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pmid:19864493
Sporadic ALS has compartment-specific aberrant exon splicing and altered cell-matrix adhesion biology.
Stuart J Rabin · Jae Mun Hugo Kim · Michael Baughn · Ryan T Libby · Young Joo Kim · Yuxin Fan · Randell T Libby · Albert La Spada · Brad Stone · John Ravits
Human molecular genetics · 2010 doi:10.1093/hmg/ddp498
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Complete file
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The fundamental pathogenic mechanisms are unknown and recent evidence is implicating a significant role for abnormal exon splicing and RNA processing. Using new comprehensive genomic technologies, we studied exon splicing directly in 12 sporadic ALS and 10 control lumbar spinal cords acquired by a rapid autopsy system that processed nervous systems specifically for genomic studies. ALS patients had rostral onset and caudally advancing disease and abundant residual motor neurons in this region. We created two RNA pools, one from motor neurons collected by laser capture microdissection and one from the surrounding anterior horns. From each, we isolated RNA, amplified mRNA, profiled whole-genome exon splicing, and applied advanced bioinformatics. We employed rigorous quality control measures at all steps and validated findings by qPCR. In the motor neuron enriched mRNA pool, we found two distinct cohorts of mRNA signals, most of which were up-regulated: 148 differentially expressed genes (P <or= 10(-3)) and 411 aberrantly spliced genes (P <or= 10(-5)). The aberrantly spliced genes were highly enriched in cell adhesion (P <or= 10(-57)), especially cell-matrix as opposed to cell-cell adhesion. Most of the enriching genes encode transmembrane or secreted as opposed to nuclear or cytoplasmic proteins. The differentially expressed genes were not biologically enriched. In the anterior horn enriched mRNA pool, we could not clearly identify mRNA signals or biological enrichment. These findings, perturbed and up-regulated cell-matrix adhesion, suggest possible mechanisms for the contiguously progressive nature of motor neuron degeneration. 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and top 25 differentially expressed genes", "structure": {"pmcid": "PMC2796893", "section_index": 5, "section_title": "Genomic analysis identifies differentially expressed gene signals in the motor neuron enriched mRNA pool", "row_count": 49, "column_count": 7}, "table": {"label": "Table 2.", "caption": "Top 25 aberrantly spliced and top 25 differentially expressed genes", "rows": [["Gene symbol", "Gene name", "RefSeq", "Alt. splice P-value", "Differential expression P-value", "Fold-change (A versus C)", "# Markers (exons)"], ["ABCA8", "ATP-binding cassette, sub-family A (ABC1), member 8", "NM_007168", "2.84E–17", "0.0147702", "2.07853", "37"], ["ACADVL", "Acyl-Coenzyme A dehydrogenase, very long chain", "NM_000018", "0.07572", "9.62E-05", "−1.36709", "20"], ["AGTRL1", "Angiotensin II receptor-like 1", "NM_005161", "0.00280309", "0.000100449", "2.80667", "6"], ["AQP4", "Aquaporin 4", "NM_001650", "1.35E-27", "1.21E−06", "3.17926", "13"], ["ASPA", "Aspartoacylase (Canavan disease)", "NM_000049", "0.199691", "0.000120487", "2.94572", "6"], ["C1orf198", "Chromosome 1 open reading frame 198", "AK096166", "2.66E−16", "0.00111187", "1.7294", "17"], ["C21orf33", "Chromosome 21 open reading frame 33", "NM_004649", "0.0218155", "0.00010392", "−1.30992", "10"], ["C3", "Complement