Identifying core biological processes distinguishing human eye tissues with systems-level gene expression analyses and weighted correlation networks

The human eye has several specialized tissues which direct, capture, and pre-process information to provide vision. RNA-seq gene expression analyses have been used extensively, for example, to profile specific eye tissues and in large consortium studies, like the GTEx project, to study tissue-specific gene expression patterning. However, there has not been an integrated study of multiple eye tissues expression patterning with other human body tissues. We have collated current publicly available healthy human RNA-seq datasets and a substantial subset of the GTEx project RNA-seq datasets and processed all in a consistent bioinformatic workflow. We use this fully integrated dataset to probe the relatedness and biological processes between the cornea, retina, RPE-choroid complex, and the rest of the human tissues with differential expression, clustering, and GO term enrichment tools. We also leverage our large collection of retina and RPE-choroid tissues to build the first human weighted gene correlation networks and use them to highlight known biological pathways and eye gene disease enrichment. Finally, we make these data, analyses, and visualizations available via a powerful interactive web application (http://eyeIntegration.nei.nih.gov).