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pmid:29201983
Data on novel DNA methylation changes induced by valproic acid in human hepatocytes.
JarnoEJ Wolters · SimoneGJ van Breda · SandraM Claessen · TheoMCM de Kok · JosCS Kleinjans
Data in brief · 2018 doi:10.1016/j.dib.2017.11.031
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Complete file
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The data presented in this DIB publication is used to further investigate the VPA-induced mechanisms of steatosis by analyzing changes in patterns of methylation. Therefore, primary human hepatocytes (PHHs) were exposed to VPA at a concentration which was shown to cause steatosis without inducing overt cytotoxicity. VPA was administered for 5 days daily to PHHs. Furthermore, after 5 days VPA-treatment parts of the PHHs were followed for a 3 days washout. Differentially methylated DNA regions (DMRs) were identified by using the 'Methylated DNA Immuno-Precipitation - sequencing' (MeDIP-seq) method. The data presented in this DIB demonstrate induced steatosis pathways by all DMRs during VPA-treatment, covering interesting drug-induced steatosis genes (persistent DMRs upon terminating VPA treatment and the EP300 network). This was illustrated in our associated article (Wolters et al., 2017) [1]. 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PHHs, primary human hepatocytes; VPA, valproic acid; DMRs, differentially methylated DNA regions.", "structure": {"pmcid": "PMC5702865", "section_index": 3, "section_title": "Data", "row_count": 31, "column_count": 4}, "table": {"label": "Table 1", "caption": "Names and functions of the 20 persistently hypermethylated DMRs annotated to 15 unique Entrez Genes (A) and the 11 hypomethylated DMRs annotated to 9 unique Entrez Genes (B) of the MEDIP-seq analysis after the exposure of PHHs for 5 days daily to VPA followed by 3 days washout. 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Mutations in this gene have been associated with seborrhea-like dermatitis with psoriasiform elements."], ["80757", "TMEM121", "transmembrane protein 121", "–"], ["114784", "CSMD2", "CUB and Sushi multiple domains 2", "–"], ["122706", "PSMB11", "proteasome (prosome, macropain) subunit, beta type, 11", "Proteasomes generate peptides that are presented by major histocompatibility complex (MHC) I molecules to other cells of the immune system."], ["254827", "NAALADL2", "N-acetylated alpha-linked acidic dipeptidase-like 2", "–"], ["338707", "B4GALNT4", "beta-1,4-N-acetyl-galactosaminyl transferase 4", "–"], ["388228", "SBK1", "SH3 domain binding kinase 1", "–"], ["440073", "IQSEC. 3", "IQ motif and Sec. 7 domain 3", "–"], ["100507290", "ZNF865", "zinc finger protein 865", "–"], [""], ["B) 11 persistently hypomethylated DMRs annotated to 9 unique Entrez Genes"], [""], ["Entrez Gene ID", "Gene Symbol", "Gene Name", "NCBI Gene Function"], [""], ["290", "ANPEP", "alanyl (membrane) aminopeptidase", "Aminopeptidase N is located in the small-intestinal and renal microvillar membrane, and also in other plasma membranes. In the small intestine aminopeptidase N plays a role in the final digestion of peptides generated from hydrolysis of proteins by gastric and pancreatic proteases."], ["29982", "NRBF2", "nuclear receptor binding factor 2", "–"], ["136051", "ZNF786", "zinc finger protein 786", "–"], ["414763", "BMS1P18", "BMS1 ribosome biogenesis factor pseudogene 18", "–"], ["643955", "ZNF733P", "zinc finger protein 733, pseudogene", "–"], ["646096", "CHEK2P2", "checkpoint kinase 2 pseudogene 