component 3", "NM_000064", "1.89E−23", "0.00107972", "2.39112", "43"], ["C4A", "Complement component 4A (Rodgers blood group)", "NM_007293", "1.88E−31", "0.000487554", "2.3395", "48"], ["CENTD1", "Centaurin, delta 1", "NM_015230", "9.18E−08", "8.68E−05", "1.86511", "37"], ["COG5", "Component of oligomeric golgi complex 5", "NM_006348", "1.79E−05", "0.000102532", "1.63965", "28"], ["COL1A2", "Collagen, type I, alpha 2", "NM_000089", "2.02E−24", "0.0319974", "1.44001", "47"], ["COL6A3", "ollagen, type VI, Calpha 3", "NM_004369", "3.34E−20", "0.0945555", "1.36456", "45"], ["CPVL", "Carboxypeptidase, vitellogenic-like", "NM_019029", "3.89E−11", "6.99E−06", "2.06165", "17"], ["CXCL16", "Chemokine (C-X-C motif) ligand 16", "NM_022059", "0.00011424", "2.01E−05", "1.99739", "10"], ["DST", "Dystonin", "NM_183380", "9.73E−24", "0.323111", "1.0925", "125"], ["EDNRB", "Endothelin receptor type B", "NM_000115", "2.64E−19", "1.64E−05", "3.01733", "17"], ["ELAVL3", "ELAV (embryonic lethal, abnormal vision, Drosophila)-like", "NM_032281", "1.12E−05", "0.000109817", "−2.14778", "18"], ["EXOSC6", "Exosome component 6", "NM_058219", "0.804989", "0.000105887", "−1.21483", "7"], ["FAM46C", "Family with sequence similarity 46, member C", "NM_017709", "6.43E−08", "0.000117789", "2.4746", "6"], ["FLJ21963", "FLJ21963 protein", "NM_024560", "2.64E−12", "2.35E−05", "3.01776", "17"], ["FLJ44874", "FLJ44874 protein", "AK126822", "0.597731", "1.44E−07", "−1.46746", "3"], ["FLNC", "Filamin C, gamma (actin-binding protein 280)", "NM_001458", "2.80E−16", "0.289023", "1.0877", "48"], ["FN1", "Fibronectin 1", "NM_212482", "2.24E−21", "0.0133788", "2.50828", "63"], ["HIF3A", "Hypoxia inducible factor 3, alpha subunit", "NM_022462", "6.33E−16", "0.0968477", "1.24509", "27"], ["HLA-B", "Major histocompatibility complex, class I, B", "NM_005514", "0.011742", "0.000145132", "2.07808", "3"], ["HLA-DMB", "Major histocompatibility complex, class II, DM beta", "NM_002118", "0.00334092", "0.000122339", "2.64162", "3"], ["HLA-DRA", "Major histocompatibility complex, class II, DR alpha", "NM_019111", "0.0176529", "9.96E−06", "3.75813", "9"], ["INPP5D", "Inositol polyphosphate-5-phosphatase, 145 kDa", "NM_005541", "2.28E−15", "0.00485491", "1.54023", "25"], ["KIAA0644", "KIAA0644 gene product", "NM_014817", "5.30E−18", "0.0764209", "1.16279", "15"], ["KRT73", "Keratin 73", "NM_175068", "0.156092", "6.78E−05", "−1.35392", "9"], ["LRP1", "Low-density lipoprotein-related protein 1 (alpha-2-macroglo", "NM_002332", "2.68E−19", "0.0219457", "1.28675", "105"], ["MACF1", "Microtubule-actin cross-linking factor 1", "NM_012090", "7.85E−22", "0.00408213", "1.24486", "115"], ["MYBPC1", "Myosin binding protein C, slow type", "NM_002465", "1.90E−21", "0.00967833", "1.31138", "31"], ["OR2W3", "Olfactory receptor, family 2, subfamily W, member 3", "NM_001001957", "0.602669", "0.000100305", "−1.45266", "13"], ["OR5AS1", "Olfactory receptor, family 5, subfamily AS, member 1", "NM_001001921", "0.548751", "0.000141626", "−1.3982", "3"], ["PADI2", "Peptidyl arginine deiminase, type II", "NM_007365", "9.72E−14", "0.000114651", "1.6916", "18"], ["PARP9", "Poly (ADP-ribose) polymerase family, member 9", "NM_031458", "0.606104", "2.15E−05", "3.48026", "3"], ["PCDHGC5", "Protocadherin gamma subfamily C, 5", "NM_018929", "2.24E−21", "0.00182203", "1.23154", "100"], ["PYGM", "Phosphorylase, glycogen; muscle (McArdle syndrome, glycogen", "NM_005609", "7.14E−19", "0.000661684", "1.64136", "20"], ["SEMA5B", "Sema