EyeTFDB: a Curated Eye Disease Transcription Factor Web-Based Platform

Background:  The TFs identify as distinct DNA sequences to regulate transcription processes and chromatin forming.   Materials and Methods: To address needs in multiple areas, we present the EyeTFDB (https://eyetfdb.databanks.behrc.ir/) web-based platform, a novel platform of curated data. It combines the eye disease-related pathways data from the KEGG and REACTOME and their associated mRNAs. Furthermore, we expanded our mRNAs data by extracting disease-related data from valuable databases like DisGeNET and OMIM.   Results: Despite the high importance of eye diseases and the global need for further research in this area, still, there is no remarkable comprehensive database for transcription factors of eye diseases. Here we integrated multiple heterogeneous datasets from different databases addressing this need. We collected 429 mRNAs from 1258 pathways for 25 types of eye disease. In addition, transcription factors are separated from this considerable amount of data.  EyeTFDB user interface is designed to facilitate multiple types of the desired use: (i) the interactive investigations of individual entries on the level of a gene, transcription factor, pathway, eye disease, and (ii) the construction of highly customized datasets using advanced searching and filtering. Conclusion: The status of eye TFs and their broad interactions could significantly influence eye health. EyeTFDB, as well as other established databases serve as rich resources for assisting the researchers in exploring eye TFs in the elevation of public health. The wealthy information generated from future investigations can be incorporated into EyeTFDB for better serving the eye TF research and exploration efforts

Transcriptomic Analysis of Human Retina Reveals Molecular Mechanisms Underlying Diabetic Retinopathy in Sexually Divergent Manner

Today, retinopathy is one of the major causes of vision loss. With the increasing prevalence of obesity, diabetes, blood fat, and hypertension, the number of patients with retinopathy is increasing. Gender is an important factor in a variety of retinal diseases but has rarely been studied in clinical and biological studies. The current understanding of the effect of gender on molecular changes and pathways involved in the onset and progression of diabetic retinopathy (DR) is limited. The aim of this study is to investigate the differences in Diabetic patients’ retinal gene expression between the two sexes. Through RNAseq analysis, mRNA expression profiles were analyzed from 40 post-mortem samples from 20 patients with diabetic macular edema (DME) stage of DR. 29 of samples were female and 11 were male. So our groups were control-female, DME-female, control-male and, DME-male. Human retinal single-cell RNA‑Sequencing data revealed 245 differently expressed genes in female-DME and male-DME patients. The results of enrichment analysis show that most up-regulated genes take part in pathways involved in Osteoclast-associated receptor (OSCAR) binds collagen and Surfactant protein D (SP-D), apoptosis, and tyrosine metabolism molecular functions. In this study, we detected a significant association between tyrosine metabolism and diabetic retinopathy in the DME stage. The increased DR risk was observed only in female patients with the abnormality of low tyrosine metabolism. Furthermore, we found a significant interaction between DR and the coexistence of low tyrosine metabolism. Suggesting that control of tyrosine metabolism might confer great risk reduction for DR in female patients