Bioinformatics: Transcriptomics Data and Tools - Cambridge, UK
The Functional Genomics Group at EMBL-EBI is responsible for management and analysis of functional genomics data, which include expression profiling, chromatin immunoprecipitate, SNP genotyping and methylation profiling experiments from both microarray and high-throughput sequencing platforms. The group provides a set of tools for biologists and researchers to access and analyze data available in the public domain. This course aims at introducing biologists to these tools.
Topics included in this workshop:
- Microarray/sequencing data standards and reporting format: MIAME, MINSEQE and MAGE-TAB
- Ontologies: Experimental Factor Ontology
- ArrayExpress: EMBL-EBI's MIAME/MINSEQE-compliant repository for functional genomics experiments. Introduction on how to browse/search, interpret and download the database content.
- Expression Atlas: A database that allows users to ask questions about which genes are up- or down-regulated in different experimental conditions, based on a set of highly curated RNA-Seq and microarray experiments from ArrayExpress that have been re-analyzed in-house. Introduction on how the database is constructed and how to interrogate the database.
|Day 1 - 28 November 2013|
|09:00 - 12:30
||The types of functional genomics data sets available in ArrayExpress||Amy Tang|
|Microarray/sequencing data standards and reporting format: MIAME, MINSEQE and MAGE-TAB||Amy Tang|
|Introduction and tour of ArrayExpress. Use of Experimental Factor Ontology (EFO) when searching ArrayExpress.||Amy Tang|
|Hands-on exercise on ArrayExpress||Amy Tang|
|Expression Atlas: How is it constructed?||Amy Tang|
|How to search the Expression Atlas by gene or condition of interest||Amy Tang|
|Hands-on exercises on Expression Atlas
Quiz - Quiz solutions
|Latest developments: Baseline Atlas and improved Differential Atlas||Amy Tang|
|Course Feedback||Amy Tang|