Literature DB >> 28093886

Regulatory elements in molecular networks.

Ashley S Doane1, Olivier Elemento1.   

Abstract

Regulatory elements determine the connectivity of molecular networks and mediate a variety of regulatory processes ranging from DNA looping to transcriptional, posttranscriptional, and posttranslational regulation. This review highlights our current understanding of the different types of regulatory elements found in molecular networks with a focus on DNA regulatory elements. We highlight technical advances and current challenges for the mapping of regulatory elements at the genome-wide scale, and describe new computational methods to uncover these elements via reconstructing regulatory networks from large genomic datasets. WIREs Syst Biol Med 2017, 9:e1374. doi: 10.1002/wsbm.1374 For further resources related to this article, please visit the WIREs website.
© 2017 Wiley Periodicals, Inc.

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Year:  2017        PMID: 28093886      PMCID: PMC5400678          DOI: 10.1002/wsbm.1374

Source DB:  PubMed          Journal:  Wiley Interdiscip Rev Syst Biol Med        ISSN: 1939-005X


  78 in total

1.  Regulatory element detection using correlation with expression.

Authors:  H J Bussemaker; H Li; E D Siggia
Journal:  Nat Genet       Date:  2001-02       Impact factor: 38.330

2.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.

Authors:  Nathaniel D Heintzman; Rhona K Stuart; Gary Hon; Yutao Fu; Christina W Ching; R David Hawkins; Leah O Barrera; Sara Van Calcar; Chunxu Qu; Keith A Ching; Wei Wang; Zhiping Weng; Roland D Green; Gregory E Crawford; Bing Ren
Journal:  Nat Genet       Date:  2007-02-04       Impact factor: 38.330

3.  Super-enhancers in the control of cell identity and disease.

Authors:  Denes Hnisz; Brian J Abraham; Tong Ihn Lee; Ashley Lau; Violaine Saint-André; Alla A Sigova; Heather A Hoke; Richard A Young
Journal:  Cell       Date:  2013-10-10       Impact factor: 41.582

4.  Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution.

Authors:  Ho Sung Rhee; B Franklin Pugh
Journal:  Cell       Date:  2011-12-09       Impact factor: 41.582

5.  A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

Authors:  Suhas S P Rao; Miriam H Huntley; Neva C Durand; Elena K Stamenova; Ivan D Bochkov; James T Robinson; Adrian L Sanborn; Ido Machol; Arina D Omer; Eric S Lander; Erez Lieberman Aiden
Journal:  Cell       Date:  2014-12-11       Impact factor: 41.582

6.  FTO Obesity Variant Circuitry and Adipocyte Browning in Humans.

Authors:  Melina Claussnitzer; Simon N Dankel; Kyoung-Han Kim; Gerald Quon; Wouter Meuleman; Christine Haugen; Viktoria Glunk; Isabel S Sousa; Jacqueline L Beaudry; Vijitha Puviindran; Nezar A Abdennur; Jannel Liu; Per-Arne Svensson; Yi-Hsiang Hsu; Daniel J Drucker; Gunnar Mellgren; Chi-Chung Hui; Hans Hauner; Manolis Kellis
Journal:  N Engl J Med       Date:  2015-08-19       Impact factor: 91.245

7.  Architecture of the human regulatory network derived from ENCODE data.

Authors:  Mark B Gerstein; Anshul Kundaje; Manoj Hariharan; Stephen G Landt; Koon-Kiu Yan; Chao Cheng; Xinmeng Jasmine Mu; Ekta Khurana; Joel Rozowsky; Roger Alexander; Renqiang Min; Pedro Alves; Alexej Abyzov; Nick Addleman; Nitin Bhardwaj; Alan P Boyle; Philip Cayting; Alexandra Charos; David Z Chen; Yong Cheng; Declan Clarke; Catharine Eastman; Ghia Euskirchen; Seth Frietze; Yao Fu; Jason Gertz; Fabian Grubert; Arif Harmanci; Preti Jain; Maya Kasowski; Phil Lacroute; Jing Jane Leng; Jin Lian; Hannah Monahan; Henriette O'Geen; Zhengqing Ouyang; E Christopher Partridge; Dorrelyn Patacsil; Florencia Pauli; Debasish Raha; Lucia Ramirez; Timothy E Reddy; Brian Reed; Minyi Shi; Teri Slifer; Jing Wang; Linfeng Wu; Xinqiong Yang; Kevin Y Yip; Gili Zilberman-Schapira; Serafim Batzoglou; Arend Sidow; Peggy J Farnham; Richard M Myers; Sherman M Weissman; Michael Snyder
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962

