f4276cd37a7c455d731f60faa9795e49180a89", "source_hash": "b1f222b62c24952b360e18202d83259818cd6f1d206bd3a7057965d4b4b9dd58", "raw_response": "<think>We need answer JSON only. Need parse task carefully. Need identify \"single numerical result that a replication of the registered target has to reproduce. Report headline number only: the value the paper itself states for the registered target, not calculated... unit paper prints. Exact contiguous quotation containing number; attribution by wording etc. Registered target: headline numerical result paper states for main finding.\"\n\nWe need infer which number is headline main finding from source. Source abstract: Analysis revealed 6763 DEGs (p &lt;0.05 and |log FC| ≥0.5), two modules for lncRNAs obtained. Which is headline numerical result? Main finding likely \"6763 DEGs\". Registered target described generically, asks single numerical result replication has reproduce. We need output 6763, unit perhaps \"DEGs\" (paper prints number followed \"DEGs\"). Evidence exact contiguous quote entire clause: \"Analysis revealed 6763 DEGs (p &lt; 0.05 and |log fold change (FC)| ≥ 0.5) that include differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA).\" Is headline number 6763 DEGs likely. Could be \"two modules for lncRNAs\" but headline numerical result main finding likely 6763 DEGs. Need unit string paper prints. \"DEGs\". parent_value number 6763. target_result likely \"6763 DEGs\" maybe concise. number_stated true.\n\nBut let's deeply inspect wording and potential traps. User says \"single numerical result that a replication of the registered target has to reproduce\" and target is \"the headline numerical result the paper itself states for its main finding\". The abstract's key quantitative result: 6763 DEGs. There are many thresholds and software versions. The central result likely count of DEGs. Quote exact contiguous. Unit could be \"DEGs\". Ensure no unit calculated. Evidence must exact quote. Exact source has \"Analysis revealed 6763 DEGs (p &lt; 0.05 and |log fold change (FC)| ≥ 0.5) that include differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA).\" We can quote that. JSON escaping fine. target_result perhaps \"6763 DEGs\". Need perhaps \"The analysis revealed 6763 differentially expressed genes.\" But report headline number only might mean target_result should simply \"6763 DEGs\". Parent value and unit separate. The evidence whole clause.\n\nCould \"two modules for lncRNAs\" be main finding? Main abstract says \"and finally, two modules for lncRNAs were obtained.\" Yet the study title novel lncRNAs; likely headline numerical result may be \"6763 DEGs\". The wording \"headline numerical result\" likely benchmark asks identify parent quantity. We need choose.\n\nLet's parse all numerics:\n- 6763 DEGs (main analysis result)\n- p cutoff etc\n- two modules\n- 10 hub genes each\n- R version, tool versions, confidence score\nNo count of novel lncRNAs explicitly in provided excerpt.\n\"single numerical result that a replication of registered target has to reproduce.\" \"REGISTERED TARGET: the headline numerical result the paper itself states for its main finding\". This is not a specific named target, so likely abstract's first result. Maybe they expect 6763 DEGs as headline number. Unit \"DEGs\" exact printed.\n\nCould target_result be explanatory string. Required always. We can say \"6763 DEGs\". Evidence exact clause. Need output strict JSON no markdown. Ensure Unicode ≥ allowed. Exact quotation must be exact, contiguous. Let's verify punctuation from source:\n\"Analysis revealed 6763 DEGs (p &lt; 0.05 and |log fold change (FC)| ≥ 0.5) that include differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA). Novel lncRNAs were identified, and to better understand the biological function of the identified lncRNAs, gene modules were constructed using weighted gene coexpression network analysis (WGCNA), and finally, two modules for lncRNAs were obtained.\"\n\nCould quote only sentence 1. It contains number and attribution. Fine.\n\nUnit might be \"DEGs\" exactly. Parent value 6763. number_stated true. target_result perhaps \"6763 DEGs\" (headline number only). Let's formulate.</think>\n\n{\"parent_value\":6763,\"unit\":\"DEGs\",\"evidence\":\"Analysis revealed 6763 DEGs (p < 0.05 and |log fold change (FC)| ≥ 0.5) that include differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA).\",\"target_result\":\"6763 DEGs\",\"number_stated\":true}", "reading": {"parent_value": 6763, "unit": "DEGs", "evidence": "Analysis revealed 6763 DEGs (p < 0.05 and |log fold change (FC)| ≥ 0.5) that include differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA).", "target_result": "6763 DEGs", "number_stated": true, "source_locator": "chars 487-670 of source sha256 b1f222b62c24952b360e18202d83259818cd6f1d206bd3a7057965d4b4b9dd58"}, "recorded_at": "2026-10-31T15:24:18.091661+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "6763 differentially expressed genes (DEGs), including differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA), were identified in colorectal cancer samples compared with normal samples.", "minimax_alt": "Analysis revealed 6763 DEGs (p < 0.05 and |log fold change (FC)| ≥ 0.5) that include differentially expressed mRNA (DEmRNA) and differentially expressed long noncoding RNA (DElncRNA).", "decisive": false}, "analysis_methods": {"minimax": ["limma", "quantile normalization", "differential expression analysis", "weighted gene coexpression network analysis (WGCNA)"], "minimax_alt": ["limma package in Bioconductor with R 4.3.3 for gene-expression preprocessing", "quantile normalization", "DEG screening using p-value and absolute log-fold-change criteria", "weighted gene coexpression network analysis (WGCNA)", "FunRich GO and KEGG enrichment analysis", "STRING protein-protein interaction network analysis", "Cytoscape and CytoHubba degree-based hub-gene selection", "GEPIA expression validation using TCGA and GTEx data"], "decisive": false}, "statistical_method": {"minimax": "limma", "minimax_alt": "limma (Bioconductor/R), followed by DEG screening using p-value and absolute log-fold-change criteria after quantile normalization", "decisive": true}}, "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "blocked", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": []}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.blocked"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:d3d8f57f44a452f1ff2fe398ca41485b479b0a179e4ec3db0e1a3a18a1ce4f04", "type": "sep_package", "label": "SEP v1 package for pmid:39949372"}], "activities": [{"id": "activity:conversion:pmid:39949372", "type": "conversion", "used": ["package:d3d8f57f44a452f1ff2fe398ca41485b479b0a179e4ec3db0e1a3a18a1ce4f04"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax", "type": "model", "label": "minimax"}, {"id": "agent:minimax_alt", "type": "model", "label": "minimax_alt"}, {"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:39949372", "parent_hash": "sha256:4c85323cf4b17502acf951aeecf7468825d268c488dd56d5795ebb11b6927a8a", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:39949372 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:39949372' does not resolve to a declared asset", "targets"]}