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pmid:41053192
Decision tree-based machine learning methods for identifying colorectal cancer-associated microRNA signatures and their regulatory networks.
Scientific reports · 2025 doi:10.1038/s41598-025-17037-7
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Complete file
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"99.87"]], "row_count": 3, "column_count": 8, "numeric_cells": 14, "header_rows": 1, "locator": "section[13]/table-wrap[1]#Tab4"}}, {"id": "asset:table:pmid:41053192:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6a448c5a5cd228d4cdbb4919a94229ff0e60265c6e2a16d8d84b99aec9a3a524", "bytes": 2968, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#Tab5", "version": null, "note": "miRNA-associated pathways listed by miranno.", "structure": {"pmcid": "PMC12500991", "section_index": 14, "section_title": "Functional annotation of the identified MiRNAs", "row_count": 46, "column_count": 4}, "table": {"label": "Table 5", "caption": "miRNA-associated pathways listed by miranno.", "rows": [["miRNA", "Pathways (N)", "Cancer/tumor pathways", "Top 5 associated molecular pathways"], ["hsa-miR-1228-5p", "144", "Signaling by ligand-responsive EGFR variants in cancer", "Metabolism of ingested SeMet, Sec, MeSec into H2Se"], ["Signaling by EGFR in cancer", "Fructose metabolism"], ["Constitutive signaling by ligand-responsive EGFR cancer variants", "Mechanism of protein import into the nucleus"], ["Signaling by EGFRvIII in cancer", "Tyrosine degradation"], ["Thyroid cancer", "Geranylgeranyl diphosphate from farnesyl diphosphate and isopentenyl diphosphate"], ["hsa-miR-6787-5p", "153", "Constitutive signaling by AKT1 E17K in cancer", "FGFRL1 modulation of FGFR1 signaling"], ["MTF1 activates gene expression"], ["Phosphoinositides and their downstream targets"], ["Lidocaine (Local Anaesthetic) Metabolism Pathway"], ["WNT ligand secretion is abrogated by the PORCN inhibitor LGK974"], ["hsa-miR-1343-3p", "102", "Estrogen responsive protein efp controls cell cycle and breast tumors growth", "PTK6 Activates STAT3"], ["Ibuprofen_Pathway_Pharmacokinetics"], ["Signaling mediated by p38-alpha and p38-beta"], ["Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling"], ["UMP biosynthesis via de novo pathway"], ["hsa-miR-6717-5p", "146", "Bladder cancer", "Benzo(a)pyrene metabolism"], ["Synthesis of bile acids and bile salts via 27-hydroxycholesterol"], ["Synthesis of bile acids and bile salts via 24-hydroxycholesterol"], ["Synthesis of bile acids and bile salts via 7alpha-Hydroxycholesterol"], ["Allopregnanolone biosynthesis"], ["hsa-miR-3184-5p", "175", "-", "NFG and proNGF binds to p75NTR"], ["Putrescine biosynthesis via L-ornithine pathway"], ["Putrescine biosynthesis I"], ["Putrescine from L-ornithine"], ["Spermidine from putrescine"], ["hsa-miR-1246", "114", "Signaling by WNT in cancer", "Interaction With Cumulus Cells"], ["Dermatan sulfate degradation (metazoa)"], ["L-cysteine degradation I"], ["phosphocholine from choline"], ["Acyl carrier protein metabolism"], ["hsa-miR-4706", "203", "-", "WNT ligand secretion / PORCN inhibitor LGK974"], ["FGFRL1 modulation of FGFR1 signaling"], ["Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane"], ["Beta agonist/Beta blocker Pathway"], ["Downstream signaling in naïve CD8 + T cells"], ["hsa-miR-8073", "131", "-", "Quinol/quinone metabolism"], ["Menaquinone biosynthesis"], ["Dopamine biosynthesis"], ["Dopamine from L-tyrosine"], ["Ascorbate and aldarate metabolism"], ["hsa-miR-5100", "89", "Methotrexate Pathway Cancer Cell Pharmacodynamics", "(S)-3-hydroxy-3-methylglutaryl-CoA degradation"], ["Acetoacetate from (S)-3-hydroxy-3-methylglutaryl-CoA"], ["TCA Cycle Nutrient Utilization and Invasiveness of Ovarian Cancer", "Metabolic intermediate metabolism"], ["Effects of Nitric Oxide"], ["4-hydroxy-2-nonenal detoxification"]], "row_count": 46, "column_count": 4, "numeric_cells": 30, "header_rows": 1, "locator": "section[14]/table-wrap[1]#Tab5"}}, {"id": "asset:table:pmid:41053192:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:08a9a99aa7133df8f6aeb5a6e057b0f12a10e08f9845e057061c4d99ea46788e", "bytes": 3831, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#Tab6", "version": null, "note": "Gene ontology reported by ToppFun for target genes of the selected