Lab 5: Gene Expression & Transcriptome Analysis
GEO: Gene Expression Omnibus
*How to query GEO Profiles and Datasets
1. GEO Profiles
The GEO Profiles database stores gene expression profiles derived from curated GEO DataSets. Each Profile is presented as a chart that displays the expression level of one gene across all Samples within a DataSet. Experimental context is provided in the bars along the bottom of the charts making it possible to see at a glance whether a gene is differentially expressed across different experimental conditions. Profiles have various types of links including internal links that connect genes that exhibit similar behaviour, and external links to relevant records in other NCBI databases.
2. GEO Datasets
Dataset clustering: good to know
The GEO DataSets database stores original submitter-supplied records (Series, Samples and Platforms) as well as curated DataSets. Curated DataSets form the basis of GEO's advanced data display and analysis features, including tools to identify differences in gene expression levels and cluster heatmaps. GEO Profiles are derived from GEO DataSets. The GEO DataSets database can be searched using many different attributes including keywords, organism, DataSet type and authors. Examples and full details about how to search for GEO DataSets of interest are provided in the Querying GEO DataSets and GEO Profiles page.
You can select the Gene List and then paste into AmiGO/GO Batch
search for GO terms corresponding to genes that you find unregulated or down regulated with your gene : http://pantherdb.org
search for the pathway your gene/protein is associated with
**The Human Protein Atlas: visually appealing database of gene expression both RNA and Protein + localization. There might be some images and info you can use from here.