[BioC] Student project at European Bioinformatics Institute
Gabriella Rustici
gabry at ebi.ac.uk
Tue Oct 27 17:36:21 CET 2009
Dear all,
the following student project is available at the EBI, Cambridge, UK.
The project description is reproduced below.
Regards,
Gabriella
--------------------------------------
Project title: Interface for Human Gene Expression Map
Project Description:
Thousands of microarray experiments are performed every year to estimate
the relative abundance of different RNA molecules in different
biological conditions. Most of these experiments concentrate on
comparing a small number of biological conditions such as a particular
disease state compared to a normal condition. However, many more
different biological states, such as rare diseases or particular cell
subtypes exist. It is impractical for a single dedicated experiment to
generate a comprehensive expression data set covering all biological
conditions but we can achieve this by using computational integration of
the wealth of experiments that have already been performed and are
available from public databases.
We collected, from the public microarray repositories GEO1 and
ArrayExpress2, over 9000 raw data files generated from the human gene
expression array Affymetrix U133A and derived a global Human Gene
Expression Map by integrating raw data and harmonizing annotations from
thousands of samples. For each gene we then computed its expression
profile characterizing its expression under each of the studied
biological conditions and sample classes. This project is part of an
ongoing effort of integrative analysis across very large collections of
microarray datasets, which has resulted in the release of a new
database, the Gene Expression Atlas2.
This project aims at implementing, based on the current prototype, a
public interface for the Human Gene Expression Map. Through this
interface, users will be able to visualize the map, explore expression
profiles and differentially expressed genes under particular
experimental and biological conditions, and link to other bioinformatics
resources providing genes functional annotation.
Project Learning Summary:
The student will acquire experience in the development of web interfaces
for explorative bioinformatics analysis, a deeper understanding of
microarray data analysis, as well as meta-analytical approaches and
statistical methods for data mining of large-scale datasets. The student
will also gain insights into the production process of a large European
transcriptomics database.
Objectives:
1. Further develop visualization and browsing features in the
existing prototype (http://wwwdev.ebi.ac.uk/microarray/hge/HGE.jsp);
2. Implement a more advanced interface for exploring the Human Gene
Expression Map;
3. Implement basic descriptive statistics for data exploration; and
4. Retrieve or link information about gene annotation from other
bioinformatics resources
Required Student Knowledge:
1. Good to expert level of programming ability with Java and R;
2. Familiarity with some of the aspects of bioinformatics would be
advantageous, especially transcriptomics and microarray data
analysis; and
3. Ability to document code and work progress
Please note that candidates must be registered at a university
throughout the entire duration of their stay at EBI and the work
completed at EBI should form part of the candidate's final year studies.
Project duration:
approx. 6 months
Please email a cv and a cover letter to Gabriella Rustici, gabry at ebi.ac.uk
--
Gabriella Rustici, PhD
Microarray Informatics Team
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge, CB10 1SD
United Kingdom
Email: gabry at ebi.ac.uk
Tel: +44 (0)1223 492539
Fax: +44 (0)1223 494468
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