domain, seven thrombospondin Repeats (type 1 and", "NM_001031702", "6.12E−25", "0.746505", "1.02067", "31"], ["SF1", "Splicing factor 1", "NM_004630", "3.25E−18", "0.0117229", "1.26463", "32"], ["SLC1A3", "Solute carrier family 1 (glial high affinity glutamate transporter)", "NM_004172", "3.81E−05", "0.000106293", "2.50395", "15"], ["SLC35A4", "Solute carrier family 35, member A4", "NM_080670", "0.793629", "7.95E−05", "−1.49356", "8"], ["SLC4A4", "Solute carrier family 4, sodium bicarbonate co-transporter", "NM_001098484", "1.64E−16", "0.000145173", "2.17261", "31"], ["TJP2", "Tight junction protein 2 (zona occludens 2)", "NM_004817", "9.14E−16", "0.000452437", "2.01894", "31"], ["TRBV19", "T-cell receptor beta variable 19", "BC073930", "1.48E−15", "0.695085", "1.02684", "30"], ["UTRN", "Utrophin", "NM_007124", "1.56E−20", "0.00473928", "1.78074", "74"]], "row_count": 49, "column_count": 7, "numeric_cells": 285, "header_rows": 1, "locator": "section[5]/table-wrap[1]#DDP498TB2"}}, {"id": "asset:table:pmid:19864493:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:167a18825f635a6874e6b6b34d466fabacebb2c90815a8da7c3531692ab1f7f3", "bytes": 2744, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#DDP498TB3", "version": null, "note": "Biological enrichment of aberrantly spliced genes", "structure": {"pmcid": "PMC2796893", "section_index": 7, "section_title": "The aberrantly spliced genes but not the differentially expressed genes in the motor neuron enriched mRNA pool are biologically enriched", "row_count": 34, "column_count": 7}, "table": {"label": "Table 3.", "caption": "Biological enrichment of aberrantly spliced genes", "rows": [["Enrichment", "Enrichment P-value", "% genes in group that are present", "Number of genes present", "Number of genes in group", "GO ID", "GO category"], ["Biological adhesion", "10−58", "8.6758", "57", "657", "22610", "BP"], ["Cell adhesion", "10−58", "8.6758", "57", "657", "7155", "BP"], ["Basement membrane", "10−48", "28.9474", "11", "38", "5604", "CC"], ["Transmembrane receptor protein tyrosine kinase activity", "10−43", "20.5882", "14", "68", "4714", "MF"], ["Collagen", "10−43", "28.5714", "10", "35", "5581", "CC"], ["Extracellular matrix structural constituent", "10−42", "18.75", "15", "80", "5201", "MF"], ["Vascular endothelial growth factor receptor activity", "10−42", "50", "6", "12", "5021", "MF"], ["Laminin-1 complex", "10−41", "62.5", "5", "8", "5606", "CC"], ["Laminin complex", "10−41", "62.5", "5", "8", "43256", "CC"], ["Transmembrane receptor protein kinase activity", "10−41", "18.2927", "15", "82", "19199", "MF"], ["Regulation of cell migration", "10−39", "29.0323", "9", "31", "30334", "BP"], ["Cell–substrate adhesion", "10−31", "17.3913", "12", "69", "31589", "BP"], ["Cell–matrix adhesion", "10−28", "17.1875", "11", "64", "7160", "BP"], ["Extracellular region part", "10−27", "6.38003", "46", "721", "44421", "CC"], ["Protein binding", "10−27", "3.32847", "228", "6850", "5515", "MF"], ["Plasma membrane part", "10−25", "4.74517", "81", "1707", "44459", "CC"], ["Regulation of cell motility", "10−25", "14.2857", "12", "84", "51270", "BP"], ["Cell–substrate junction assembly", "10−25", "60", "3", "5", "7044", "BP"], ["Cell junction assembly", "10−25", "60", "3", "5", "34329", "BP"], ["Extracellular matrix organization and biogenesis", "10−24", "19.5122", "8", "41", "30198", "BP"], ["Collagen binding", "10−23", "29.4118", "5", "17", "5518", "MF"], ["Phosphate