EyeDiseases: an integrated resource for dedicating to genetic variants, gene expression and epigenetic factors of human eye diseases.
Jian YuanFukun ChenDandan FanQi JiangZhengbo XueJi ZhangXiangyi YuKai LiJia QuJianzhong SuPublished in: NAR genomics and bioinformatics (2021)
Eye diseases are remarkably common and encompass a large and diverse range of morbidities that affect different components of the visual system and visual function. With advances in omics technology of eye disorders, genome-scale datasets have been rapidly accumulated in genetics and epigenetics field. However, the efficient collection and comprehensive analysis of different kinds of omics data are lacking. Herein, we developed EyeDiseases (https://eyediseases.bio-data.cn/), the first database for multi-omics data integration and interpretation of human eyes diseases. It contains 1344 disease-associated genes with genetic variation, 1774 transcription files of bulk cell expression and single-cell RNA-seq, 105 epigenomics data across 185 kinds of human eye diseases. Using EyeDiseases, we investigated SARS-CoV-2 potential tropism in eye infection and found that the SARS-CoV-2 entry factors, ACE2 and TMPRSS2 are highly correlated with cornea and keratoconus, suggest that ocular surface cells are susceptible to infection by SARS-CoV-2. Additionally, integrating analysis of Age-related macular degeneration (AMD) GWAS loci and co-expression data revealed 9 associated genes involved in HIF-1 signaling pathway and voltage-gate potassium channel complex. The EyeDiseases provides a valuable resource for accelerating the discovery and validation of candidate loci and genes contributed to the molecular diagnosis and therapeutic vulnerabilities with various eyes diseases.
Keyphrases
- single cell
- rna seq
- sars cov
- endothelial cells
- gene expression
- electronic health record
- high throughput
- big data
- genome wide
- age related macular degeneration
- signaling pathway
- poor prognosis
- induced pluripotent stem cells
- induced apoptosis
- epithelial mesenchymal transition
- data analysis
- small molecule
- optical coherence tomography
- squamous cell carcinoma
- machine learning
- mesenchymal stem cells
- angiotensin ii
- lymph node metastasis
- genome wide association study
- cell proliferation
- artificial intelligence
- oxidative stress
- climate change
- adverse drug
- single molecule