HiCPlotter integrates genomic data with interaction matrices

被引：179

作者：

Akdemir, Kadir Caner ^{[1
]}

Chin, Lynda ^{[1
,2
]}

机构：

[1] Univ Texas MD Anderson Canc Ctr, Dept Genom Med, Div Canc Med, Houston, TX 77030 USA

[2] Univ Texas MD Anderson Canc Ctr, Inst Appl Canc Sci, Houston, TX 77030 USA

来源：

GENOME BIOLOGY | 2015年 / 16卷

关键词：

3D GENOME; ARCHITECTURE; ORGANIZATION; DOMAINS; PRINCIPLES; OCCURS; LINK; MAP;

D O I：

10.1186/s13059-015-0767-1

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 [微生物学]; 090105 [作物生产系统与生态工程];

摘要：

Metazoan genomic material is folded into stable non-randomly arranged chromosomal structures that are tightly associated with transcriptional regulation and DNA replication. Various factors including regulators of pluripotency, long non-coding RNAs, or the presence of architectural proteins have been implicated in regulation and assembly of the chromatin architecture. Therefore, comprehensive visualization of this multi-faceted structure is important to unravel the connections between nuclear architecture and transcriptional regulation. Here, we present an easy-to-use open-source visualization tool, HiCPlotter, to facilitate juxtaposition of Hi-C matrices with diverse genomic assay outputs, as well as to compare interaction matrices between various conditions. https://github.com/kcakdemir/HiCPlotter

引用

页数：8

共 36 条

[1]

Genome Architecture: Domain Organization of Interphase Chromosomes [J].

Bickmore, Wendy A. ;

van Steensel, Bas .

CELL, 2013, 152 (06) :1270-1284

[2]

A mechanistic link between gene regulation and genome architecture in mammalian development [J].

Bonora, Giancarlo ;

Plath, Kathrin ;

Denholtz, Matthew .

CURRENT OPINION IN GENETICS & DEVELOPMENT, 2014, 27 :92-101

[3]

Capturing chromosome conformation [J].

Dekker, J ;

Rippe, K ;

Dekker, M ;

Kleckner, N .

SCIENCE, 2002, 295 (5558) :1306-1311

[4]

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data [J].

Dekker, Job ;

Marti-Renom, Marc A. ;

Mirny, Leonid A. .

NATURE REVIEWS GENETICS, 2013, 14 (06) :390-403

[5]

Variation in FTO contributes to childhood obesity and severe adult obesity [J].

Dina, Christian ;

Meyre, David ;

Gallina, Sophie ;

Durand, Emmanuelle ;

Koerner, Antje ;

Jacobson, Peter ;

Carlsson, Lena M. S. ;

Kiess, Wieland ;

Vatin, Vincent ;

Lecoeur, Cecile ;

Delplanque, Jerome ;

Vaillant, Emmanuel ;

Pattou, Francois ;

Ruiz, Juan ;

Weill, Jacques ;

Levy-Marchal, Claire ;

Horber, Fritz ;

Potoczna, Natascha ;

Hercberg, Serge ;

Le Stunff, Catherine ;

Bougneres, Pierre ;

Kovacs, Peter ;

Marre, Michel ;

Balkau, Beverley ;

Cauchi, Stephane ;

Chevre, Jean-Claude ;

Froguel, Philippe .

NATURE GENETICS, 2007, 39 (06) :724-726

[6]

Topological domains in mammalian genomes identified by analysis of chromatin interactions [J].

Dixon, Jesse R. ;

Selvaraj, Siddarth ;

Yue, Feng ;

Kim, Audrey ;

Li, Yan ;

Shen, Yin ;

Hu, Ming ;

Liu, Jun S. ;

Ren, Bing .

NATURE, 2012, 485 (7398) :376-380

[7]

Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes [J].

Dowen, Jill M. ;

Fan, Zi Peng ;

Hnisz, Denes ;

Ren, Gang ;

Abraham, Brian J. ;

Zhang, Lyndon N. ;

Weintraub, Abraham S. ;

Schuijers, Jurian ;

Lee, Tong Ihn ;

Zhao, Keji ;

Young, Richard A. .

CELL, 2014, 159 (02) :374-387

[8]

SMC complexes link gene expression and genome architecture [J].

Dowen, Jill M. ;

Young, Richard A. .

CURRENT OPINION IN GENETICS & DEVELOPMENT, 2014, 25 :131-137

[9]

Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription [J].

Giorgetti, Luca ;

Galupa, Rafael ;

Nora, Elphege P. ;

Piolot, Tristan ;

Lam, France ;

Dekker, Job ;

Tiana, Guido ;

Heard, Edith .

CELL, 2014, 157 (04) :950-963

[10]

Architectural proteins: regulators of 3D genome organization in cell fate [J].

Gomez-Diaz, Elena ;

Corces, Victor G. .

TRENDS IN CELL BIOLOGY, 2014, 24 (11) :703-711

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