Center for Human and Clinical
Genetics - LUMC
(Centrum voor Humane en Klinische Genetica)
Microarray Analysis Group
- Maarten van Iterson:
statistical tools for design and analysis of microrray experiments
(supported by Biorange, the NBIC
research programme and the CMSB)
- Vacancy: integration of omics data
from multiple sources in complex phenotypes and disease (supported by the
European FP7 project ENGAGE)
- Peter-Bram 't Hoen: superuser and
co-developer of microarray analysis tools
- Judith Boer: superuser and co-developer
of microarray analysis tools
Microarrays are increasingly used
in life sciences to investigate molecular processes on a genome-wide scale and
to identify biomarkers for molecular diagnostics. We work on different aspects
of microarray data analysis, including platform comparison, sample size
determination and study design. In addition to expression profiling, we work on
the analysis of different types of microarray data, e.g. array-CGH, SNP arrays
and methylation arrays. We develop new statistical tools for optimizing study
design and for the analysis and integration of microarray experiments and apply
them to genomics projects carried out within our institute.
- We developed a statistical
approach to integrate gene expression and genotype (e.g. copy number or
SNP) data to
identify regions of association and candidate genes for tumorigenesis and
- We compared the performance
of five different microarray platforms and RNA-Seq with samples from
transgenic and wildtype mice. We found good correlation between the
different platforms, but also differences related to platform and method: one-color
vs two-color and RNA-Seq vs microarrays.
- We developed an R package
for the estimation of sample size in relation to power, based on pilot
Our lectures, courses and course material
To be included on the mailing list for microarray-related
lectures and courses organized by the Center for Human and Clinical Genetics,
send me an email.
lectures: Tuesdays at lunchtime
- including R users group: collection of
packages with our experiences and example scripts
started in R: How-To: information for first time R users including
several practicals for microarray data analysis
- MGC 3-day course
"Analysis of microarray gene expression data"
Edition: June 16-19, 2008 at ErasmusMC, Rotterdam
- CMSB 3-day course
"Microarray analysis using R"
LUMC microarray analysis infrastructure
- Experimental design of
microarray analyses including a short introduction to experimental
design and designing a microarray experiment
- DNA microarray analysis
flow chart including publicly available software regularly used at the
Center for Human and Clinical Genetics
available at the Leiden
- Rosetta Resolver Server
for DNA chip and microarray data storage and analysis (access restricted
to registered users from participating institutes)
- Microarray-related software
tools developed at the Microarray Analysis Group (Marten Boetzer, Maarten
van Iterson, Renée X. de Menezes, Judith M. Boer, Peter-Bram 't Hoen):
Integrated Analysis of gene expression and copynumber data.
- SSPA, Power and sample size analysis R package
for microarray experiments on the basis of pilot data.
- TurboNorm: A fast scatterplot smoother suitable for microarray normalization
- GPSS: General power
and sample size calculations for high-dimensional genomic data (Source)
- miRNAmRNA: Integrated analysis of microRNA and mRNA (Source)
- Microarray Retriever:
a web-based tool for searching and large scale retrieval of public
- Microarray-related software
tools developed at the Pathology department (Ronald van Eijk, Jan Oosting
and Anne-Marie Cleton-Jansen):
- Sorting of cDNA
microarray data on chromosomal position (Spotfire plug-in)
- Tool in R voor cDNA
microarray data, selection of valid signals and normalisation in combined
high and low intensity scans
- exprSetBuilder Excel
Addin, to build exprSets to use in R and the Global Test GUI
- Global Test GUI, to run
Global Test on GO terms and KEGG pathways
- Microarray-related software
tools developed at the Department of Medical Statistics and Bioinformatics
(Jelle Goeman, Paul Eilers):
R/BioC package for testing the association of gene sets with a response
for enhancing scatterplots with smoothed densities
- Quantsmooth, for quantile smoothing of array-CGH data
- M. van Iterson, S. Bervoets, E.J. de Meijer, H.P. Buermans, P.A.C. 't
Hoen, R.X. Menezes and J.M. Boer. Integrated analysis of microRNA and mRNA expression: adding biological
significance to microRNA target predictions (submitted). (Supplementary tables)
- van Iterson M, Boer JM, Menezes RX. Filtering, FDR and power. BMC
Bioinformatics, 2010 Sep 7;11:450.
