RNAnet a Map of Human Gene Expression

TL;DR

RNAnet offers rapid, normalized access to extensive human gene expression data from GEO, enabling efficient data mining and new insights into RNA systems biology.

Contribution

RNAnet bridges Ensembl and GEO databases, providing immediate access to normalized gene expression data for human genes, simplifying cross-experiment comparisons.

Findings

Access to thousands of normalized gene expression measurements in seconds

Discovery of large, sparse gene co-expression networks

New insights into RNA systems biology through data mining

Abstract

RNAnet provides a bridge between two widely used Human gene databases. Ensembl describes DNA sequences and transcripts but not experimental gene expression. Whilst NCBI's GEO contains actual expression levels from Human samples. RNAnet provides immediate access to thousands of Affymetrix HG-U133 2plus GeneChip measurements Homo sapiens genes in most medically interesting tissues. Without RNAnet comparison across experiments in GEO is very labour intensive requiring man months of effort to down load and clean data. With RNAnet anyone can access cleaned quantile normalised data in seconds. It can be used to data mine patterns of co-expression. The network of strongly correlated genes is huge but sparse. Thousands of genes interact strongly with thousands of others. Conversely there are tens of thousands of genes which interact strongly with less than 100 others. I.e. RNAnet gives new views for RNA Systems Biology.