HeatMapper:: powerful combined visualization of gene expression profile correlations, genotypes, phenotypes and sample characteristics

被引：27

作者：

Verhaak, Roel G. W. ^{[1
]}

Sanders, Mathijs A.

Bijl, Maarten A.

Delwel, Ruud

Horsman, Sebastiaan

Moorhouse, Michael J.

van der Spek, Peter J.

Lowenberg, Bob

Valk, Peter J. M.

机构：

[1] Erasmus Univ, Med Ctr, Dept Hematol, Rotterdam, Netherlands

[2] Erasmus Univ, Med Ctr, Dept Bioinformat, Rotterdam, Netherlands

来源：

BMC BIOINFORMATICS | 2006年 / 7卷 / 1期

关键词：

D O I：

10.1186/1471-2105-7-337

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Background: Accurate interpretation of data obtained by unsupervised analysis of large scale expression profiling studies is currently frequently performed by visually combining sample-gene heatmaps and sample characteristics. This method is not optimal for comparing individual samples or groups of samples. Here, we describe an approach to visually integrate the results of unsupervised and supervised cluster analysis using a correlation plot and additional sample metadata. Results: We have developed a tool called the HeatMapper that provides such visualizations in a dynamic and flexible manner and is available from http://www.erasmusmc.nl/hematologie/heatmapper/. Conclusion: The HeatMapper allows an accessible and comprehensive visualization of the results of gene expression profiling and cluster analysis.

引用

页数：4

共 12 条

[1] Gene expression profiling in acute myeloid leukemia [J].

Bullinger, L ;

Valk, PJM .

JOURNAL OF CLINICAL ONCOLOGY, 2005, 23 (26) :6296-6305

[2] Comparison of discrimination methods for the classification of tumors using gene expression data [J].

Dudoit, S ;

Fridlyand, J ;

Speed, TP .

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 2002, 97 (457) :77-87

[3] Cluster analysis and display of genome-wide expression patterns [J].

Eisen, MB ;

Spellman, PT ;

Brown, PO ;

Botstein, D .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (25) :14863-14868

[4]

Raychaudhuri S, 2000, Pac Symp Biocomput, P455

[5] Gene expression profiling of pediatric acute myelogenous leukemia [J].

Ross, ME ;

Mahfouz, R ;

Onciu, M ;

Liu, HC ;

Zhou, XD ;

Song, GC ;

Shurtleff, SA ;

Pounds, S ;

Cheng, C ;

Ma, J ;

Ribeiro, RC ;

Rubnitz, JE ;

Girtman, K ;

Williams, WK ;

Raimondi, SC ;

Liang, DC ;

Shih, LY ;

Pui, CH ;

Downing, JR .

BLOOD, 2004, 104 (12) :3679-3687

[6] Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization [J].

Spellman, PT ;

Sherlock, G ;

Zhang, MQ ;

Iyer, VR ;

Anders, K ;

Eisen, MB ;

Brown, PO ;

Botstein, D ;

Futcher, B .

MOLECULAR BIOLOGY OF THE CELL, 1998, 9 (12) :3273-3297

[7] Gene expression profiling in acute myeloid leukemia [J].

Valk, PJM ;

Delwel, R ;

Löwenberg, B .

CURRENT OPINION IN HEMATOLOGY, 2005, 12 (01) :76-81

[8] Prognostically useful gene-expression profiles in acute myeloid leukemia [J].

Valk, PJM ;

Verhaak, RGW ;

Beijen, MA ;

Erpelinck, CAJ ;

van Doorn-Khosrovani, SBV ;

Boer, JM ;

Beverloo, HB ;

Moorhouse, MJ ;

van der Spek, PJ ;

Löwenberg, B ;

Delwel, R .

NEW ENGLAND JOURNAL OF MEDICINE, 2004, 350 (16) :1617-1628

[9] The common viral insertion site Evi12 is located in the 5′-noncoding region of Gnn, a novel gene with enhanced expression in two subclasses of human acute myeloid leukemia [J].

van den Akker, E ;

Vankan-Berkhoudt, Y ;

Valk, PJM ;

Löwenberg, B ;

Delwel, R .

JOURNAL OF VIROLOGY, 2005, 79 (09) :5249-5258

[10] Gene expression profiling predicts clinical outcome of breast cancer [J].

van't Veer, LJ ;

Dai, HY ;

van de Vijver, MJ ;

He, YDD ;

Hart, AAM ;

Mao, M ;

Peterse, HL ;

van der Kooy, K ;

Marton, MJ ;

Witteveen, AT ;

Schreiber, GJ ;

Kerkhoven, RM ;

Roberts, C ;

Linsley, PS ;

Bernards, R ;

Friend, SH .

NATURE, 2002, 415 (6871) :530-536

← 1 2 →