- van Iterson M, 't
Hoen PA, Pedotti P, Hooiveld GJ, den Dunnen JT, van Ommen GJ, Boer JM,
Menezes RX. Relative power and sample size analysis on gene
expression profiling data. BMC Genomics. 2009 Sep 17;10:439.
- Menezes RX, Boetzer M,
Sieswerda M, van Ommen GJ, Boer JM. Integrated analysis of DNA copy number
and gene expression microarray data using gene sets. BMC Bioinformatics.
2009 Jun 29;10:203.
- 't Hoen PA, Ariyurek Y, Thygesen HH,
Vreugdenhil E, Vossen RH, de Menezes RX, Boer JM, van Ommen GJ, den Dunnen
JT. Deep sequencing-based expression analysis shows major advances
in robustness, resolution and inter-lab portability over five microarray
platforms. Nucleic Acids Res. 2008 Dec;36(21):e141.
- Ivliev AE, 't Hoen
PA, Villerius MP, den Dunnen JT, Brandt BW. Microarray retriever: a
web-based tool for searching and large scale retrieval of public
microarray data. Nucleic Acids Res. 2008 May 7.
- Alagaratnam S, Mertens BJ, Dalebout JC,
Deelder AM, van Ommen GJ, den Dunnen JT, 't Hoen
PA. Serum protein profiling in mice: identification of Factor XIIIa
as a potential biomarker for muscular dystrophy. Proteomics. 2008 Apr;8(8):1552-63.
- Pedotti P, 't Hoen
PA, Vreugdenhil E, Schenk GJ, Vossen RH, Ariyurek Y, de Hollander M,
Kuiper R, van Ommen GJ, den Dunnen JT, Boer JM, de Menezes RX. Can
subtle changes in gene expression be consistently detected with different
microarray platforms? BMC Genomics. 2008 Mar 10;9:124.
- Vinciotti V, Liu X, Turk R, de Meijer EJ, 't Hoen PA. Exploiting the full power of
temporal gene expression profiling through a new statistical test:
application to the analysis of muscular dystrophy data. BMC
Bioinformatics. 2006 Apr 3;7:183.
- de Graaf JM, de Menezes RX, Boer JM, Kosters
itemsets for genomic profiling. CompLife 2005, Lecture Notes in
Computer Science 3695: 104-116.
- Eilers PH, de Menezes RX. Quantile
smoothing of array CGH data. Bioinformatics. 2005 Apr 1;21(7):1146-53.
- Menezes RX, Boer JM, van Houwelingen HC. Microarray
data analysis : a hierarchical T-test to handle
heteroscedasticity. Appl Bioinformatics. 2004;3(4):229-35.
- Cardoso J, Molenaar L, de Menezes RX,
Rosenberg C, Morreau H, Moslein G, Fodde R, Boer JM. Genomic
profiling by DNA amplification of laser capture
microdissected tissues and array CGH. Nucleic Acids Res. 2004 Oct 28;32(19):e146.
- Turk R, 't Hoen PA,
Sterrenburg E, de Menezes RX, de Meijer EJ, Boer JM, van Ommen GJ, den
Dunnen JT. Gene
expression variation between mouse inbred
strains. BMC Genomics. 2004 Aug 18;5(1):57.
- 't Hoen PA, Turk R, Boer JM, Sterrenburg E, de
Menezes RX, van Ommen GJ, den Dunnen JT. Intensity-based analysis
of two-colour microarrays enables efficient and flexible hybridization
designs. Nucleic Acids Res. 2004 Feb 24;32(4):e41.
If you have any comments or suggestions be sure to let me know
! Judith M. Boer
Last modified: September 8th, 2010 (IF)
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