8.  Genome-wide mapping of in vivo protein-DNA interactions.

Authors:  David S Johnson; Ali Mortazavi; Richard M Myers; Barbara Wold
Journal:  Science       Date:  2007-05-31       Impact factor: 47.728

9.  The role of DNA shape in protein-DNA recognition.

Authors:  Remo Rohs; Sean M West; Alona Sosinsky; Peng Liu; Richard S Mann; Barry Honig
Journal:  Nature       Date:  2009-10-29       Impact factor: 49.962

10.  Integrative analysis of 111 reference human epigenomes.

Authors:  Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi-Moussavi; Pouya Kheradpour; Zhizhuo Zhang; Jianrong Wang; Michael J Ziller; Viren Amin; John W Whitaker; Matthew D Schultz; Lucas D Ward; Abhishek Sarkar; Gerald Quon; Richard S Sandstrom; Matthew L Eaton; Yi-Chieh Wu; Andreas R Pfenning; Xinchen Wang; Melina Claussnitzer; Yaping Liu; Cristian Coarfa; R Alan Harris; Noam Shoresh; Charles B Epstein; Elizabeta Gjoneska; Danny Leung; Wei Xie; R David Hawkins; Ryan Lister; Chibo Hong; Philippe Gascard; Andrew J Mungall; Richard Moore; Eric Chuah; Angela Tam; Theresa K Canfield; R Scott Hansen; Rajinder Kaul; Peter J Sabo; Mukul S Bansal; Annaick Carles; Jesse R Dixon; Kai-How Farh; Soheil Feizi; Rosa Karlic; Ah-Ram Kim; Ashwinikumar Kulkarni; Daofeng Li; Rebecca Lowdon; GiNell Elliott; Tim R Mercer; Shane J Neph; Vitor Onuchic; Paz Polak; Nisha Rajagopal; Pradipta Ray; Richard C Sallari; Kyle T Siebenthall; Nicholas A Sinnott-Armstrong; Michael Stevens; Robert E Thurman; Jie Wu; Bo Zhang; Xin Zhou; Arthur E Beaudet; Laurie A Boyer; Philip L De Jager; Peggy J Farnham; Susan J Fisher; David Haussler; Steven J M Jones; Wei Li; Marco A Marra; Michael T McManus; Shamil Sunyaev; James A Thomson; Thea D Tlsty; Li-Huei Tsai; Wei Wang; Robert A Waterland; Michael Q Zhang; Lisa H Chadwick; Bradley E Bernstein; Joseph F Costello; Joseph R Ecker; Martin Hirst; Alexander Meissner; Aleksandar Milosavljevic; Bing Ren; John A Stamatoyannopoulos; Ting Wang; Manolis Kellis
Journal:  Nature       Date:  2015-02-19       Impact factor: 69.504

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  7 in total

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Journal:  Exp Dermatol       Date:  2020-12-20       Impact factor: 3.960

2.  Multi-omic profiling of histone variant H3.3 lysine 27 methylation reveals a distinct role from canonical H3 in stem cell differentiation.

Authors:  Yekaterina Kori; Peder J Lund; Matteo Trovato; Simone Sidoli; Zuo-Fei Yuan; Kyung-Min Noh; Benjamin A Garcia
Journal:  Mol Omics       Date:  2022-05-11

3.  A Bayesian data fusion based approach for learning genome-wide transcriptional regulatory networks.

Authors:  Elisabetta Sauta; Andrea Demartini; Francesca Vitali; Alberto Riva; Riccardo Bellazzi
Journal:  BMC Bioinformatics       Date:  2020-05-29       Impact factor: 3.169

4.  lncRNAfunc: a knowledgebase of lncRNA function in human cancer.

Authors:  Mengyuan Yang; Huifen Lu; Jiajia Liu; Sijia Wu; Pora Kim; Xiaobo Zhou
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 16.971

Review 5.  Artificial intelligence and machine learning approaches for drug design: challenges and opportunities for the pharmaceutical industries.

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Journal:  Mol Divers       Date:  2021-10-23       Impact factor: 2.943

Review 6.  Genome Editing Human Pluripotent Stem Cells to Model β-Cell Disease and Unmask Novel Genetic Modifiers.

Authors:  Matthew N George; Karla F Leavens; Paul Gadue
Journal:  Front Endocrinol (Lausanne)       Date:  2021-06-02       Impact factor: 6.055

7.  Key elements involved in Epstein-Barr virus-associated gastric cancer and their network regulation.

Authors:  Jing-Jing Jing; Ze-Yang Wang; Hao Li; Li-Ping Sun; Yuan Yuan
Journal:  Cancer Cell Int       Date:  2018-09-21       Impact factor: 5.722

  7 in total

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