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Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context Journal article
Cell Reports, 2018,Volume: 23,Issue: 1,Page: 297-312.e12
Authors:  Chiu H.-S.;  Somvanshi S.;  Patel E.;  Chen T.-W.;  Singh V.P.;  Zorman B.;  Patil S.L.;  Pan Y.;  Chatterjee S.S.;  Caesar-Johnson S.J.;  Demchok J.A.;  Felau I.;  Kasapi M.;  Ferguson M.L.;  Hutter C.M.;  Sofia H.J.;  Tarnuzzer R.;  Wang Z.;  Yang L.;  Zenklusen J.C.;  Zhang J.J.;  Chudamani S.;  Liu J.;  Lolla L.;  Naresh R.;  Pihl T.;  Sun Q.;  Wan Y.;  Wu Y.;  Cho J.;  DeFreitas T.;  Frazer S.;  Gehlenborg N.;  Getz G.;  Heiman D.I.;  Kim J.;  Lawrence M.S.;  Lin P.;  Meier S.;  Noble M.S.;  Saksena G.;  Voet D.;  Zhang H.;  Bernard B.;  Chambwe N.;  Dhankani V.;  Knijnenburg T.;  Kramer R.;  Leinonen K.;  Liu Y.;  Miller M.;  Reynolds S.;  Shmulevich I.;  Thorsson V.;  Zhang W.;  Akbani R.;  Broom B.M.;  Hegde A.M.;  Ju Z.;  Kanchi R.S.;  Korkut A.;  Li J.;  Liang H.;  Ling S.;  Liu W.;  Lu Y.;  Mills G.B.;  Ng K.-S.;  Rao A.;  Ryan M.;  Wang J.;  Weinstein J.N.;  Zhang J.;  Abeshouse A.;  Armenia J.;  Chakravarty D.;  Chatila W.K.;  de Bruijn I.;  Gao J.;  Gross B.E.;  Heins Z.J.;  Kundra R.;  La K.;  Ladanyi M.;  Luna A.;  Nissan M.G.;  Ochoa A.;  Phillips S.M.;  Reznik E.;  Sanchez-Vega F.;  Sander C.;  Schultz N.;  Sheridan R.;  Sumer S.O.;  Sun Y.;  Taylor B.S.;  Wang J.;  Zhang H.;  Anur P.;  Peto M.;  Spellman P.;  Benz C.;  Stuart J.M.;  Wong C.K.;  Yau C.;  Hayes D.N.;  Parker J.S.;  Wilkerson M.D.;  Ally A.;  Balasundaram M.;  Bowlby R.;  Brooks D.;  Carlsen R.;  Chuah E.;  Dhalla N.;  Holt R.;  Jones S.J.M.;  Kasaian K.;  Lee D.;  Ma Y.;  Marra M.A.;  Mayo M.;  Moore R.A.;  Mungall A.J.;  Mungall K.;  Robertson A.G.;  Sadeghi S.;  Schein J.E.;  Sipahimalani P.;  Tam A.;  Thiessen N.;  Tse K.;  Wong T.;  Berger A.C.;  Beroukhim R.;  Cherniack A.D.;  Cibulskis C.;  Gabriel S.B.;  Gao G.F.;  Ha G.;  Meyerson M.;  Schumacher S.E.;  Shih J.;  Kucherlapati M.H.;  Kucherlapati R.S.;  Baylin S.;  Cope L.;  Danilova L.;  Bootwalla M.S.;  Lai P.H.;  Maglinte D.T.;  Van Den Berg D.J.;  Weisenberger D.J.;  Auman J.T.;  Balu S.;  Bodenheimer T.;  Fan C.;  Hoadley K.A.;  Hoyle A.P.;  Jefferys S.R.;  Jones C.D.;  Meng S.;  Mieczkowski P.A.;  Mose L.E.;  Perou A.H.;  Perou C.M.;  Roach J.;  Shi Y.;  Simons J.V.;  Skelly T.;  Soloway M.G.;  Tan D.;  Veluvolu U.;  Fan H.;  Hinoue T.;  Laird P.W.;  Shen H.;  Zhou W.;  Bellair M.;  Chang K.;  Covington K.;  Creighton C.J.;  Dinh H.;  Doddapaneni H.;  Donehower L.A.;  Drummond J.;  Gibbs R.A.;  Glenn R.;  Hale W.;  Han Y.;  Hu J.;  Korchina