Functional Genomics and Bioinformatics

Research

Research Projects

”Bioinformatics in Microarray Gene Expression Analysis” is a project for analyzing and extracting the vital information from the massive amounts of data produced by microarrays. Various clustering algorithms are used including heierarchial clustering and self-organizing-maps, a neuron based machine learning algorithm. The current emphasis is geared toward improved visualization of clustered microarray produced data. 

"Neurodegenerative Models in C. elegans” is a project that focuses on building transgenic worm models to understand the molecular and celluar events leading to neurodegeneration. Various putative or candidate neurotoxicity causing genes are overexpressed in worms using coexpression of green-fluorescent protein (GFP) in neurons as a marker, followed by fluorescent microscopy. Various worm phenotypes are scored and characterized.

”Pharmacologic and Toxicologic Actions of Clinically Used NMDA Receptor Antagonists” is one project that focuses on understanding the effects and mechanisms of drugs in this class which are anti-Parkinson’s, anti-dementia, anti-addictive and antidepressant. Using rats as a model, gene expression changes are monitored and profiled using macro- and microarrays, in situ hybridizaton histochemistry together with bioinformatic tools. Underlying changes in src kinases, b-ZIP transcription factor, small molecule transporters, and receptor associated molecules have been found and characterized. To help understand some of the drug side effects, which resemble psychosis, similar studies with both macro- and microarrays have been performed with antipsychotic drugs.

Selected Publications

| 2006 | 2005 | 2004 | 2003 | 2002 |

2006

• Kankainen M, Pehkonen P, Rosenstom P, Toronen P, Wong G, Holm L. POXO: a web-enabled tool series to discover transcription factor binding sites. Nucleic Acids Res. 2006:34(Web Server issue):W534-540.
• Paananen J, Storvik M, Wong G. CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies. BMC  Bioinformatics. 2006: 7:418.
• Paananen J, Wong G. Integration of genomic data for pharmacology and toxicology using Internet resources. SAR QSAR Environ Res. 2006:17(1):25-36.
• Storvik M, Tiikkainen P, van Iersel M, Wong G. Distinct gene expression profiles in adult rat brains after acute MK-801 and cocaine treatments. Eur Neuropsychopharmacol. 2006:16(3):211-219.
• Vartiainen S, Aarnio V, Lakso M, Wong G. Increased lifespan in transgenic Caenorhabditis elegans overexpressing human alpha-synuclein. Exp Gerontol. 2006:16 [Epub ahead of print]
• Vartiainen S, Pehkonen P, Lakso M, Nass R, Wong G. Identification of gene expression changes in transgenic C. elegans overexpressing human alpha-synuclein. Neurobiol Dis. 2006: 22(3):477-486.

2005

• Aarnio V, Paananen J, Wong G. Analysis of microarray studies performed in the neurosciences. J Mol Neurosci. 2005;27(3):261-268.
• Asikainen S, Vartiainen S, Lakso M, Nass R, Wong G. Selective sensitivity of Caenorhabditis elegans neurons to RNA interference. Neuroreport. 2005:16(18):1995-1999.
• Pehkonen P, Wong G, Toronen P. Theme discovery from gene lists for identification and viewing of multiple functional groups. BMC Bioinformatics 2005, 6:162 doi:10.1186/1471-2105-6-162
• Reisner K, Asikainen S, Vartiainen S, Wong G. Development and biological insights obtained from gene expression profiling of the nematode Caenorhabditis elegans. Curr Genomics 2005:6:97-107.
• Vartiainen S, Wong G. C. elegans models of Parkinson disease. In: LeDoux M, ed. Animal Models of Movement Disorders, p. 219-225. USA: Elsevier, 2005.

