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.
Highlights
Global gene expression profiling studies offer an unparalleled opportunity to further our understanding of gene function
Studies have focused on a particular subset of these conditions, but “atlas”-type resources such as the Genomics Institute of the Novartis Research Foundation (GNF) Gene Expression Atlas (Su et al, 2004) that encompasses a wide variety of tissue
We present a tool that enables the user to visualize large-scale human gene expression data sets directly on representations of the human body—the Human eFP Browser at http://bar. utoronto.ca/efp_human/, which is based on an open source framework developed by Winter et al (2007)
Summary
Global gene expression profiling studies offer an unparalleled opportunity to further our understanding of gene function. The ability to decipher when a given gene is expressed, and to what level in certain tissues and developmental stages can prove useful for human biomedical studies. Experimental protein-level evidence for at least 30% of the ~21,000 genes is lacking [3], leaving a sizeable void in our understanding of gene function. Expression levels of human genes vary across a multitude of tissue types, developmental stages and disease states. Studies have focused on a particular subset of these conditions, but “atlas”-type resources such as the Genomics Institute of the Novartis Research Foundation (GNF) Gene Expression Atlas (Su et al, 2004) that encompasses a wide variety of tissue
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