V.;  Lee S.;  Lewis L.;  Li W.;  Liu X.;  Morgan M.;  Morton D.;  Muzny D.;  Santibanez J.;  Sheth M.;  Shinbrot E.;  Wang L.;  Wang M.;  Wheeler D.A.;  Xi L.;  Zhao F.;  Hess J.;  Appelbaum E.L.;  Bailey M.;  Cordes M.G.;  Ding L.;  Fronick C.C.;  Fulton L.A.;  Fulton R.S.;  Kandoth C.;  Mardis E.R.;  McLellan M.D.;  Miller C.A.;  Schmidt H.K.;  Wilson R.K.;  Crain D.;  Curley E.;  Gardner J.;  Lau K.;  Mallery D.;  Morris S.;  Paulauskis J.;  Penny R.;  Shelton C.;  Shelton T.;  Sherman M.;  Thompson E.;  Yena P.;  Bowen J.;  Gastier-Foster J.M.;  Gerken M.;  Leraas K.M.;  Lichtenberg T.M.;  Ramirez N.C.;  Wise L.;  Zmuda E.;  Corcoran N.;  Costello T.;  Hovens C.;  Carvalho A.L.;  de Carvalho A.C.;  Fregnani J.H.;  Longatto-Filho A.;  Reis R.M.;  Scapulatempo-Neto C.;  Silveira H.C.S.;  Vidal D.O.;  Burnette A.;  Eschbacher J.;  Hermes B.;  Noss A.;  Singh R.;  Anderson M.L.;  Castro P.D.;  Ittmann M.;  Huntsman D.;  Kohl B.;  Le X.;  Thorp R.;  Andry C.;  Duffy E.R.;  Lyadov V.;  Paklina O.;  Setdikova G.;  Shabunin A.;  Tavobilov M.;  McPherson C.;  Warnick R.;  Berkowitz R.;  Cramer D.;  Feltmate C.;  Horowitz N.;  Kibel A.;  Muto M.;  Raut C.P.;  Malykh A.;  Barnholtz-Sloan J.S.;  Barrett W.;  Devine K.;  Fulop J.;  Ostrom Q.T.;  Shimmel K.;  Wolinsky Y.;  Sloan A.E.;  De Rose A.;  Giuliante F.;  Goodman M.;  Karlan B.Y.;  Hagedorn C.H.;  Eckman J.;  Harr J.;  Myers J.;  Tucker K.;  Zach L.A.;  Deyarmin B.;  Hu H.;  Kvecher L.;  Larson C.;  Mural R.J.;  Somiari S.;  Vicha A.;  Zelinka T.;  Bennett J.;  Iacocca M.;  Rabeno B.;  Swanson P.;  Latour M.;  Lacombe L.;  Tetu B.;  Bergeron A.;  McGraw M.;  Staugaitis S.M.;  Chabot J.;  Hibshoosh H.;  Sepulveda A.;  Su T.;  Wang T.;  Potapova O.;  Voronina O.;  Desjardins L.;  Mariani O.;  Roman-Roman S.;  Sastre X.;  Stern M.-H.;  Cheng F.;  Signoretti S.;  Berchuck A.;  Bigner D.;  Lipp E.;  Marks J.;  McCall S.;  McLendon R.;  Secord A.;  Sharp A.;  Behera M.;  Brat D.J.;  Chen A.;  Delman K.;  Force S.;  Khuri F.;  Magliocca K.;  Maithel S.;  Olson J.J.;  Owonikoko T.;  Pickens A.;  Ramalingam S.;  Shin D.M.;  Sica G.;  Van Meir E.G.;  Zhang H.;  Eijckenboom W.;  Gillis A.;  Korpershoek E.;  Looijenga L.;  Oosterhuis W.;  Stoop H.;  van Kessel K.E.;  Zwarthoff E.C.;  Calatozzolo C.;  Cuppini L.;  Cuzzubbo S.;  DiMeco F.;  Finocchiaro G.;  Mattei L.;  Perin A.;  Pollo B.;  Chen C.;  Houck J.;  Lohavanichbutr P.;  Hartmann A.;  Stoehr C.;  Stoehr R.;  Taubert H.;  Wach S.;  Wullich B.;  Kycler W.;  Murawa D.;  Wiznerowicz M.;  Chung K.;  Edenfield W.J.;  Martin J.;  Baudin E.;  Bubley G.;  Bueno R.;  De Rienzo A.;  Richards