2", "–"], ["647121", "EMBP1", "embigin pseudogene 1", "–"], ["100101266", "HAVCR1P1", "hepatitis A virus cellular receptor 1 pseudogene 1", "–"], ["101927554", "LINC01250", "long intergenic non-protein coding RNA 1250", "–"]], "row_count": 31, "column_count": 4, "numeric_cells": 58, "header_rows": 2, "locator": "section[3]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:29201983:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c6f21f6213cb8cc77cd1a615eb078d7ef244d8e9a81be872f33d60ef4d672509", "bytes": 10824, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[2]#t0010", "version": null, "note": "The ‘enriched pathway-based sets’ from the HOMER annotated genes of the 3006 hypermethylated DMRs and the 3077 hypomethylated DMRs after the exposure of PHHs for 5 days daily to VPA. PHHs, primary human hepatocytes; VPA, valproic acid; DMRs, differentially methylated DNA regions.", "structure": {"pmcid": "PMC5702865", "section_index": 3, "section_title": "Data", "row_count": 120, "column_count": 6}, "table": {"label": "Table 2", "caption": "The ‘enriched pathway-based sets’ from the HOMER annotated genes of the 3006 hypermethylated DMRs and the 3077 hypomethylated DMRs after the exposure of PHHs for 5 days daily to VPA. PHHs, primary human hepatocytes; VPA, valproic acid; DMRs, differentially methylated DNA regions.", "rows": [["Pathway name", "Set size", "Candidates, contained", "p-value", "q-value", "Pathway source"], ["Developmental Biology", "586", "129 (22.0%)", "3.23E-10", "8.02E-07", "Reactome"], ["Axon guidance", "459", "101 (22.0%)", "3.06E-08", "3.81E-05", "Reactome"], ["Wnt signaling pathway - Homo sapiens (human)", "140", "36 (25.7%)", "3.17E-05", "0.0262", "KEGG"], ["Axon guidance - Homo sapiens (human)", "127", "33 (26.0%)", "5.33E-05", "0.0331", "KEGG"], ["Signalling by NGF", "386", "76 (19.7%)", "9.86E-05", "0.0447", "Reactome"], ["Signaling by SCF-KIT", "264", "56 (21.2%)", "0.000108", "0.0447", "Reactome"], ["Hippo signaling pathway - Homo sapiens (human)", "154", "36 (23.4%)", "0.000257", "0.0914", "KEGG"], ["Diseases of signal transduction", "180", "40 (22.2%)", "0.000373", "0.097", "Reactome"], ["Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)", "20", "9 (45.0%)", "0.00044", "0.097", "Reactome"], ["Oxytocin signaling pathway - Homo sapiens (human)", "159", "36 (22.6%)", "0.000494", "0.097", "KEGG"], ["BMP2 signaling TGF-beta MV", "56", "17 (30.4%)", "0.000501", "0.097", "INOH"], ["Fc gamma R-mediated phagocytosis - Homo sapiens (human)", "92", "24 (26.1%)", "0.000502", "0.097", "KEGG"], ["effects of calcineurin in keratinocyte differentiation", "13", "7 (53.8%)", "0.000508", "0.097", "BioCarta"], ["NOTCH1 Intracellular Domain Regulates Transcription", "47", "15 (31.9%)", "0.000587", "0.104", "Reactome"], ["Calcium signaling pathway - Homo sapiens (human)", "180", "39 (21.7%)", "0.000741", "0.118", "KEGG"], ["Signaling by ERBB4", "263", "52 (19.8%)", "0.00107", "0.118", "Reactome"], ["Signaling by PDGF", "301", "58 (19.3%)", "0.0011", "0.118", "Reactome"], ["Signaling by FGFR3", "270", "53 (19.6%)", "0.00114", "0.118", "Reactome"], ["Signaling by FGFR4", "270", "53 (19.6%)", "0.00114", "0.118", "Reactome"], ["Signaling by FGFR1", "271", "53 (19.6%)", "0.00125", "0.118", "Reactome"], ["Extrinsic Pathway of Fibrin Clot Formation", "5", "4 (80.0%)", "0.00126", "0.118", "Reactome"], ["G alpha (12/13) signalling events", "76", "20 (26.3%)", "0.00127", "0.118", "Reactome"], ["alk in cardiac myocytes", "27", "10 (37.0%)", "0.00134", "0.118", "BioCarta"], ["TGF-beta super family signaling