transport", "10−23", "13.1868", "12", "91", "6817", "BP"], ["Hemidesmosome", "10−23", "100", "2", "2", "30056", "CC"], ["Integrin-mediated signaling pathway", "10−23", "16.3636", "9", "55", "7229", "BP"], ["Proteinaceous extracellular matrix", "10−22", "9.00901", "20", "222", "5578", "CC"], ["Regulation of embryonic development", "10−22", "50", "3", "6", "45995", "BP"], ["Stereocilium", "10−22", "50", "3", "6", "32420", "CC"], ["Fibroblast growth factor receptor activity", "10−22", "50", "3", "6", "5007", "MF"], ["Extracellular matrix", "10−21", "8.77193", "20", "228", "31012", "CC"], ["Anatomical structure development", "10−21", "5.15464", "55", "1067", "48856", "BP"], ["Structural molecule activity", "10−21", "5.91716", "40", "676", "5198", "MF"], ["Integrin complex", "10−20", "21.4286", "6", "28", "8305", "CC"], ["Developmental process", "10−20", "4.04485", "101", "2497", "32502", "BP"]], "row_count": 34, "column_count": 7, "numeric_cells": 166, "header_rows": 1, "locator": "section[7]/table-wrap[1]#DDP498TB3"}}, {"id": "asset:table:pmid:19864493:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:27df59ef0bbcab5fe899ab576caf8625d52ef6a07105270e098704567bb94bcd", "bytes": 6199, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[2]#DDP498TB4", "version": null, "note": "Aberrantly spliced cell adhesion genes", "structure": {"pmcid": "PMC2796893", "section_index": 7, "section_title": "The aberrantly spliced genes but not the differentially expressed genes in the motor neuron enriched mRNA pool are biologically enriched", "row_count": 58, "column_count": 8}, "table": {"label": "Table 4.", "caption": "Aberrantly spliced cell adhesion genes", "rows": [["Gene symbol", "Gene name", "RefSeq", "Alt. splice P-value", "Differential expression P-value", "Fold change (A versus C)", "Number of markers", "Protein location"], ["AEBP1", "AE binding protein 1", "NM_001129", "2.44E−10", "0.0186655", "1.69315", "27", "sec"], ["ANXA9", "Annexin A9", "NM_003568", "8.62E−07", "0.971328", "−1.00249", "14", "cyt"], ["CDH11", "Cadherin 11, type 2, OB-cadherin (osteoblast)", "NM_001797", "2.94E−06", "0.00458728", "1.65623", "21", "tm"], ["CDH5", "Cadherin 5, type 2, VE-cadherin (vascular epithelium)", "NM_001795", "2.36E−06", "0.102509", "1.27449", "19", "tm"], ["CDH23", "Cadherin-like 23", "NM_022124", "1.61E−07", "0.156179", "1.12818", "71", "tm"], ["CTNNA3", "Catenin (cadherin-associated protein), alpha 3", "NM_013266", "6.53E−06", "0.00648134", "1.79781", "25", "cyt"], ["CTNND2", "Catenin (cadherin-associated protein), delta 2", "NM_001332", "1.59E−06", "0.0867763", "1.1616", "32", "cyt"], ["CD44", "CD44 molecule (Indian blood group)", "NM_000610", "5.13E−12", "0.000479249", "1.89535", "21", "tm"], ["CLDN10", "Claudin 10", "NM_182848", "6.03E−06", "0.162268", "1.20723", "12", "tm"], ["CLDN11", "Claudin 11 (oligodendrocyte transmembrane protein)", "NM_005602", "1.94E−06", "0.00435624", "1.53442", "6", "tm"], ["COL3A1", "Collagen, type III, alpha 1 (Ehlers-Danlos syndrome type)", "NM_000090", "3.84E−09", "0.221719", "1.17435", "49", "sec"], ["COL6A3", "Collagen, type VI, alpha 3", "NM_004369", "3.34E−20", "0.0945555", "1.36456", "45", "sec"], ["COL11A1", "Collagen, type XI, alpha 1", "NM_001854", "2.33E−09", "0.178053", "1.20705", "46", "sec"], ["COL12A1", "Collagen, type XII, alpha 1", "NM_004370", "1.69E−10", "0.0105983", "1.79078", "69", "sec"], ["COL13A1", "Collagen, type XIII, alpha 