W.G.;  Kalkanis S.;  Mikkelsen T.;  Noushmehr H.;  Scarpace L.;  Girard N.;  Aymerich M.;  Campo E.;  Gine E.;  Guillermo A.L.;  Van Bang N.;  Hanh P.T.;  Phu B.D.;  Tang Y.;  Colman H.;  Evason K.;  Dottino P.R.;  Martignetti J.A.;  Gabra H.;  Juhl H.;  Akeredolu T.;  Stepa S.;  Hoon D.;  Ahn K.;  Kang K.J.;  Beuschlein F.;  Breggia A.;  Birrer M.;  Bell D.;  Borad M.;  Bryce A.H.;  Castle E.;  Chandan V.;  Cheville J.;  Copland J.A.;  Farnell M.;  Flotte T.;  Giama N.;  Ho T.;  Kendrick M.;  Kocher J.-P.;  Kopp K.;  Moser C.;  Nagorney D.;  O'Brien D.;  O'Neill B.P.;  Patel T.;  Petersen G.;  Que F.;  Rivera M.;  Roberts L.;  Smallridge R.;  Smyrk T.;  Stanton M.;  Thompson R.H.;  Torbenson M.;  Yang J.D.;  Zhang L.;  Brimo F.;  Ajani J.A.;  Gonzalez A.M.A.;  Behrens C.;  Bondaruk J.;  Broaddus R.;  Czerniak B.;  Esmaeli B.;  Fujimoto J.;  Gershenwald J.;  Guo C.;  Lazar A.J.;  Logothetis C.;  Meric-Bernstam F.;  Moran C.;  Ramondetta L.;  Rice D.;  Sood A.;  Tamboli P.;  Thompson T.;  Troncoso P.;  Tsao A.;  Wistuba I.;  Carter C.;  Haydu L.;  Hersey P.;  Jakrot V.;  Kakavand H.;  Kefford R.;  Lee K.;  Long G.;  Mann G.;  Quinn M.;  Saw R.;  Scolyer R.;  Shannon K.;  Spillane A.;  Stretch J.;  Synott M.;  Thompson J.;  Wilmott J.;  Al-Ahmadie H.;  Chan T.A.;  Ghossein R.;  Gopalan A.;  Levine D.A.;  Reuter V.;  Singer S.;  Singh B.;  Tien N.V.;  Broudy T.;  Mirsaidi C.;  Nair P.;  Drwiega P.;  Miller J.;  Smith J.;  Zaren H.;  Park J.-W.;  Hung N.P.;  Kebebew E.;  Linehan W.M.;  Metwalli A.R.;  Pacak K.;  Pinto P.A.;  Schiffman M.;  Schmidt L.S.;  Vocke C.D.;  Wentzensen N.;  Worrell R.;  Yang H.;  Moncrieff M.;  Goparaju C.;  Melamed J.;  Pass H.;  Botnariuc N.;  Caraman I.;  Cernat M.;  Chemencedji I.;  Clipca A.;  Doruc S.;  Gorincioi G.;  Mura S.;  Pirtac M.;  Stancul I.;  Tcaciuc D.;  Albert M.;  Alexopoulou I.;  Arnaout A.;  Bartlett J.;  Engel J.;  Gilbert S.;  Parfitt J.;  Sekhon H.;  Thomas G.;  Rassl D.M.;  Rintoul R.C.;  Bifulco C.;  Tamakawa R.;  Urba W.;  Hayward N.;  Timmers H.;  Antenucci A.;  Facciolo F.;  Grazi G.;  Marino M.;  Merola R.;  de Krijger R.;  Gimenez-Roqueplo A.-P.;  Piche A.;  Chevalier S.;  McKercher G.;  Birsoy K.;  Barnett G.;  Brewer C.;  Farver C.;  Naska T.;  Pennell N.A.;  Raymond D.;  Schilero C.;  Smolenski K.;  Williams F.;  Morrison C.;  Borgia J.A.;  Liptay M.J.;  Pool M.;  Seder C.W.;  Junker K.;  Omberg L.;  Dinkin M.;  Manikhas G.;  Alvaro D.;  Bragazzi M.C.;  Cardinale V.;  Carpino G.;  Gaudio E.;  Chesla D.;  Cottingham S.;  Dubina M.;  Moiseenko F.;  Dhanasekaran R.;  Becker K.-F.;  Janssen K.