Dr Helen Lockstone

Head of Functional Data Analysis

 Helen Lockstone

Research Summary

I am primarily involved in the analysis and interpretation of microarray data generated within the WTCHG and through other collaborations. This is usually gene expression data obtained for different groups of samples (disease and healthy subjects for example). The rationale behind these studies is that differences in transcript abundance between groups can give insights into the biological mechanisms underlying the disease or condition being studied.

Microarray studies generate a vast amount of data, which can be difficult to interpret even once it has been reduced to a list of differentially expressed genes. Many software tools (often freely available) have been developed to extract useful biological information from microarray data. These tools aim to identify particular groups of genes that are enriched among the genes found differentially expressed. For example, if genes involved in a particular biological process are found to be enriched, that process may be important in the disease.

In addition to gene expression profiling, high-throughput array technology now has a wide variety of other applications, including the investigation of alternative splicing, microRNAs, identification of transcription factor binding sites (ChIP-chip), methylation and DNaseI hypersensitivity sites. These datasets provide information about regulatory features on a genome-wide scale.

Several large-scale studies being conducted in the Centre use one or more of these complementary approaches to identify not only the genes showing altered expression, but to investigate the regulatory mechanisms responsible for the observed differences as well. These studies have great potential to help understand the highly complex system of gene regulation and expression, and the aberrations that occur in disease.

Recently I have become involved in the analysis of High-throughput Sequencing data, e.g. ChiP-Seq and digital transcriptomics.

Publications

Transcriptional signature of human adipose tissue-derived stem cells (hASCs) preconditioned for chondrogenesis in hypoxic conditions.
Pilgaard L, Lund P, Duroux M, Lockstone H, Taylor J, Emmersen J, Fink T, Ragoussis J, Zachar V.
Exp Cell Res. 2009 Feb 2. [Epub ahead of print] PMID: 19331821
 
The cerebral microvasculature in schizophrenia: a laser capture microdissection study.
Harris LW, Wayland M, Lan M, Ryan M, Giger T, Lockstone H, Wuethrich I, Mimmack M, Wang L, Kotter M, Craddock R, Bahn S.
PLoS ONE. 2008;3(12):e3964. Epub 2008 Dec 17. PMID: 19088852
 
Metabolic changes in schizophrenia and human brain evolution.
Khaitovich P, Lockstone HE, Wayland MT, Guo AJ, Zhou J, Somel M, Tsang TM, Jayatilaka SD, Harris LJW, Holmes E, Pääbo S, Bahn S.
Genome Biol.2008;9(8):R124. Epub 2008 Aug 5. PMID: 18681948
 
Gene expression profiling in the human adult Down syndrome brain.
Lockstone HE, Harris LJW, Swatton JE, Wayland MT, Holland A, Bahn S.
Genomics. 2007 Dec;90(6):647-60. Epub 2007 Oct 22. PMID: 17950572
 
Independent protein profiling studies show a decrease in apolipoprotein A1 levels in schizophrenia CSF, brain and peripheral tissues.
Huang J-TJ, Wang L, Prabakaran S, Wengenroth M, Lockstone HE, Koethe D, Gerth CW, Gross S, Schreiber D, Lilley KS, Wayland MT, Oxley D, Leweke FM, Bahn S.
Mol Psychiatry. 2008 Dec; 13(12):1118-28. Epub 2007 Oct 16. PMID: 17938634

Further Publications - see under listing
 

Research Areas
Functional genomics Bioinformatics

Keywords
Microarrays Gene expression Data analysis Functional profiling

 

Contact Details
Helen Lockstone
Bioinformatics Core Group
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive
Oxford OX37BN
United Kingdom

E-mail: hel23@well.ox.ac.uk
Telephone: +44 1865 287590