1", "NM_005203", "6.71E−09", "0.169929", "1.15626", "25", "sec"], ["COL14A1", "Collagen, type XIV, alpha 1 (undulin)", "NM_021110", "1.06E−08", "0.00638787", "1.58704", "24", "sec"], ["COL27A1", "Collagen, type XXVII, alpha 1", "NM_032888", "1.43E−06", "0.243964", "−1.10262", "46", "sec"], ["CSF3R", "Colony stimulating factor 3 receptor (granulocyte)", "NM_156039", "2.04E−06", "0.126098", "1.10957", "24", "tm"], ["CYR61", "Cysteine-rich, angiogenic inducer, 61", "NM_001554", "1.17E−07", "0.0315499", "1.55961", "8", "sec"], ["DDR1", "Discoidin domain receptor family, member 1", "NM_013993", "4.24E−08", "0.103136", "1.15821", "31", "tm"], ["DST", "Dystonin", "NM_183380", "9.73E−24", "0.323111", "1.0925", "125", "cyt"], ["ENG", "Endoglin (Osler-Rendu-Weber syndrome 1)", "NM_000118", "5.65E−06", "0.342529", "1.19248", "20", "tm"], ["ERBB2IP", "Erbb2 interacting protein", "NM_018695", "6.83E−07", "0.000240051", "2.08535", "30", "cyt"], ["ECM2", "Extracellular matrix protein 2, female organ and adipocyte", "NM_001393", "4.60E−06", "0.0461937", "1.59777", "20", "sec"], ["FAT", "FAT // FAT tumor suppressor homolog 1 (Drosophila)", "NM_005245", "1.45E−08", "0.00159728", "1.86066", "31", "tm"], ["FN1", "Fibronectin 1", "NM_212482", "2.24E−21", "0.0133788", "2.50828", "63", "sec"], ["HMCN1", "Hemicentin 1", "NM_031935", "7.81E−07", "0.209353", "1.1854", "116", "sec"], ["HSPG2", "Heparan sulfate proteoglycan 2", "NM_005529", "2.11E−09", "0.938373", "−1.00658", "101", "sec"], ["HEPACAM", "Hepatocyte cell adhesion molecule", "NM_152722", "2.96E−06", "0.0223096", "1.54885", "13", "tm"], ["IGSF11", "Immunoglobulin superfamily, member 11", "NM_001015887", "5.57E−08", "0.0724414", "1.24835", "13", "tm"], ["ITGA6", "Integrin, alpha 6", "NM_000210", "9.56E−08", "0.0229754", "2.06743", "29", "tm"], ["ITGAX", "Integrin, alpha X (complement component 3 receptor 4 subunit)", "NM_000887", "7.10E−08", "0.305373", "1.09177", "29", "tm"], ["ITGB3", "Integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)", "NM_000212", "1.12E−06", "0.394661", "1.16482", "20", "tm"], ["ITGB4", "Integrin, beta 4", "NM_000213", "4.07E−15", "0.183707", "1.14822", "44", "tm"], ["ITGB7", "integrin, beta 7", "NM_000889", "1.28E−12", "0.345837", "−1.07065", "17", "tm"], ["ITGBL1", "ITGBL1 // integrin, beta-like 1 (with EGF-like repeat domains)", "NM_004791", "2.24E−14", "0.00392462", "1.97861", "16", "tm"], ["JAM2", "Junctional adhesion molecule 2", "NM_021219", "3.87E−08", "0.00548407", "2.02731", "13", "tm"], ["LAMB1", "Laminin, beta 1", "NM_002291", "2.61E−13", "0.0290629", "1.61794", "36", "sec"], ["LAMB2", "Laminin, beta 2 (laminin S)", "NM_002292", "3.16E−06", "0.155571", "1.21405", "40", "sec"], ["LAMC3", "Laminin, gamma 3", "NM_006059", "8.59E−06", "0.370666", "−1.06083", "35", "sec"], ["LPP", "LIM domain containing preferred translocation partner in lip", "NM_005578", "1.40E−06", "0.147014", "1.51955", "13", "cyt"], ["MYBPC1", "Myosin binding protein C, slow type", "NM_002465", "1.90E−21", "0.00967833", "1.31138", "31", "cyt"], ["NCAN", "Neurocan", "NM_004386", "4.77E−10", "0.206516", "1.13639", "25", "sec"], ["NRP2", "Neuropilin 2", "NM_003872", "5.65E−07", "0.0447044", "1.29315", "36", "tm"], ["PARVG", "Parvin, gamma", "NM_022141", "2.03E−07", "0.015984", "1.25824", "14", "cyt"], ["PDZD2", "PDZ domain containing 2", "NM_178140", "2.86E−07", "0.0529539", "1.34362", "44", "cyt"], ["PECAM1", "Platelet/endothelial cell adhesion molecule (CD31 