Making the Most of GEO Data: Query and Analysis Tools

Friday, November 08, 2013 — Poster Session III
10:00 a.m. – 12:00 p.m.	FAES Academic Center (Upper-Level Terrace)	NLM	GEN-13

Authors

M. Holko
C. Evangelista
I.F. Kim
P. Ledoux
H. Lee
K. Marshall
K. Phillippy
N. Serova
P.M. Sherman
A. Soboleva
M. Tomashevsky
S.E. Wilhite
A. Yefanov
N. Zhang
T. Barrett

Abstract

The Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) is the world's largest open repository and distribution hub for microarray data. GEO currently holds nearly 38,000 studies, encompassing almost a million samples, spanning almost 2,000 organisms, and addressing a huge variety of biological phenomena. Here, we present tips and methods to help users effectively query, visualize, analyze and download GEO data. The new GEO holdings browser, together with the complex query builder, can help users identify GEO data relevant to their own interests. The data can then be downloaded directly, or analyzed using GEO’s web-based analysis tools. These tools do not require specialized knowledge of microarray analysis methods, nor do they require time-consuming download of large data sets. Data may be queried and visualized from both experiment- and gene-centric perspectives, on either small or large scale. Additionally, GEO data are richly interconnected with other NCBI databases including Gene, GenBank, and PubMed, adding further value to the data and providing opportunity to discover previously unidentified relationships between diverse data types. GEO data can be used in a variety of ways to supplement laboratory findings and aid in discovery.