RNAnet a Map of Human Gene Expression

RNAnet provides a bridge between two widely used Human gene databases. Ensembl describes DNA sequences and transcripts but not experimental gene expression. Whilst GEO contains actual expression levels from many thousands of Human samples but, although samples in GEO can be queried by experiment, comparison across the whole of GEO is not supported. RNAnet provides immediate access to thousands of Affymetrix HG-U133 2+ measurements provided by GEO covering Human genes in most medically interesting tissues. Data have been quantile normalised and scanned for a variety of common GeneChip errors. There are copious links back into GEO and Ensembl. Without RNAnet comparison across experiments in GEO is very labour intensive requiring down loading and manual cleaning of data files for each microarray in each experiment. Previously normalising more than a few dozens GeneChips was tricky. Having downloaded tens of thousands of microarray datasets, before RNAnet, we could normalise all HG-U133 2+ in ten hours. With RNAnet anyone can access cleaned quantile normalised data in seconds. Further, since we have data from across many different tissues and medical conditions GEO data can be used to find patterns of co-expression. RNAnet shows that the network of strong correlations is huge but sparse. Thousands of genes interact strongly with thousands of others. Conversely, tens of thousands of genes interact strongly with less than 100 others. I.e. RNAnet gives new views for RNA Systems Biology. It builds on free but very valuable databases.