{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina_HumanHT-12v4"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00010000869"],"sample_count":["62"],"description":["EGA dataset EGAD00010000869"],"repository":["EGA"],"title":["Rna_expression"],"pubmed_abstract":["Gliomas represent approximately 30% of all central nervous system tumors and 80% of malignant brain tumors. To understand the molecular mechanisms underlying the malignant progression of low-grade gliomas with mutations in IDH1 (encoding isocitrate dehydrogenase 1), we studied paired tumor samples from 41 patients, comparing higher-grade, progressed samples to their lower-grade counterparts. Integrated genomic analyses, including whole-exome sequencing and copy number, gene expression and DNA methylation profiling, demonstrated nonlinear clonal expansion of the original tumors and identified oncogenic pathways driving progression. These include activation of the MYC and RTK-RAS-PI3K pathways and upregulation of the FOXM1- and E2F2-mediated cell cycle transitions, as well as epigenetic silencing of developmental transcription factor genes bound by Polycomb repressive complex 2 in human embryonic stem cells. Our results not only provide mechanistic insight into the genetic and epigenetic mechanisms driving glioma progression but also identify inhibition of the bromodomain and extraterminal (BET) family as a potential therapeutic approach."],"pubmed_title":["Integrated genomic characterization of IDH1-mutant glioma malignant progression."],"pubmed_authors":["Bai Hanwen H, Harmancı Akdes Serin AS, Erson-Omay E Zeynep EZ, Li Jie J, Coşkun Süleyman S, Simon Matthias M, Krischek Boris B, Özduman Koray K, Omay S Bülent SB, Sorensen Eric A EA, Turcan Şevin Ş, Bakırcığlu Mehmet M, Carrión-Grant Geneive G, Murray Phillip B PB, Clark Victoria E VE, Ercan-Sencicek A Gulhan AG, Knight James J, Sencar Leman L, Altınok Selin S, Kaulen Leon D LD, Gülez Burcu B, Timmer Marco M, Schramm Johannes J, Mishra-Gorur Ketu K, Henegariu Octavian O, Moliterno Jennifer J, Louvi Angeliki A, Chan Timothy A TA, Tannheimer Stacey L SL, Pamir M Necmettin MN, Vortmeyer Alexander O AO, Bilguvar Kaya K, Yasuno Katsuhito K, Günel Murat M"],"name_synonyms":["Non-Polyadenylated RNA, ribonucleic acid, Acid, RNA, Ribonucleic, ribose nucleic acid, yeast nucleic acid, Ribonukleinsaeure, Non Polyadenylated RNA, Gene Products, ribonucleic acids, pentosenucleic acids, Non-Polyadenylated, Ribonucleic acids, RNS, Ribonucleic Acid, Non Polyadenylated, RNA Gene Products."],"description_synonyms":["Non-Polyadenylated RNA, ribonucleic acid, Acid, RNA, Ribonucleic, microarray., ribose nucleic acid, yeast nucleic acid, Ribonukleinsaeure, Non Polyadenylated RNA, Gene Products, ribonucleic acids, pentosenucleic acids, Non-Polyadenylated, Ribonucleic acids, RNS, Ribonucleic Acid, Non Polyadenylated, RNA Gene Products"],"pubmed_title_synonyms":["Glioma 1, Glioma NOS, Glioma (except Nasal glioma, GLM, glial tumors, IDH, malignant, neuroglial tumor, IDP, obsolete_glioma, Mixed Glioma, Malignant Glioma, Neuroglial Tumor, tumour of the neuroglia, Tumor, Malignant, IDCD, neoplasm of neuroglia, [M]Glioma NOS (morphologic abnormality), AI314845, tumor of the neuroglia, HEL-S-26, [M]Gliomas (morphologic abnormality), Gliomas, Mixed, Glial Cell Tumor, [M]Glioma NOS, HEL-216, AI788952, Mixed Gliomas, Id-1, PICD, Glial Tumor, Idh-1, NOS (except Nasal glioma, Neuroglial Neoplasm, glioma (morphologic abnormality), Neuroglial