A Human "eFP" Browser for Generating Gene Expression Anatograms

Abstract

Transcriptomic studies help to further our understanding of gene function. Human transcriptomic studies tend to focus on a particular subset of tissue types or a particular disease state; however, it is possible to collate into a compendium multiple studies that have been profiled using the same expression analysis platform to provide an overview of gene expression levels in many different tissues or under different conditions. In order to increase the knowledge and understanding we gain from such studies, intuitive visualization of gene expression data in such a compendium can be useful. The Human eFP ("electronic Fluorescent Pictograph") Browser presented here is a tool for intuitive visualization of large human gene expression data sets on pictographic representations of the human body as gene expression "anatograms". Pictographic representations for new data sets may be generated easily. The Human eFP Browser can also serve as a portal to other gene-specific information through link-outs to various online resources.

Fig 1. Human eFP Browser output showing expression patterns of the INS gene in the “Skeletal Immune Digestive” compendium.

Strong expression of INS, as denoted by the red colour, is observed in Islet cell cultures, and to a lesser extent in RNA samples generated from the whole pancreas, where these specialized cells are found.

Fig 2. Human eFP Browser output for the SIX homeobox 3 (SIX3) gene using the “Nervous” Data Source, showing strong levels of expression in the putamen and nucleus accumbens, as denoted by the red colouring.

Fig 3. Human eFP Browser output for the calcium/calmodulin-dependant protein kinase II beta (CAMK2B) gene using the “Human Body Map 2 Illumina” Data Source.

Highest expression levels are found in the brain and to a lesser extent in the skeletal muscle, as denoted by the red colouring.