pathway canonical", "115", "27 (23.5%)", "0.00135", "0.118", "INOH"], ["nuclear receptors coordinate the activities of chromatin remodeling complexes and coactivators to facilitate initiation of transcription in carcinoma cells", "8", "5 (62.5%)", "0.00145", "0.118", "BioCarta"], ["Signaling by FGFR2", "273", "53 (19.4%)", "0.00148", "0.118", "Reactome"], ["Interleukin-3, 5 and GM-CSF signaling", "211", "43 (20.4%)", "0.00152", "0.118", "Reactome"], ["Downstream signaling of activated FGFR2", "267", "52 (19.5%)", "0.00152", "0.118", "Reactome"], ["Downstream signaling of activated FGFR1", "267", "52 (19.5%)", "0.00152", "0.118", "Reactome"], ["Downstream signaling of activated FGFR3", "267", "52 (19.5%)", "0.00152", "0.118", "Reactome"], ["Downstream signaling of activated FGFR4", "267", "52 (19.5%)", "0.00152", "0.118", "Reactome"], ["Signaling by FGFR", "274", "53 (19.3%)", "0.00161", "0.118", "Reactome"], ["Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human)", "83", "21 (25.3%)", "0.00167", "0.118", "KEGG"], ["Signaling by Insulin receptor", "262", "51 (19.5%)", "0.0017", "0.118", "Reactome"], ["Androgen receptor signaling pathway", "89", "22 (24.7%)", "0.00181", "0.118", "Wikipathways"], ["Signaling by NOTCH1", "73", "19 (26.0%)", "0.00191", "0.118", "Reactome"], ["Ectoderm Differentiation", "141", "31 (22.0%)", "0.00194", "0.118", "Wikipathways"], ["Signaling by ERBB2", "277", "53 (19.1%)", "0.00206", "0.118", "Reactome"], ["Interleukin-2 signaling", "202", "41 (20.3%)", "0.00209", "0.118", "Reactome"], ["HTLV-I infection - Homo sapiens (human)", "259", "50 (19.3%)", "0.00224", "0.118", "KEGG"], ["Arrhythmogenic Right Ventricular Cardiomyopathy", "74", "19 (25.7%)", "0.00227", "0.118", "Wikipathways"], ["Arrhythmogenic right ventricular cardiomyopathy (ARVC) - Homo sapiens (human)", "74", "19 (25.7%)", "0.00227", "0.118", "KEGG"], ["Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants", "53", "15 (28.3%)", "0.0023", "0.118", "Reactome"], ["Constitutive Signaling by NOTCH1 PEST Domain Mutants", "53", "15 (28.3%)", "0.0023", "0.118", "Reactome"], ["Signaling by NOTCH1 PEST Domain Mutants in Cancer", "53", "15 (28.3%)", "0.0023", "0.118", "Reactome"], ["Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer", "53", "15 (28.3%)", "0.0023", "0.118", "Reactome"], ["Signaling by NOTCH1 in Cancer", "53", "15 (28.3%)", "0.0023", "0.118", "Reactome"], ["Platelet activation - Homo sapiens (human)", "131", "29 (22.1%)", "0.00239", "0.118", "KEGG"], ["Adipogenesis", "131", "29 (22.1%)", "0.00239", "0.118", "Wikipathways"], ["Downstream signal transduction", "279", "53 (19.0%)", "0.00242", "0.118", "Reactome"], ["Signaling by EGFR", "292", "55 (18.8%)", "0.00246", "0.118", "Reactome"], ["Regulation of nuclear beta catenin signaling and target gene transcription", "80", "20 (25.0%)", "0.00248", "0.118", "PID"], ["Validated nuclear estrogen receptor alpha network", "64", "17 (26.6%)", "0.00257", "0.118", "PID"], ["NCAM signaling for neurite out-growth", "223", "44 (19.7%)", "0.0026", "0.118", "Reactome"], ["Downstream signaling events of B Cell Receptor (BCR)", "120", "27 (22.5%)", "0.0026", "0.118", "Reactome"], ["BMP signaling Dro", "34", "11 (32.4%)", "0.00275", "0.122", "INOH"], ["Signaling by Leptin", "193", "39 (20.2%)", "0.00287", "0.124", "Reactome"], ["Inactivation of Cdc42 and Rac", "9", "5 (55.6%)", "0.00291", "0.124", "Reactome"], ["DAP12 signaling", "282", "53 (18.8%)", "0.00306", "0.129", "Reactome"], ["Mesodermal Commitment Pathway", "76", "19 (25.0%)", "0.00314", "0.129", "Wikipathways"], ["Insulin