Volume 17, Issue 6 | June 2007

COMMENTARY
- - ENCODE: More genomic empowerment
    George M. Weinstock
    First Published June 13, 2007
PERSPECTIVES
- - What is a gene, post-ENCODE? History and updated definition
    Mark B. Gerstein
    Can Bruce
    Joel S. Rozowsky
    Deyou Zheng
    Jiang Du
    Jan O. Korbel
    ...[+1 authors]...,
    Olof Emanuelsson
    Zhengdong D. Zhang
    Sherman Weissman
    Michael Snyder
    First Published June 13, 2007
  - Origin of phenotypes: Genes and transcripts
    Thomas R. Gingeras
    First Published June 13, 2007
ARTICLES
- - The landscape of histone modifications across 1% of the human genome in five human cell lines
    Christoph M. Koch
    Robert M. Andrews
    Paul Flicek
    Shane C. Dillon
    Ulaş Karaöz
    Gayle K. Clelland Sarah Wilcox David M. Beare Joanna C. Fowler Phillippe Couttet Keith D. James Gregory C. Lefebvre Alexander W. Bruce Oliver M. Dovey Peter D. Ellis Pawandeep Dhami Cordelia F. Langford Zhiping Weng
    ...[+13 authors]...,
    Ewan Birney
    Nigel P. Carter
    David Vetrie
    Ian Dunham
    First Published June 13, 2007
  - Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes
    Alvaro Rada-Iglesias
    Stefan Enroth
    Adam Ameur
    Christoph M. Koch
    Gayle K. Clelland
    Patricia Respuela-Alonso Sarah Wilcox Oliver M. Dovey Peter D. Ellis
    ...[+4 authors]...,
    Cordelia F. Langford
    Ian Dunham
    Jan Komorowski
    Claes Wadelius
    First Published June 13, 2007
  - Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome
    Nathan D. Trinklein
    Ulaş Karaöz
    Jiaqian Wu
    Anason Halees
    Shelley Force Aldred
    Patrick J. Collins Deyou Zheng Zhengdong D. Zhang
    ...[+3 authors]...,
    Mark B. Gerstein
    Michael Snyder
    Richard M. Myers
    Zhiping Weng
    First Published June 13, 2007
  - The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci
    Joel S. Rozowsky
    Daniel Newburger
    Fred Sayward
    Jiaqian Wu
    Greg Jordan
    Jan O. Korbel Ugrappa Nagalakshmi Jin Yang Deyou Zheng Roderic Guigó Thomas R. Gingeras
    ...[+6 authors]...,
    Sherman Weissman
    Perry Miller
    Michael Snyder
    Mark B. Gerstein
    First Published June 13, 2007
  - Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions
    France Denoeud
    Philipp Kapranov
    Catherine Ucla
    Adam Frankish
    Robert Castelo
    Jorg Drenkow Julien Lagarde Tyler Alioto Caroline Manzano Jacqueline Chrast Sujit Dike Carine Wyss Charlotte N. Henrichsen Nancy Holroyd Mark C. Dickson Ruth Taylor Zahra Hance Sylvain Foissac Richard M. Myers Jane Rogers Tim Hubbard Jennifer Harrow
    ...[+17 authors]...,
    Roderic Guigó
    Thomas R. Gingeras
    Stylianos E. Antonarakis
    Alexandre Reymond
    First Published June 13, 2007
  - Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
    Elliott H. Margulies
    Gregory M. Cooper
    George Asimenos
    Daryl J. Thomas
    Colin N. Dewey
    Adam Siepel Ewan Birney Damian Keefe Ariel S. Schwartz Minmei Hou James Taylor Sergey Nikolaev Juan I. Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham James B. Brown Peter Bickel Ian Holmes James C. Mullikin Abel Ureta-Vidal Benedict Paten Eric A. Stone Kate R. Rosenbloom W. James Kent Gerard G. Bouffard Xiaobin Guan Nancy F. Hansen Jacquelyn R. Idol Valerie V.B. Maduro Baishali Maskeri Jennifer C. McDowell Morgan Park Pamela J. Thomas Alice C. Young Robert W. Blakesley Donna M. Muzny Erica Sodergren David A. Wheeler Kim C. Worley Huaiyang Jiang George M. Weinstock Richard A. Gibbs Tina Graves Robert Fulton Elaine R. Mardis Richard K. Wilson Michele Clamp James Cuff Sante Gnerre David B. Jaffe Jean L. Chang Kerstin Lindblad-Toh Eric S. Lander Angie Hinrichs Heather Trumbower Hiram Clawson Ann Zweig Robert M. Kuhn Galt Barber Rachel Harte Donna Karolchik Matthew A. Field Richard A. Moore Carrie A. Matthewson Jacqueline E. Schein Marco A. Marra Stylianos E. Antonarakis Serafim Batzoglou Nick Goldman Ross Hardison David Haussler
