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eyeIntegration Dataset

Probe the relatedness and biological processes between the cornea, retina, RPE (choroid), and the rest of the human tissues by using a fully integrated dataset with differential expression, clustering, and GO term enrichment tools.

Details

We have collated publicly available (deposited between January 1st, 2019 and November 1st, 2023) healthy human RNA-seq datasets and a substantial subset of the GTEx project RNA-seq datasets and processed all of these samples in a consistent bioinformatic workflow. We use this fully integrated dataset to build informative visualizations, a novel PCA tool, and UCSC genome browser to provide the ophthalmic community with a powerful and quick means to formulate and test hypotheses on human gene and transcript expression.

Citation(s)

If any portion of this software is used, please cite the following paper in your publication:

  • 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

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