receptor signalling cascade", "238", "46 (19.3%)", "0.00321", "0.129", "Reactome"], ["regulation of pgc-1a", "21", "8 (38.1%)", "0.00332", "0.129", "BioCarta"], ["EPH-ephrin mediated repulsion of cells", "30", "10 (33.3%)", "0.00332", "0.129", "Reactome"], ["Retinoic acid receptors-mediated signaling", "30", "10 (33.3%)", "0.00332", "0.129", "PID"], ["FoxO signaling pathway - Homo sapiens (human)", "134", "29 (21.6%)", "0.0034", "0.13", "KEGG"], ["Interleukin receptor SHC signaling", "195", "39 (20.0%)", "0.00346", "0.13", "Reactome"], ["NGF signalling via TRKA from the plasma membrane", "310", "57 (18.4%)", "0.00361", "0.133", "Reactome"], ["NRAGE signals death through JNK", "45", "13 (28.9%)", "0.00363", "0.133", "Reactome"], ["Constitutive Signaling by Aberrant PI3K in Cancer", "61", "16 (26.2%)", "0.00389", "0.14", "Reactome"], ["AMPK signaling pathway - Homo sapiens (human)", "124", "27 (21.8%)", "0.00422", "0.148", "KEGG"], ["MAPK1/MAPK3 signaling", "191", "38 (19.9%)", "0.00424", "0.148", "Reactome"], ["Signaling by VEGF", "274", "51 (18.6%)", "0.00444", "0.149", "Reactome"], ["Wnt Signaling Pathway and Pluripotency", "101", "23 (22.8%)", "0.00445", "0.149", "Wikipathways"], ["VEGFR2 mediated cell proliferation", "198", "39 (19.7%)", "0.00455", "0.149", "Reactome"], ["FRS-mediated FGFR2 signaling", "186", "37 (19.9%)", "0.00475", "0.149", "Reactome"], ["FRS-mediated FGFR1 signaling", "186", "37 (19.9%)", "0.00475", "0.149", "Reactome"], ["FRS-mediated FGFR3 signaling", "186", "37 (19.9%)", "0.00475", "0.149", "Reactome"], ["FRS-mediated FGFR4 signaling", "186", "37 (19.9%)", "0.00475", "0.149", "Reactome"], ["Dilated cardiomyopathy - Homo sapiens (human)", "90", "21 (23.3%)", "0.00475", "0.149", "KEGG"], ["repression of WNT target genes", "10", "5 (50.0%)", "0.00519", "0.16", "Reactome"], ["MAPK family signaling cascades", "225", "43 (19.1%)", "0.00529", "0.16", "Reactome"], ["MAPK signaling pathway - Homo sapiens (human)", "257", "48 (18.7%)", "0.00529", "0.16", "KEGG"], ["transcription regulation by methyltransferase of carm1", "14", "6 (42.9%)", "0.00556", "0.16", "BioCarta"], ["Netrin-1 signaling", "37", "11 (29.7%)", "0.0057", "0.16", "Reactome"], ["IRS-related events triggered by IGF1R", "239", "45 (18.8%)", "0.00583", "0.16", "Reactome"], ["IGF1R signaling cascade", "239", "45 (18.8%)", "0.00583", "0.16", "Reactome"], ["Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R)", "239", "45 (18.8%)", "0.00583", "0.16", "Reactome"], ["Neuronal System", "291", "53 (18.2%)", "0.00595", "0.16", "Reactome"], ["DAP12 interactions", "298", "54 (18.1%)", "0.00614", "0.16", "Reactome"], ["Gastric acid secretion - Homo sapiens (human)", "75", "18 (24.0%)", "0.00631", "0.16", "KEGG"], ["Fatty acid, triacylglycerol, and ketone body metabolism", "98", "22 (22.4%)", "0.00637", "0.16", "Reactome"], ["PIP3 activates AKT signaling", "98", "22 (22.4%)", "0.00637", "0.16", "Reactome"], ["PI-3K cascade:FGFR2", "98", "22 (22.4%)", "0.00637", "0.16", "Reactome"], ["PI-3K cascade:FGFR1", "98", "22 (22.4%)", "0.00637", "0.16", "Reactome"], ["PI-3K cascade:FGFR3", "98", "22 (22.4%)", "0.00637", "0.16", "Reactome"], ["PI-3K cascade:FGFR4", "98", "22 (22.4%)", "0.00637", "0.16", "Reactome"], ["PI3K events in ERBB4 signaling", "98", "22 (22.4%)", "0.00637", "0.16", "Reactome"], ["PI3K events in ERBB2 signaling", "98", "22 (22.4%)", "0.00637", "0.16", "Reactome"], ["VEGFA-VEGFR2 Pathway", "266", "49 (18.4%)", "0.00639", "0.16", "Reactome"], ["Collagen biosynthesis and modifying enzymes", "64", "16 (25.0%)", "0.00644", "0.16", "Reactome"], ["IRS-mediated signalling", "235", "44 (18.7%)", "0.00704", "0.173", "Reactome"], ["O-linked glycosylation", "105", "23 (21.9%)", "0.00731", "0.173", "Reactome"], ["RAF/MAP kinase cascade", "185", "36 (19.5%)", "0.00759", "0.173", "Reactome"], ["SHC1 events in EGFR signaling", "185", "36 (19.5%)", "0.00759", "0.173", "Reactome"], ["SOS-mediated signalling", "185", "36 (19.5%)", "0.00759", "0.173", "Reactome"], ["GRB2 events in EGFR signaling", "185", "36 (19.5%)", "0.00759", "0.173", "Reactome"], ["SHC1 events in ERBB2 signaling", "185", "36 (19.5%)", "0.00759", "0.173", "Reactome"], ["SHC1 events in ERBB4 signaling", "185", "36 (19.5%)", "0.00759", "0.173", "Reactome"], ["GRB2 events in ERBB2 signaling", "185", "36 (19.5%)", "0.00759", "0.173", "Reactome"], ["Regulation of Commissural axon pathfinding by Slit and Robo", "4", "3 (75.0%)", "0.00784", "0.175", "Reactome"], ["Fosphenytoin (Antiarrhythmic) Metabolism Pathway", "4", "3 (75.0%)", "0.00784", "0.175", "SMPDB"], ["Ephrin B reverse signaling", "24", "8 (33.3%)", "0.0084", "0.186", "PID"], ["Signaling by Interleukins", "270", "49 (18.1%)", "0.00851", "0.186", "Reactome"], ["Transport of organic anions", "11", "5 (45.5%)", "0.00852", "0.186", "Reactome"], ["Rho GTPase cycle", "125", "26 (20.8%)", "0.00914", "0.194", "Reactome"], ["PI3K/AKT activation", "101", "22 (21.8%)", "0.00918", "0.194", "Reactome"], ["Thyroid hormone signaling pathway - Homo sapiens (human)", "119", "25 (21.0%)", "0.0092", "0.194", "KEGG"], ["Signaling by NOTCH", "107", "23 (21.5%)", "0.00923", "0.194", "Reactome"], ["Cell death signalling via NRAGE, NRIF and NADE", "61", "15 (24.6%)", "0.0096", "0.2", "Reactome"]], "row_count": 120, "column_count": 6, "numeric_cells": 489, "header_rows": 1, "locator": "section[3]/table-wrap[2]#t0010"}}, {"id": "asset:table:pmid:29201983:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e78853399a1c568de357199c8a538754a6fb4926905f7241b56431765a03fa06", "bytes": 3733, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[3]#t0015", "version": null, "note": "Names and FCs of the 33 neighbors of the EntrezGene ID 2033 (see Fig. 1) after the exposure of PHHs for 5 days daily to VPA. PHHs, primary human hepatocytes; VPA, valproic acid; FCs, fold changes.", "structure": {"pmcid": "PMC5702865", "section_index": 3, "section_title": "Data", "row_count": 53, "column_count": 5}, "table": {"label": "Table 3", "caption": "Names and FCs of the 33 neighbors of the EntrezGene ID 2033 (see Fig. 1) after the exposure of PHHs for 5 days daily to VPA. PHHs, primary human hepatocytes; VPA, valproic acid; FCs, fold changes.", "rows": [["Entrez Gene ID", "Gene Symbol", "Gene Name", "MeDIP-seq FCs", "Steatosis-related pathway(s)"], ["354", "KLK3", "kallikrein-related peptidase 3", "1.9", "–"], ["595", "CCND1", "cyclin D1", "2.1", "–"], ["864", "RUNX3", "runt-related transcription factor 3", "2", "–"], ["", "", "", "", ""], ["1026", "CDKN1A", "cyclin-dependent kinase inhibitor 1 A (p21, Cip1)", "-3.5", "Adipogenesis"], ["Signaling events mediated by HDAC Class III"], ["", "", "", "", ""], ["1387", "CREBBP", "CREB binding protein", "-3.2", "Signaling events mediated by HDAC Class III"], ["Transcriptional regulation of white adipocyte differentiation"], ["Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)"], ["Signaling events mediated by HDAC Class I"], ["Fatty acid, triacylglycerol, and ketone body metabolism"], ["1488", "CTBP2", "C-terminal binding protein 2", "-3.9", "–"], ["1844", "DUSP2", "dual specificity phosphatase 