waviCGH: a web application for the analysis and visualization of genomic copy number alterations

被引：14

作者：

Carro, Angel ^{[2
]}

Rico, Daniel ^{[1
]}

Rueda, Oscar M. ^{[3
]}

Diaz-Uriarte, Ramon ^{[1
]}

Pisano, David G. ^{[2
]}

机构：

[1] Spanish Natl Canc Res Ctr CNIO, Struct Computat Biol Grp, Struct Biol & Biocomp Programme, Cambridge, England

[2] Spanish Natl Canc Res Ctr CNIO, Bioinformat Unit, Cambridge, England

[3] Canc Res UK, Breast Canc Funct Gen, Cambridge, England

来源：

NUCLEIC ACIDS RESEARCH | 2010年 / 38卷

关键词：

ARRAY CGH DATA; GENE-EXPRESSION; HYBRIDIZATION; ABERRATIONS; SEGMENTATION; TOOL;

D O I：

10.1093/nar/gkq441

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

waviCGH is a versatile web server for the analysis and comparison of genomic copy number alterations in multiple samples from any species. waviCGH processes data generated by high density SNP-arrays, array-CGH or copy-number calls generated by any technique. waviCGH includes methods for pre-processing of the data, segmentation, calling of gains and losses, and minimal common regions determination over a set of experiments. The server is a user-friendly interface to the analytical methods, with emphasis on results visualization in a genomic context. Analysis tools are introduced to the user as the different steps to follow in an experimental protocol. All the analysis steps generate high quality images and tables ready to be imported into spreadsheet programs. Additionally, for human, mouse and rat, altered regions are represented in a biological context by mapping them into chromosomes in an integrated cytogenetic browser. waviCGH is available at http://wavi.bioinfo.cnio.es.

引用

页码：W182 / W187

页数：6

共 35 条

[1] A fast and flexible method for the segmentation of aCGH data [J].

Ben-Yaacov, Erez ;

Eldar, Yonina C. .

BIOINFORMATICS, 2008, 24 (16) :I139-I145

[2] Methods and strategies for analyzing copy number variation using DNA microarrays [J].

Carter, Nigel P. .

NATURE GENETICS, 2007, 39 (Suppl 7) :S16-S21

[3] CNVDetector: locating copy number variations using array CGH data [J].

Chen, Peng-An ;

Liu, Hsiao-Fei ;

Chao, Kun-Mao .

BIOINFORMATICS, 2008, 24 (23) :2773-2775

[4] CGHPRO - A comprehensive data analysis tool for array CGH [J].

Chen, W ;

Erdogan, F ;

Ropers, HH ;

Lenzner, S ;

Ullmann, R .

BMC BIOINFORMATICS, 2005, 6 (1)

[5] ISACGH:: a web-based environment for the analysis of array CGH and gene expression which includes functional profiling [J].

Conde, Lucia ;

Montaner, David ;

Burguet-Castell, Jordi ;

Tarraga, Joaquin ;

Medina, Ignacio ;

Al-Shahrour, Fatima ;

Dopazo, Joaquin .

NUCLEIC ACIDS RESEARCH, 2007, 35 :W81-W85

[6] ADaCGH: A Parallelized Web-Based Application and R Package for the Analysis of aCGH Data [J].

Diaz-Uriarte, Ramon ;

Rueda, Oscar M. .

PLOS ONE, 2007, 2 (08)

[7] STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments [J].

Diskin, Sharon J. ;

Eck, Thomas ;

Greshock, Joel ;

Mosse, Yael P. ;

Naylor, Tara ;

Stoeckert, Christian J., Jr. ;

Weber, Barbara L. ;

Maris, John M. ;

Grant, Gregory R. .

GENOME RESEARCH, 2006, 16 (09) :1149-1158

[8] Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms [J].

Diskin, Sharon J. ;

Li, Mingyao ;

Hou, Cuiping ;

Yang, Shuzhang ;

Glessner, Joseph ;

Hakonarson, Hakon ;

Bucan, Maja ;

Maris, John M. ;

Wang, Kai .

NUCLEIC ACIDS RESEARCH, 2008, 36 (19)

[9] Array CGH and gene-expression profiling reveals distinct genomic instability patterns associated with DNA repair and cell-cycle checkpoint pathways in Ewing's sarcoma [J].

Ferreira, B. I. ;

Alonso, J. ;

Carrillo, J. ;

Acquadro, F. ;

Largo, C. ;

Suela, J. ;

Teixeira, M. R. ;

Cerveira, N. ;

Molares, A. ;

Gomez-Lopez, G. ;

Pestana, A. ;

Sastre, A. ;

Garcia-Miguel, P. ;

Cigudosa, J. C. .

ONCOGENE, 2008, 27 (14) :2084-2090

[10] Comparative genome profiling across subtypes of low-grade B-cell lymphoma identifies type-specific and common aberrations that target genes with a role in B-cell neoplasia [J].

Ferreira, Bibiana, I ;

Garcia, Juan F. ;

Suela, Javier ;

Mollejo, Manuela ;

Camacho, Francisca, I ;

Carro, Angel ;

Montes, Santiago ;

Piris, Miguel A. ;

Cigudosa, Juan C. .

HAEMATOLOGICA, 2008, 93 (05) :670-679

← 1 2 3 4 →