    ...[+68 authors]...,
    Webb Miller
    Lior Pachter
    Eric D. Green
    Arend Sidow
    First Published June 13, 2007
LETTERS
- - Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data
    David C. King
    James Taylor
    Ying Zhang
    Yong Cheng
    Heather A. Lawson
    First Published June 13, 2007
  - Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions
    Zhengdong D. Zhang
    Alberto Paccanaro
    Yutao Fu
    Sherman Weissman
    Zhiping Weng
    First Published June 13, 2007
  - Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1
    Hualin Xi
    Yong Yu
    Yutao Fu
    Jonathan Foley
    Anason Halees
    First Published June 13, 2007
  - Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches
    Victor X. Jin
    Henriette O’Geen
    Sushma Iyengar
    Roland Green
    Peggy J. Farnham
    First Published June 13, 2007
  - Transcription factor binding and modified histones in human bidirectional promoters
    Jane M. Lin
    Patrick J. Collins
    Nathan D. Trinklein
    Yutao Fu
    Hualin Xi
    First Published June 13, 2007
  - Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)
    Yijun Ruan
    Hong Sain Ooi
    Siew Woh Choo
    Kuo Ping Chiu
    Xiao Dong Zhao
    K.G. Srinivasan Fei Yao Chiou Yu Choo Jun Liu Pramila Ariyaratne Wilson G.W. Bin Vladimir A. Kuznetsov Atif Shahab
    ...[+8 authors]...,
    Wing-Kin Sung
    Guillaume Bourque
    Nallasivam Palanisamy
    Chia-Lin Wei
    First Published June 13, 2007
  - Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution
    Deyou Zheng
    Adam Frankish
    Robert Baertsch
    Philipp Kapranov
    Alexandre Reymond
    Siew Woh Choo Yontao Lu France Denoeud Stylianos E. Antonarakis Michael Snyder Yijun Ruan Chia-Lin Wei
    ...[+7 authors]...,
    Thomas R. Gingeras
    Roderic Guigó
    Jennifer Harrow
    Mark B. Gerstein
    First Published June 13, 2007
  - Structured RNAs in the ENCODE selected regions of the human genome
    Stefan Washietl
    Jakob S. Pedersen
    Jan O. Korbel
    Claudia Stocsits
    Andreas R. Gruber
    Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Reiche Andrea Tanzer Catherine Ucla Carine Wyss Stylianos E. Antonarakis France Denoeud Julien Lagarde Jorg Drenkow Philipp Kapranov Thomas R. Gingeras Roderic Guigó Michael Snyder
    ...[+15 authors]...,
    Mark B. Gerstein
    Alexandre Reymond
    Ivo L. Hofacker
    Peter F. Stadler
    First Published June 13, 2007
  - Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas
    Neerja Karnani
    Christopher Taylor
    Ankit Malhotra
    Anindya Dutta
    First Published June 13, 2007
Methods
- - FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin
    Paul G. Giresi
    Jonghwan Kim
    Ryan M. McDaniell
    Vishwanath R. Iyer
    Jason D. Lieb
    First Published December 19, 2006
  - Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
    Olof Emanuelsson
    Ugrappa Nagalakshmi
    Deyou Zheng
    Joel S. Rozowsky
    Alexander E. Urban
    Jiang Du Zheng Lian
    ...[+2 authors]...,
    Viktor Stolc
    Sherman Weissman
    Michael Snyder
    Mark B. Gerstein
    First Published November 21, 2006
  - Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies
    Ghia M. Euskirchen
    Joel S. Rozowsky
    Chia-Lin Wei
    Wah Heng Lee
    Zhengdong D. Zhang
    Stephen Hartman Olof Emanuelsson Viktor Stolc
    ...[+3 authors]...,
    Sherman Weissman
    Mark B. Gerstein
    Yijun Ruan
