The human eye has several specialized tissues which direct, capture, and pre-process information to provide vision. In order to profile specific eye tissues, researchers have widely used RNA-seq gene expression analyses. They've used it in large consortium studies - like the GTEx project - to study tissue-specific gene expression patterning.
However, there hasn't been an integrated study of multiple eye tissues expression patterning with other human body tissues. That's why NEI has collated publicly available healthy human RNA-seq datasets and a substantial subset of the GTEx project RNA-seq datasets - and processed all of them in a consistent bioinformatic workflow.
We used this fully integrated dataset to probe the relatedness and biological processes between the cornea, retina, RPE (choroid), and the rest of the human tissues with differential expression, clustering, and GO term enrichment tools. We also leveraged our large collection of retina and RPE tissues to build the first human weighted gene correlation networks and use them to highlight known biological pathways and eye gene disease enrichment.
John M Bryan, Temesgen D Fufa, Kapil Bharti, Brian P Brooks, Robert B Hufnagel, David M McGaughey, Identifying core biological processes distinguishing human eye tissues with precise systems-level gene expression analyses and weighted correlation networks, Human Molecular Genetics, Volume 27, Issue 19, 1 October 2018, Pages 3325–3339, https://doi.org/10.1093/hmg/ddy239
Success! Citation copied to clipboard.
Copy to clipboard failed.
First, check the FAQ on the main Eye lntegration page by clicking on Information in the header.
Then click on FAQs.
You can report issues in 2 ways:
The source code and data for this web application is available here.
The following have made contributions to this project:
- David McGaughey conceived of and implemented the project
- John Bryan created the retina and RPE gene networks and the accompanying web pages
- Vinay Swamy created the automated pipeline datasets