Gitools: Analysis and Visualisation of Genomic Data Using Interactive Heat-Maps

被引：234

作者：

Perez-Llamas, Christian ^{[1
]}

Lopez-Bigas, Nuria ^{[1
]}

机构：

[1] Univ Pompeu Fabra, Dept Expt & Hlth Sci, Res Unit Biomed Informat, Barcelona, Spain

来源：

PLOS ONE | 2011年 / 6卷 / 05期

关键词：

GENE SET ENRICHMENT; ONTOLOGY TOOL; EXPRESSION; PLATFORM; SUITE;

D O I：

10.1371/journal.pone.0019541

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Intuitive visualization of data and results is very important in genomics, especially when many conditions are to be analyzed and compared. Heat-maps have proven very useful for the representation of biological data. Here we present Gitools (http://www.gitools.org), an open-source tool to perform analyses and visualize data and results as interactive heat-maps. Gitools contains data import systems from several sources (i.e. IntOGen, Biomart, KEGG, Gene Ontology), which facilitate the integration of novel data with previous knowledge.

引用

页数：6

共 33 条

[1]

[Anonymous], MAV MAV SOFTW PROJ M

[2]

[Anonymous], FLEX PROJ MAN WEB AP

[3] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[4] CONTROLLING THE FALSE DISCOVERY RATE - A PRACTICAL AND POWERFUL APPROACH TO MULTIPLE TESTING [J].

BENJAMINI, Y ;

HOCHBERG, Y .

JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY, 1995, 57 (01) :289-300

[5] ToppGene Suite for gene list enrichment analysis and candidate gene prioritization [J].

Chen, Jing ;

Bardes, Eric E. ;

Aronow, Bruce J. ;

Jegga, Anil G. .

NUCLEIC ACIDS RESEARCH, 2009, 37 :W305-W311

[6] Whole genome analysis of p38 SAPK-mediated gene expression upon stress [J].

Ferreiro, Isabel ;

Joaquin, Manel ;

Islam, Abul ;

Gomez-Lopez, Gonzalo ;

Barragan, Montserrat ;

Lombardia, Luis ;

Dominguez, Orlando ;

Pisano, David G. ;

Lopez-Bigas, Nuria ;

Nebreda, Angel R. ;

Posas, Francesc .

BMC GENOMICS, 2010, 11

[7] geWorkbench: an open source platform for integrative genomics [J].

Floratos, Aris ;

Smith, Kenneth ;

Ji, Zhou ;

Watkinson, John ;

Califano, Andrea .

BIOINFORMATICS, 2010, 26 (14) :1779-1780

[8] IntOGen: integration and data mining of multidimensional oncogenomic data [J].

Gundem, Gunes ;

Perez-Llamas, Christian ;

Jene-Sanz, Alba ;

Kedzierska, Anna ;

Islam, Abul ;

Deu-Pons, Jordi ;

Furney, Simon J. ;

Lopez-Bigas, Nuria .

NATURE METHODS, 2010, 7 (02) :92-93

[9]

Hall M., 2009, SIGKDD Explorations, V11, P10, DOI DOI 10.1145/1656274.1656278

[10]

HOLM S, 1979, SCAND J STAT, V6, P65

← 1 2 3 4 →