    Michael Snyder
    First Published June 13, 2007
  - Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE)
    Akshay A. Bhinge
    Jonghwan Kim
    Ghia M. Euskirchen
    Michael Snyder
    Vishwanath R. Iyer
    First Published June 13, 2007
  - Identification of higher-order functional domains in the human ENCODE regions
    Robert E. Thurman
    Nathan Day
    William S. Noble
    John A. Stamatoyannopoulos
    First Published June 13, 2007
  - Independent and complementary methods for large-scale structural analysis of mammalian chromatin
    Jonathan H. Dennis
    Hua-Ying Fan
    Sheila M. Reynolds
    Guocheng Yuan
    James C. Meldrim
    Daniel J. Richter
    ...[+1 authors]...,
    Daniel G. Peterson
    Oliver J. Rando
    William S. Noble
    Robert E. Kingston
    First Published June 13, 2007
  - Detection of DNA structural motifs in functional genomic elements
    Jason A. Greenbaum
    Stephen C.J. Parker
    Thomas D. Tullius
    First Published June 13, 2007
RESOURCES
- - Construction of a genome-scale structural map at single-nucleotide resolution
    Jason A. Greenbaum
    Bo Pang
    Thomas D. Tullius
    First Published June 13, 2007
  - The ENCODEdb portal: Simplified access to ENCODE Consortium data
    Laura L. Elnitski
    Prachi Shah
    R. Travis Moreland
    Lowell Umayam
    Tyra G. Wolfsberg
    First Published June 13, 2007
  - A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly
    Daniel Blankenberg
    James Taylor
    Ian Schenck
    Jianbin He
    Yi Zhang
    Matthew Ghent Narayanan Veeraraghavan Istvan Albert
    ...[+3 authors]...,
    Webb Miller
    Kateryna D. Makova
    Ross C. Hardison
    Anton Nekrutenko
    First Published June 13, 2007

Table of Contents

Volume 17, Issue 6 | June 2007

COMMENTARY

ENCODE: More genomic empowerment

PERSPECTIVES

What is a gene, post-ENCODE? History and updated definition

Origin of phenotypes: Genes and transcripts

ARTICLES

The landscape of histone modifications across 1% of the human genome in five human cell lines

Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes

Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome

The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci

Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

LETTERS

Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data

Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions

Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1

Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches

Transcription factor binding and modified histones in human bidirectional promoters

Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)

Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution

Structured RNAs in the ENCODE selected regions of the human genome

Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas

Methods

FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin

Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome

Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies

Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE)

Identification of higher-order functional domains in the human ENCODE regions

Independent and complementary methods for large-scale structural analysis of mammalian chromatin

Detection of DNA structural motifs in functional genomic elements

RESOURCES

Construction of a genome-scale structural map at single-nucleotide resolution

The ENCODEdb portal: Simplified access to ENCODE Consortium data

A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly

Table of Contents

Volume 17, Issue 6 | June 2007

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COMMENTARY

PERSPECTIVES

ARTICLES

LETTERS

Methods

RESOURCES