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Bioinformatics Tools: Expression Analysis

This guide contains a curated set of resources and tools that will help you with your research data analysis. It also includes those medical library workshops available at Yale University on many of these bioinformatics tools.

NCBI Resources

Gene Expression Omnibus DataSets is an NCBI repository that contains curated gene expression DataSets, as well as original Series and Platform records in the Gene Expression Omnibus (GEO) repository.

Gene Expression Omnibus Profiles is an NCBI repository that contains individual gene expression profiles from curated DataSets.

Gene Enrichment Analysis

Gene Ontology Enrichment Analysis Software (GOEAST) identifies significantly enriched GO terms among give lists of genes

EMBL-EBI Resources

The ArrayExpress is the EMBL-EBI database that includes gene expression data from microarray and high throughput sequencing studies. Experiments are submitted directly to ArrayExpress or are imported from the NCBI GEO database.

The Expression Atlas is the EMBLEBI expression repository and provides information on gene expression patterns under different biological conditions.


Gene Expression Databases

Allen Brain Atlas Gene expression and neuroanatomical data

The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes.

The International Cancer Genome Consortium (ICGC) Data Portal provides tools for visualizing, querying and downloading the data released quarterly by the consortium's member projects. It contains copy number, rearrangement, expression, and mutation data.

Gene Expression across Normal and Tumor tissue (GENT) is a web-accessible database which provides gene expression patterns across diverse human cancer and normal tissues.

Cell Miner is a Repository of gene expression and GI 50 drug concentration data from NCI60 cell lines