2004

• Marvanová M, Lakso M, Wong G. Identification of genes regulated by memantine and MK-801 in adult rat brain by cDNA microarray analysis. Neuropsychopharmacology 2004:29:1070-1079.
• Marvanová M,  Wong G. Adenosine A2A receptor mRNA expression is increased in rat striatum and nucleus accumbens after memantine administration.  Brain Res Mol Brain Research 2004:120(2):193-196.
• Sinkkonen ST, Lindén A-M, Korpi ER, Wong G. Selective reduction of gamma-aminobutyric acid type A receptor delta subunit mRNA levels by MK-801 in rat dentate gyrus. Neurosci Lett 2004:364:106-109.

2003

• Kankainen M, Wong G. DANCER: a program for digital anatomical reconstruction of gene expression data. Nucleic Acids Research 2003:31(21):e132.
• Lakso M, Vartiainen S, Moilanen A-M, Sirviö J, Thomas JH, Nass R, Blakely RD, Wong G. Dopaminergic neuronal loss and motor deficits in Caenorhabditis elegans overexpressing human alfa-synuclein. J Neurochem 2003:86(1):165-172.
• Marvanová M, Ménager J, Bezard E, Bontrop RE, Pradier L, Wong G. Microarray analysis of nonhuman primates: validation of experimental models in neurological disorders. FASEB J 2003:17:929-931.
• Marvanová M, Storvik M, Wong G. Microarray data analysis - applications  for studies on gene expression in addiction and human/nonhuman primates. In: Kotila S, Haataja J, Forsström P-L, Ignatius J, Jukka L, Laine MM, Runeberg N, Råback P, Savolainen V, eds. CSC Report on Scientific Computing 2001-2003, p. 151-154. 2003.
• Storvik M., Lindén A-M, Lakso M, Wong G. Subunit selective decrease of AMPA and metabotropic glutamate receptor mRNA expression in rat brain by systemic adminstratin fo the NMDA receptor blocker MK-801. J Mol Neurosci 2003:21:29-34.
• Törönen P, Wong G, Castren E. Methods for quantitation and clustering of gene expression data. Current Genomics 2003:4:445-463. 
• Wong G. Introduction. In: Tuimala J, Laine MM, eds. DNA Microarray Data Analysis, p. 15-24. Helsinki: Picaset, 2003.
• Wong G. Experimental design. In: Tuimala J, Laine MM, eds. DNA Microarray Data Analysis, p. 38-41. Helsinki: Picaset, 2003.

2002

• Haapasalo A, Sipola I, Larsson K, Åkerman KEO, Stoilov P, Stamm S, Wong G, Castrén E. Regulation of TRKB surface expression by brain-derived  neurotrophic factor and truncated TRKB isoforms. J Biol Chem  2002:277(45):43160-43167.
• Kontkanen O, Lakso M, Wong G, Castrén E. Chronic antipsychotic drug treatment induces long-lasting expression of fos and jun family genes and activator protein 1 complex in the rat prefrontal cortex. Neuropsychopharmacology 2002:27:152-162.
• Kontkanen O, Törönen P, Lakso M, Wong G, Castrén E. Antipsychotic drug treatment induces differential gene expression in the rat cortex. J Neurochem 2002:83:1043-1053.
• Marvanova M, Törönen P, Storvik M, Lakso M, Castrén E, Wong G. Synexpression analysis of ESTs in the rat brain reveals distinct patterns and potential drug targets. Mol Brain Res 2002:104(2):176-183.
• Nikkilä J, Törönen P, Kaski S, Venna J, Castrén E, Wong G. Analysis and visualization of gene expression data using self-organizing maps. Neural Netw 2002:15(8-9):953-966.
• Oja M, Nikkilä J, Törönen P, Wong G, Castrén E, Kaski S. Exploratory clustering on gene expression profiles of mutated yeast strains. In: Zhang W, Shmulevich I, eds. Computational and statistical approaches to genomics, p. 65-78. Boston: Kluwer, 2002.
• Törönen P, Storvik M, Lindén A-M, Kontkanen O, Marvanova M, Lakso M, Castrén E, Wong G. Expression profiling to understand actions of NMDA/glutamate receptor antagonists in rat brain. Neurochem Res 2002:27(10):1209-1220.