mirnas.", "structure": {"pmcid": "PMC12500991", "section_index": 14, "section_title": "Functional annotation of the identified MiRNAs", "row_count": 44, "column_count": 4}, "table": {"label": "Table 6", "caption": "Gene ontology reported by ToppFun for target genes of the selected mirnas.", "rows": [["GO: biological process", "GO: molecular function"], ["ID", "Name", "ID", "Name"], ["GO:0045934", "negative regulation of nucleobase-containing compound metabolic process", "GO:0043565", "sequence-specific DNA binding"], ["GO:0051253", "negative regulation of RNA metabolic process", "GO:0003690", "double-stranded DNA binding"], ["GO:0010558", "negative regulation of macromolecule biosynthetic process", "GO:1,990,837", "sequence-specific double-stranded DNA binding"], ["GO:0031327", "negative regulation of cellular biosynthetic process", "GO:0000976", "transcription cis-regulatory region binding"], ["GO:1,902,679", "negative regulation of RNA biosynthetic process", "GO:0019904", "protein domain specific binding"], ["GO:0045892", "negative regulation of DNA-templated transcription", "GO:0001067", "transcription regulatory region nucleic acid binding"], ["GO:0060322", "head development", "GO:0060090", "molecular adaptor activity"], ["GO:0031647", "regulation of protein stability", "GO:0008134", "transcription factor binding"], ["GO:0000122", "negative regulation of transcription by RNA polymerase II", "GO:0000977", "RNA polymerase II transcription regulatory region sequence-specific DNA binding"], ["GO:0043066", "negative regulation of apoptotic process", "GO:0003700", "DNA-binding transcription factor activity"], ["GO:0051960", "regulation of nervous system development", "GO:0000978", "RNA polymerase II cis-regulatory region sequence-specific DNA binding"], ["GO:0043069", "negative regulation of programmed cell death", "GO:0030674", "protein-macromolecule adaptor activity"], ["GO:0007420", "brain development", "GO:0044389", "ubiquitin-like protein ligase binding"], ["GO:0007417", "central nervous system development", "GO:0000987", "cis-regulatory region sequence-specific DNA binding"], ["GO:0050767", "regulation of neurogenesis", "GO:0140262", "mRNA cap binding complex binding"], ["GO:0045893", "positive regulation of DNA-templated transcription", "GO:0000981", "DNA-binding transcription factor activity, RNA polymerase II-specific"], ["GO:1,902,680", "positive regulation of RNA biosynthetic process", "GO:0031625", "ubiquitin protein ligase binding"], ["GO:0043067", "regulation of programmed cell death", "GO:0042393", "histone binding"], ["GO:0000902", "cell morphogenesis", "GO:0140110", "transcription regulator activity"], ["GO:0042981", "regulation of apoptotic process", "GO:0001221", "transcription coregulator binding"], ["GO:0050821", "protein stabilization", "", ""], ["GO:0007628", "adult walking behavior", "", ""], ["GO:1,903,169", "regulation of calcium ion transmembrane transport", "", ""], ["GO:0045597", "positive regulation of cell differentiation", "", ""], ["GO:0043523", "regulation of neuron apoptotic process", "", ""], ["GO:0048666", "neuron development", "", ""], ["GO:0044087", "regulation of cellular component biogenesis", "", ""], ["GO:0045184", "establishment of protein localization", "", ""], ["GO:0014009", "glial cell proliferation", "", ""], ["GO:0015031", "protein transport", "", ""], ["GO:0090659", "walking behavior", "", ""], ["GO:0042063", "gliogenesis", "", ""], ["GO:0051402", "neuron apoptotic process", "", ""], ["GO:0003181", "atrioventricular valve morphogenesis", "", ""], ["GO:0006974", "DNA damage response", "", ""], ["GO:0010626", "negative regulation of Schwann cell proliferation", "", ""], ["GO:0050768", "negative regulation of neurogenesis", "", ""], ["GO:0048598", "embryonic morphogenesis", "", ""], ["GO:1,901,339", "regulation of store-operated calcium channel activity", "", ""], ["GO:0043524", "negative regulation of neuron apoptotic process", "", ""], ["GO:0097193", "intrinsic apoptotic signaling pathway", "", ""], ["GO:0071824", "protein-DNA complex organization", "", ""]], "row_count": 44, "column_count": 4, "numeric_cells": 62, "header_rows": 2, "locator": "section[14]/table-wrap[2]#Tab6"}}], "gaps": ["asset:source:pmid:41053192 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:41053192", "asset:table:pmid:41053192:1", 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