-P.;  Slotta-Huspenina J.;  Abdel-Rahman M.H.;  Aziz D.;  Bell S.;  Cebulla C.M.;  Davis A.;  Duell R.;  Elder J.B.;  Hilty J.;  Kumar B.;  Lang J.;  Lehman N.L.;  Mandt R.;  Nguyen P.;  Pilarski R.;  Rai K.;  Schoenfield L.;  Senecal K.;  Wakely P.;  Hansen P.;  Lechan R.;  Powers J.;  Tischler A.;  Grizzle W.E.;  Sexton K.C.;  Kastl A.;  Henderson J.;  Porten S.;  Waldmann J.;  Fassnacht M.;  Asa S.L.;  Schadendorf D.;  Couce M.;  Graefen M.;  Huland H.;  Sauter G.;  Schlomm T.;  Simon R.;  Tennstedt P.;  Olabode O.;  Nelson M.;  Bathe O.;  Carroll P.R.;  Chan J.M.;  Disaia P.;  Glenn P.;  Kelley R.K.;  Landen C.N.;  Phillips J.;  Prados M.;  Simko J.;  Smith-McCune K.;  VandenBerg S.;  Roggin K.;  Fehrenbach A.;  Kendler A.;  Sifri S.;  Steele R.;  Jimeno A.;  Carey F.;  Forgie I.;  Mannelli M.;  Carney M.;  Hernandez B.;  Campos B.;  Herold-Mende C.;  Jungk C.;  Unterberg A.;  von Deimling A.;  Bossler A.;  Galbraith J.;  Jacobus L.;  Knudson M.;  Knutson T.;  Ma D.;  Milhem M.;  Sigmund R.;  Godwin A.K.;  Madan R.;  Rosenthal H.G.;  Adebamowo C.;  Adebamowo S.N.;  Boussioutas A.;  Beer D.;  Giordano T.;  Mes-Masson A.-M.;  Saad F.;  Bocklage T.;  Landrum L.;  Mannel R.;  Moore K.;  Moxley K.;  Postier R.;  Walker J.;  Zuna R.;  Feldman M.;  Valdivieso F.;  Dhir R.;  Luketich J.;  Pinero E.M.M.;  Quintero-Aguilo M.;  Carlotti C.G.;  Dos Santos J.S.;  Kemp R.;  Sankarankuty A.;  Tirapelli D.;  Catto J.;  Agnew K.;  Swisher E.;  Creaney J.;  Robinson B.;  Shelley C.S.;  Godwin E.M.;  Kendall S.;  Shipman C.;  Bradford C.;  Carey T.;  Haddad A.;  Moyer J.;  Peterson L.;  Prince M.;  Rozek L.;  Wolf G.;  Bowman R.;  Fong K.M.;  Yang I.;  Korst R.;  Rathmell W.K.;  Fantacone-Campbell J.L.;  Hooke J.A.;  Kovatich A.J.;  Shriver C.D.;  DiPersio J.;  Drake B.;  Govindan R.;  Heath S.;  Ley T.;  Van Tine B.;  Westervelt P.;  Rubin M.A.;  Lee J.I.;  Aredes N.D.;  Mariamidze A.;  Sood A.K.;  Gunaratne P.H.;  Sumazin P.
Favorite | View/Download:13/0 | TC[WOS]:88 TC[Scopus]:0 | Submit date:2019/01/16
cancer gene  interactome  lncRNA  microRNA  modulation  noncoding RNA  pan-cancer  regulation  RNA-binding proteins  
Analysis of Genomes and Transcriptomes of Hepatocellular Carcinomas Identifies Mutations and Gene Expression Changes in the Transforming Growth Factor-β Pathway Journal article
Gastroenterology, 2018,Volume: 154,Issue: 1,Page: 195-210
Authors:  Chen J.;  Zaidi S.;  Rao S.;  Chen J.-S.;  Phan L.;  Farci P.;  Su X.;  Shetty K.;  White J.;  Zamboni F.;  Wu X.;  Rashid A.;  Pattabiraman N.;  Mazumder R.;  Horvath A.;  Wu R.-C.;  Li S.;  Xiao C.;  Deng C.-X.;  Wheeler D.A.;  Mishra B.;  Akbani R.;  Mishra L.
