Microarray analysis                  Medisch Genetisch Centrum Zuid-West Nederland


Svensson JP, Stalpers LJ, Esveldt-van Lange RE, Franken NA, Haveman J, Klein B, Turesson I, Vrieling H and Giphart-Gassler M. (2006) "Analysis of gene expression using gene sets discriminates cancer patients with and without late radiation toxicity." PLoS Med 3(10): e422 Full text
[Raw data at ArrayExpress (E-TABM-90)] Originally the samples were wrongly annotated at ArrayExpress, this file contains the correct annotation.
[Updated R-scripts Nov2007] [Additional files] [Original R-scripts]

Kruse JJ*, Svensson JP*, Huigsloot M*, Giphart-Gassler M, Schoonen WG, Polman JE, Horbach GJ, van de Water B and Vrieling H. (2007) "A portrait of cisplatin-induced transcriptional changes in mouse embryonic stem cells reveals a dominant p53-like response." Mutation Research 2007 Apr 1;617(1-2):58-70 [R-scripts] [Additional info]
[Raw data at ArrayExpress (E-TABM-89)] * these authors contributed equally

van Bezooijen RL, Svensson JP, Eefting D, Visser A, van der Horst G, Karperien M, Quax PH, Vrieling H, Papapoulos SE, ten Dijke P, Lwik CW. (2007) "Sclerostin abrogates BMP-stimulated bone formation by antagonizing Wnt signaling." J Bone Miner Res. 2007 Jan;22(1):19-28

Svensson JP, de Menezes RX, Turesson I, Giphart-Gassler M and Vrieling H. (2005) "Dissecting systems-wide data using mixture models: application to identify affected cellular processes". BMC Bioinformatics Jul 14;6:177 Full text [Supplementary information]

Jahangir Tafrechi RS, Svensson JP, Janssen GM, Szuhai K, Maassen JA and Raap AK (2005) "Distinct nuclear gene expression profiles in cells with mtDNA depletion and homoplasmic A3243G mutation." Mutation Research. Oct 15;578(1-2):43-52. Full text

Boerma M, Van der Wees CG, Vrieling H, Svensson JP, Wondergem J, Van der Laarse A, Mullenders LH and Van Zeeland AA. (2005) "Microarray analysis of gene expression profiles of cardiac myocytes and fibroblasts after mechanical stress, ionising or ultraviolet radiation." BMC Genomics Jan 18;6(1):6 Full text


Thresholds: R code to decompose populations of p-values.
PLA: R-package containing functions for probe level analysis of oligonucleotide array from Affymetrix.


Harry Vrieling, Ph.D., Department of Toxicogenetics, LUMC, The Netherlands