Neoplasms, Glioma NOS (morphologic abnormality), Idpc, neuroglial tumour, Glial Cell, Malignant glioma, Neoplasm of the Neuroglia, Tumor of Neuroglia, Glial Neoplasm, E030024J03Rik, neuroglial neoplasm, tumor of neuroglia, Neoplasm of Neuroglia, glial tumor, no ICD-O subtype, Neoplasms of Neuroglia., Tumor of the Neuroglia, IDPC, tumour of neuroglia, glial tumour, Glial Cell Tumors, not neoplastic), Gliomas (morphologic abnormality), Malignant Gliomas, Glioma, glial neoplasm, [M]Gliomas, malignant (morphologic abnormality), glioma, Tumors of Neuroglia, neoplasm of the neuroglia, Tumors"],"pubmed_abstract_synonyms":["isocitrate dehydrogenase, BB238854, T-cell leukemia, RAS, Ras, l(1)G0098, Materials, dP60, Kinship, GLM, Vps34, Brain Neoplasms, AGL4, Stem Cells, BcDNA:LD15217, Mixed Glioma, MYC, Myc, Scc-1, Tumor, Ras-1, VPS34, Brain Metastases, 11621, B430311C09Rik, Mutations, PI-3 kinase, p110-alpha, ras, c-ras2, INTRACRANIAL NEOPL, EG:BACN5I9.1, tumor of the neuroglia, Life Cycle, [M]Gliomas (morphologic abnormality), (trimethylammoniumyl)acetate, Whole Transcriptome, Transcriptome Sequencing, TGT3, myc, tumour of brain, \"CNS neoplasm\" EXACT [CSP2005:2012-5421], foxm1l, Id-1, PICD, Cell Division Cycles, Dp60, Kinship Network, glioma (morphologic abnormality), brain neoplasms, Idpc, PI3K_59F, dm/dMyc, fkhl16, N, dE2F-2, Brain Malignant Neoplasms, F10N7_150, Neoplasm of the Neuroglia, PI3-kinase activity, Brain Tumor, D17Mit170, PI3Kgamma, Epigenomic, Primary Central Nervous System Neoplasm, MCAP, Brain Neoplasm, IDPC, PI3K 68D, tumour of neuroglia, BET, Bet, acidol, Gliomas (morphologic abnormality), zinc ion regulated proximal promoter sequence-specific DNA binding, ATP - 1-phosphatidyl-1D-myo-inositol 3-phosphotransferase activity, TRANSCRIPTION FACTOR, CG1799, Tumors, RNA polymerase II distal enhancer sequence-specific binding, RNA polymerase II core promoter proximal region sequence-specific binding, dVps34, NAD Isocitrate, Intracranial Neoplasm, brain neoplasm, Malignant Brain Neoplasms, Ras2, RAS2, Brain Benign Neoplasm, dmyc1, Ras1, RAS1, rea, Exome, bet, familial, p50alpha, l(3)L3852, Malignant Glioma, Primary Brain Neoplasm, Tl3, Tl2, Isocitrate Dehydrogenase-I, CG2699, Isocitrate Dehydrogenase, DmelCG5373, Primary Brain Tumor, Central Nervous System Tumor, Benign, C530050K14, Dm, Brain Malignant Neoplasm, type-1 PI3K, dRas85D, N-trimethylammonioacetate, sequence-specific distal enhancer binding RNA polymerase II transcription factor activity, mMyc, ras1, ras2, activation, PIG29, Malignant Brain Neoplasm, BcDNA:RE36103, Primary Malignant, Idh-1, CG11621, AA408308, Complete Transcriptome, polycomb repressive complex 2, CT22171, Hras-1, F14P3_4, Benign Neoplasms, Dm Ras1, Tumor of Neuroglia, DmelCG4141, Transcription factor, D-Myc, F8A5_4, Malignant Neoplasms, APDS, HFH-11B, RasI, hfh-11, neoplasm of the brain, Material, PI3KBETA, Cells, Whole Exome Sequencing, NAD, copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, trimethylglycocoll, not neoplastic), Glioma, N-trimethylammonio acetate, glial neoplasm, PTPbeta2, dMyc1, Epigenetics, malignant (morphologic abnormality), other neoplasm, metal ion regulated sequence-specific DNA binding, Harvey-ras, Neoplasms of Neuroglia, Hras1, Bret, Brain, CG10798, Glioma NOS, Brain Tumors, dm/myc, Dehydrogenase, Neoplasms, dRas, MPP-2, neuroglial tumor, number, CG1167, H-ras, DRAS1, AI450271, DRas2, Neuroglial Tumor, IMPDH, SEPALLATA 2, HFH-11, Transcription