antigen)", "NM_000442", "3.50E−06", "0.023662", "2.42764", "17", "tm"], ["PCDHGC5", "Protocadherin gamma subfamily C, 5", "NM_018929", "2.24E−21", "0.00182203", "1.23154", "100", "tm"], ["RELN", "Reelin", "NM_173054", "3.03E−06", "0.0459772", "1.59369", "73", "sec"], ["SSPN", "Sarcospan (Kras oncogene-associated gene)", "NM_005086", "1.23E−07", "0.00153469", "1.87677", "8", "tm"], ["SEMA5A", "Sema domain, seven thrombospondin Repeats", "NM_003966", "6.24E−06", "0.132723", "1.27857", "29", "tm"], ["SOX9", "SRY (sex determining region Y)-box 9 (campomelic dysplasia)", "NM_000346", "3.07E−07", "0.584737", "1.05446", "9", "nuc"], ["TNC", "Tenascin C (hexabrachion)", "NM_002160", "2.55E−08", "0.125224", "1.66206", "36", "sec"], ["TESK2", "Testis-specific kinase 2", "NM_007170", "6.75E−07", "0.0632463", "1.36536", "14", "nuc"], ["TRIP6", "Thyroid hormone receptor interactor 6", "NM_003302", "2.74E−07", "0.194651", "1.16145", "13", "cyt"], ["VCAN", "Versican", "NM_004385", "8.36E−11", "0.000148832", "2.61415", "26", "sec"], ["VWF", "von Willebrand factor", "NM_000552", "5.40E−12", "0.085195", "1.51082", "46", "sec"]], "row_count": 58, "column_count": 8, "numeric_cells": 340, "header_rows": 1, "locator": "section[7]/table-wrap[2]#DDP498TB4"}}, {"id": "asset:table:pmid:19864493:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:cb39ffe1309f40377acf6f558aed4924f91f8e52c05ec36c84a5fd318e286629", "bytes": 985, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#DDP498TB5", "version": null, "note": "Summary of key findings", "structure": {"pmcid": "PMC2796893", "section_index": 12, "section_title": "DISCUSSION", "row_count": 7, "column_count": 3}, "table": {"label": "Table 5.", "caption": "Summary of key findings", "rows": [["", "Motor neuron enriched mRNA pool", "Anterior horn enriched mRNA pool"], ["Cellularity", "Homogeneous (single-cell enriched)", "Heterogeneous (glia, endothelium, small neurons, degenerating neurons)"], ["Anatomic size", "Highly discrete", "Comparatively vast"], ["Differential gene expression", "148 genes", "Not detectable above noise"], ["Biological enrichment of differentially expressed genes", "Not detectable above noise", "Not detectable above noise"], ["Aberrant exon splicing", "411 genes", "Not detectable above noise"], ["Biological enrichment of aberrantly spliced genes", "Cell–matrix adhesion and extracellular matrix biology; also transmembrane receptor protein tyrosine kinase activity, vascular endothelial growth factor receptor activity, and regulation of cell motility", "Not detectable above noise"]], "row_count": 7, "column_count": 3, "numeric_cells": 2, "header_rows": 1, "locator": "section[12]/table-wrap[1]#DDP498TB5"}}], "gaps": ["asset:data:geo:GSE18920 not downloaded", "asset:data:geo:GSE18920 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To determine aberrant exon splicing, we used an ANOVA-based analysis that generates P-values indicating the probability of aberrant splicing occurring in a particular gene."}}], "targets": [], "gaps": []}, "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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["GSE18920"], "resolved_accessions": ["GSE18920"], "statements": ["Data deposition: GeneChip raw data (CEL-files) have been deposited for public access in the Gene Expression Omnibus (GEO), www.ncbi.nlm.nih.gov/geo, accession number GSE18920."], "basis": "The paper names GSE18920 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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