Notes: Gene expression

compare gene expression over genome two technologies microarray - hybridization strength

RNAseq - quantify reads

Gene Expression Omnibus

Analyze with GEO2R

set groups, look at top 20, then compare data

write wiki page for usage (view tutorial)


For this session, we were looking at NCBI's Gene Expression Omnibus (GEO). I had never worked with this database and I did not even know such a resource existed. The GEO is a collection of expression level data submitted in the format of array studies and high-throughput sequencing data.

The database also can be used to compare and explore conditions that cause variance in gene expression. My previously selected gene, p53, plays a critical role in cancer and tumor prevention, and this database has a tremendous amount of studies involving this particular gene. Some of the hallmarks of cancer are changes in gene expression within a cell, and the GEO is an excellent tool for finding and analyzing these changes.

(Hanahan and Weinberg, 2000)

The study I selected was from a 2011 study of pituitary gland tumors in humans.

From the dataset browser, you can access a heat map to illustrate the scope of the entire study.

With this map, you can compare the genes involved and immediately see differences in expression levels.

For customized searches and comparisons, the GEO has the GEO2R tool to let you designate groups and see gene specific comparisons of expression.

From these groups, you can then select individual genes and compare expression levels.

I was completely unaware of this online resource, but I was very impressed with the ability to search through and analyze the expression level data. One comment about the site would be that there are some inconsistencies with how the metadata is entered into the site. For example, the study that I eventually used had the samples thoroughly described for easier grouping.

Another study, on the other hand, had a lot of information on the samples, but the grouping was much more difficult.

A third study, had much less information, and due to limitations with the web tools, grouping and comparison was impossible.

These growing pains are not uncommon with these types of public-access databases, but it does add a bit of a wrinkle to using the GEO as a tool.


Great Brad! I like this. I actually couldn't make the relationship thing. But I knew that not all GEO entries can be evaluated by using GEO2R.

b2gof15/students/bradbows/class_sessions/2015.10.27.txt · Last modified: 2015/10/29 13:11 by jbuddika
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