Factor, dMyc, dMYC, LD06825, Dras2, Dras1, PIK3, zinc ion regulated core promoter proximal region sequence-specific DNA binding, Recurrent Brain Tumors, D-Ras, dVps34/PI3K59F, Pi3Kp60, Isocitrate Dehydrogenase (NAD+), PI3K-dp110, Kras-2, central nervous system tumour, Nop30, dPI3K, bHLHe57, anon-92Ed, IMPdH, Ha-ras, trimethylglycine, Dras, class I, ras 1, Cycles, Transcription, Complete, Exome Sequencings, CNS, Glioma NOS (morphologic abnormality), raspberry/impd, Cell Division Cycle, cell-division cycle, Dmyc, DMYc, central nervous system tumors, Glial Neoplasm, E2F, Ras[V12], Pi3Kp110, Expressions, EK3-4, DmelCG1071, Sequencing, neuroglial neoplasm, DRas, P110BETA, Neoplasias, DRas85D/Ras, Dmras64B, AW554517, malignant tumor of CNS, Whole Exome, IDH-NADP, glial tumor, PI3K21B, Nird, RNCMYC, RNA polymerase II proximal promoter sequence-specific DNA binding, Whole, copper ion regulated proximal promoter sequence-specific DNA binding, 2-N, Expression, MCM, bHLHe39, constitutitional genetic, Tumors of Neuroglia, dmyc, NEOPL INTRACRANIAL, Cancer, Cpk, Idh-NADP, Fkh16, Malignant Neoplasm, cou, Complete Exome Sequencings, AA414921, Family Research, class II, type III phosphoinositide 3-kinase activity, TRIDENT, Betaine, zinc ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, homeobox 1, Primary, e2f2, Factor, D-ras-1, dE2f2, PI(3)K, Cell, cpk, E(faf), PI3K-92E/Dp110, Family Members, Exome Sequencing, DmelCG1167, PIK3C1, Lr, Foxm1b, CWS5, Neoplasm, S35097, RNA polymerase II transcription factor activity, de2f2, CD148, HNF-3, Human Embryonic, \"neoplasm of central nervous system (disorder)\" EXACT [SNOMEDCT_2005_07_31:126951006], RAS85D, brain neoplasm (disease), Dmras85D, CG1071, l(1)9Eb, Neuroglial Neoplasms, UNQ26, Glial Cell, Cancers, DmelCG11621, E2F2, metal ion regulated core promoter proximal region sequence-specific binding, INS-1, F10N7.150, caPI3K, CLOVE, DmVps34, IMD14, Families, PI3K_68D, PI3K-92D, Central Nervous System Tumors, Bra, Malignant Gliomas, Central Nervous System, Benign Brain Neoplasm, Dmp110, brain tumour, hereditary, Relatives, Neoplasia, dE2F2, \"central nervous system tumors\" EXACT [NCI2004_11_17:C9293], Glioma 1, Networks, Ras1/RAs85D, CG5373, ATVPS34, glial tumors, DEP-1, central nervous system tumor, myc-B, c-rasHa, PI3K, DmelCG10798, E(sev)3C, Dp110, Isocitrate:NAD+ oxidoreductase (decarboxylating), Trident, tumour of the neuroglia, neoplasm of central nervous system, CG11485, c-MYC, c-Myc, PHOSPHATIDYLINOSITOL 3-KINASE, [M]Glioma NOS (morphologic abnormality), DmelCG2699, F8A5.4, RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity, AI314845, ARC, Family Life Cycle., p110alpha, phosphatidylinositol 3-kinase activity, D-Ras1, abromine, c-myc, me75, Gene Expressions, RTK, Pi3K92D, CG4141, Mpm2, Complete Exome Sequencing, Whole Transcriptome Sequencing, l(1)G0436, neuroglial tumour, catalyst activity, Primary Brain Tumors, Pi3k, ras85B, ras85D, PI[[3]]K, RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity, T1, genetic, Trimethylammonioacetate, D-ras-2, p55alpha, neoplasm of brain, Primary Malignant Brain Tumors, Human Embryonic Stem, Recurrent Brain Tumor, Cell Cycles, AGAMOUS-like 4, Malignancies, Pi3K, PI3k, CNS Neoplasms, sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity, Family Life Cycles, glioma, MCMTC, neoplasm of the neuroglia, l(3)s1747, PI3K68D, Glioma (except Nasal glioma, AU016757, N-Trimethylglycine, IDH, Ki-ras, P110DELTA, PtdIns-3-kinase