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Cosmic  Gene Regulation  Genetics  Immune Response  Liver Cancer  
TFmapper: A Tool for Searching Putative Factors Regulating Gene Expression Using ChIP-seq Data Journal article
International journal of biological sciences, 2018,Volume: 14,Issue: 12,Page: 1724-1731
Authors:  Zeng J.;  Li G.
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Chromatin Immunoprecipitation  Next-generation Sequencing  Regulation Of Gene Expression  
Analysis of Genomes and Transcriptomes of Hepatocellular Carcinomas Identifies Mutations and Gene Expression Changes in the Transforming Growth Factor-β Pathway Journal article
Gastroenterology, 2018,Volume: 154,Issue: 1,Page: 195-210
Authors:  Chen,Jian;  Zaidi,Sobia;  Rao,Shuyun;  Chen,Jiun Sheng;  Phan,Liem;  Farci,Patrizia;  Su,Xiaoping;  Shetty,Kirti;  White,Jon;  Zamboni,Fausto;  Wu,Xifeng;  Rashid,Asif;  Pattabiraman,Nagarajan;  Mazumder,Raja;  Horvath,Anelia;  Wu,Ray Chang;  Li,Shulin;  Xiao,Cuiying;  Deng,Chu Xia;  Wheeler,David A.;  Mishra,Bibhuti;  Akbani,Rehan;  Mishra,Lopa
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COSMIC  Gene Regulation  Genetics  Immune Response  Liver Cancer  
Genome-wide methylome and chromatin interactome identify abnormal enhancer to be risk factor of breast cancer Journal article
ONCOTARGET, 2017,Volume: 8,Issue: 27,Page: 44705-44719
Authors:  Wang, Yuan;  Hao, Da-Peng;  Li, Jing-Jing;  Wang, Li;  Di, Li-Jun
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Enhancer Methylation  Breast Cancer  Chromatin Interaction  Polii Chia-pet  Gene Regulation  
Mediator Undergoes a Compositional Change during Transcriptional Activation Journal article
Molecular Cell, 2016,Volume: 64,Issue: 3,Page: 443
Authors:  Petrenko N.;  Jin Y.;  Wong K.H.;  Struhl K.
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Enhancer  Gene Regulation  Mediator  Promoter  Rna Polymerase Ii  Rna Polymerase Ii C-terminal Domain  Tfiih Kinase  Transcription  Transcriptional Co-activator  
The dual lives of bidirectional promoters Journal article
Biochimica et Biophysica Acta, 2012,Volume: 1819,Issue: 2012,Page: 688–693
Authors:  Clay Wakano;  Jung S.Byun;  Li-JunDi;  Kevin Gardner
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Promoter  Transcription  Chromatin  Gene Regulation  
Transcriptional regulation of co-expressed microRNA target genes Journal article
Genomics, 2011,Volume: 98,Issue: 6,Page: 445-452
Authors:  Wang Y.;  Li X.;  Hu H.
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Cis-regulatory module  Co-expression  Co-regulation  MicroRNA  Target gene  
The Cyc8-Tup1 complex inhibits transcription primarily by masking the activation domain of the recruiting protein Journal article
Genes and Development, 2011,Volume: 25,Issue: 23,Page: 2525-2539
Authors:  Wong K.H.;  Struhl K.
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Cyc8-tup1  Gene Regulation  Stress Responses Transcriptional Activation  Transcriptional Corepressor  Transcriptional Repression  
Extensive divergence of yeast stress responses through transitions between induced and constitutive activation Journal article
Proceedings of the National Academy of Sciences of the United States of America, 2011,Volume: 108,Issue: 40,Page: 16693-16698
Authors:  Tirosh I.;  Wong K.H.;  Barkai N.;  Struhl K.
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Biological Function  Evolutionary Conservation  Functional Evolution  Gene Regulation