2", "2.4", "–"], ["1958", "EGR1", "early growth response 1", "-3.6", "–"], ["", "", "", "", ""], ["2033", "EP300", "E1A binding protein p300", "-5.2", "Signaling events mediated by HDAC Class III"], ["Transcriptional regulation of white adipocyte differentiation"], ["Signaling events mediated by HDAC Class I"], ["2309", "FOXO3", "forkhead box O3", "2.2", "Signaling events mediated by HDAC Class III"], ["2353", "FOS", "FBJ murine osteosarcoma viral oncogene homolog", "-3.5", "–"], ["2626", "GATA4", "GATA binding protein 4", "2.5", "Adipogenesis"], ["4088", "SMAD3", "SMAD family member 3", "2.4", "Adipogenesis"], ["4205", "MEF2A", "myocyte enhancer factor 2 A", "2.2", "Adipogenesis"], ["4772", "NFATC1", "nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1", "1.8", "–"], ["5594", "MAPK1", "mitogen-activated protein kinase 1", "2.3", "–"], ["5914", "RARA", "retinoic acid receptor, alpha", "-3.8", "Adipogenesis"], ["6095", "RORA", "RAR-related orphan receptor A", "-4", "Adipogenesis"], ["", "", "", "", ""], ["6256", "RXRA", "retinoid X receptor, alpha", "-3.8", "Adipogenesis"], ["Transcriptional regulation of white adipocyte differentiation"], ["Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)"], ["Fatty acid, triacylglycerol, and ketone body metabolism"], ["6670", "SP3", "Sp3 transcription factor", "-4.1", "–"], ["6776", "STAT5A", "signal transducer and activator of transcription 5 A", "2.2", "Adipogenesis"], ["6925", "TCF4", "transcription factor 4", "-4", "–"], ["6929", "TCF3", "transcription factor 3", "2.1", "–"], ["6934", "TCF7L2", "transcription factor 7-like 2 (T-cell specific, HMG-box)", "-3.4", "–"], ["6938", "TCF12", "transcription factor 12", "2.12", "–"], ["7026", "NR2F2", "nuclear receptor subfamily 2, group F, member 2", "2.6", "–"], ["7161", "TP73", "tumor protein p73", "2.5", "–"], ["9252", "RPS6KA5", "ribosomal protein S6 kinase, 90 kDa, polypeptide 5", "-3.9", "–"], ["9314", "9314", "Kruppel-like factor 4 (gut)", "2.7", "–"], ["", "", "", "", ""], ["9611", "NCOR1", "nuclear receptor corepressor 1", "-3.4", "Adipogenesis"], ["Transcriptional regulation of white adipocyte differentiation"], ["Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)"], ["Signaling events mediated by HDAC Class I"], ["Fatty acid, triacylglycerol, and ketone body metabolism"], ["10365", "KLF2", "Kruppel-like factor 2", "-3.3", "Signaling events mediated by HDAC Class III"], ["23411", "SIRT1", "sirtuin 1", "-3.5", ""], ["90427", "BMF", "Bcl2 modifying facto", "2.2", ""]], "row_count": 53, "column_count": 5, "numeric_cells": 94, "header_rows": 1, "locator": "section[3]/table-wrap[3]#t0015"}}], "gaps": ["asset:data:geo:E-MTAB-4437 not downloaded", "asset:data:geo:E-MTAB-4437 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "edger", "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": "Statistical analysis was performed applying the default parameters of MEDIPS, using the edgeR module, an empirical analysis of digital gene expression data in R that uses Bayes estimation and exact tests based on the negative binomial distribution [8]."}}], "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": ["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: edger."}, "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": ["E-MTAB-4437"], "resolved_accessions": ["E-MTAB-4437"], "statements": ["MeDIP-seq raw data are available on ArrayExpress (accession number: E-MTAB-4437)."], "basis": "The paper names E-MTAB-4437 in ArrayExpress and the accession resolves in the repository. 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