activity, UNQ262/PRO299, Malignant Primary Brain Neoplasms, IDP, obsolete_glioma, mpp2, NEOPL BRAIN, metal ion regulated sequence-specific DNA binding RNA polymerase II transcription factor activity, DNA methylation profiling, CNS Neoplasm, vacuolar protein sorting 34, results, IDCD, Division Cycles, dPIK, 1-phosphatidylinositol 3-kinase activity, Brain Benign Neoplasms, idh, NOP, Malignant Primary Brain Tumors, Genetic Materials, p21[Ras1], Gliomas, dRas1, dRAS1, Glial Cell Tumor, Scc1, Filiation, Dras85D, Genetic Material, ras-2, HFH11, l(1)G0354, F14P3.4, l(1)G0351, LD02673, Factors, p85alpha, Division Cycle, DmelCG1799, Epigenetic, Cancer of the Brain, c-Ha-ras, l(1)G0359, D-ras1, l(1)G0238, D-ras2, C-ras1, tumor of the Brain, CNS neoplasm, Dras64B, PI3K 68_D, Byp, d-myc, C-ras2, l(3)06677, Myc2, Intracranial, l(1)G0002, MPP2, Life Cycles, Niard, l(1)G0482, p110D, myc2, brain tumor, Patient, Human Embryonic Stem Cell, c-H-ras, Tumor of the Neuroglia, l(1)G0127, glial tumour, Cistron, inherited genetic, p120-PI3K, MRTL, RPTPJ, Transcriptome Sequencings, MPHOSPH2, droPIK57, N-trimethylmethanaminium inner salt, metal ion regulated proximal promoter sequence-specific DNA binding, Primary Malignant Brain Neoplasms, Family Member, RasV12, Extra Sex Combs/Enhancer of Zeste complex, 1-carboxy-N, Complete Exome, Primary Brain Neoplasms, Cancer of Brain, l(1)G0139, PI3K92E, Isocitrate Dehydrogenase I, Kras2, Benign Neoplasm, Gene, Pi3K_59F, Network, DmelCG9375, type I phosphatidylinositol kinase activity, Malignant, presence, phosphatidylinositol 3-kinase, l(1)G0388, E130207A07, anon-WO03040301.171, MYCC, Recurrent, p60, Cycle, c-myc II, PHOSPATIDYLINOSITOL 3-KINASE, Low, Primary Central Nervous System Neoplasms, HEL-216, AI788952, l(1)G0380, Mixed Gliomas, Dp110/PI3K, Central Nervous System Neoplasm, PI3K-68D/E, p21B, Ptpb2, WES, Central Nervous System Neoplasms, dras1, Dm-ras-64B, Genetic, tumour of the Brain, PRC2 complex, Malignancy, Research, malignant neoplasm of central nervous system, Cell Division, PI3'K, E030024J03Rik, l(1)G0391, E2F-2, DmelCG7176, BHLHE39, Ras 85D, PI3K-68D, PRIMARY BRAIN NEOPL, Trimethylaminoacetate, Clients, [M]Gliomas, Kinship Networks, ras-l, Family, tumor of brain, l(1)G0056, dP110, 6330412C24Rik, CG9375, p120, malignant, Benign Brain Neoplasms, p110, K-ras, Vps34p, Cistrons, Client, neoplasm of neuroglia, transcription factor activity, count in organism, fs(3)05703, ATP:1-phosphatidyl-1D-myo-inositol 3-phosphotransferase activity, vps34, 9230110J10, EP(X)1093, HEL-S-26, dp110, Brain Cancers, Mixed, Isocitrate, [M]Glioma NOS, AI929937, PI3CG, Brain Metastase, metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity, KNOTTED1-like homeobox gene 5, WIN, Intracranial Neoplasms, PI-3-K, Glial Tumor, NOS (except Nasal glioma, PI3K-59F, Complete Transcriptome Sequencing, Neuroglial Neoplasm, PI3K-Dp110, CG7176, Malignant glioma, class III, p110gamma, FOXM1B, copper ion regulated core promoter proximal region sequence-specific binding, Brain Cancer, FKHL16, Su(tor)3-2, hESC, tumor of neuroglia, Neoplasm of Neuroglia, NAD Isocitrate Dehydrogenase, no ICD-O subtype, cardinality, Glial Cell Tumors, hESCs"],"additional_accession":[]},"is_claimable":false,"name":"Rna_expression","description":"RNA expression microarray","dates":{"updated":"2019-04-11 11:51:29"},"accession":"EGAD00010000869","cross_references":{"TAXONOMY":["9606"],"pubmed":["26618343"],"EGA":["EGAC00001000406","EGAS00001001588"]}}