Epitomy is a database to integrate epitranscriptome sequencing data for exploring post-transcriptionally modifications of RNAs. Epitomy provides various search options such as searching by modification name, Pubmed ID, coordinates and gene name and is powered by IGV JS genome browser, plotly heatmap module for seamless data visualization and elastic search in the back-end for efficient data storage and retrieval.
Category: Softwares
Lantern: A genome-scale lncRNA ontology annotation extractor and cellular network repository
Lantern is a repository of high quality controlled lncRNA ontology annotations, extracted by mining recent lncRNA literature using a robust NLP based approach. It also houses extensive lncRNA omics annotations like: tissue specific lncRNA expression, RBP interactions, lncRNA-protein co-expression, coding potential, sub-cellular localization and SNPs in lncRNA. Thereby making it a holistic resource for improving the understanding of the noncoding transcriptome. The extracted annotations for around 11,000 lncRNAs are available at
SliceIt: CRISPR/Cas9 guide RNA prediction search engine
SliceIt is a genome-wide database of predicted sgRNAs based on CRISPR/Cas9 system to enable the systematic design of both low (gene or binding site centric) and high-throughput (genome-wide) CRISPR screens to understand the impact of editing the RNA-Binding Proteins’ binding sites in the human genome. SliceIt is powered by IGV JS genome browser for seamless data visualization and elastic search in the backend for efficient data storage and retrieval.
Express: Transcriptome database for mouse eye tissues across multiple developmental stages
Express contains transcript level expression data obtained from 21 lens and 35 retina RNA-Seq mouse samples. We downloaded the raw datasets, aligned them to reference genome and quantified transcript level expression for known and novel transcripts. When then downloaded the reference gene and transcript information and organized them along with the expression data in a MySQL database. We finally developed a PHP backend to interact with the database and a frontend to interact with the user and to visualize the query results.
Eye Splicer: Explore alternative splicing events across different developmental stages in lens from mouse samples
Eye Splicer is a genome browser powered by Biodalliance JavaScript library that lets you explore alternative splicing events across different developmental stages in lens from mouse samples. Eye Splicer contains the most abundant alternative splicing events, skipped exons and retained introns, from our analysis on mouse RNA-Seq datasets covering developmental stages from E15 (embryo 15 days old) to P9 (post-natal 9 days old).
ExSurv: A web resource for prognostic analyses of exons across human cancers using clinical transcriptomes
ExSurv is a web resource for studying the survival contributions of exons across human cancers using RNA-seq data. ExSurv is the first web server which provides exon level survival significance by using the RNA-seq expression datasets and the clinical metadata for four cancer types from The Cancer Genome Atlas (TCGA) project. We pre-calculated the prognostic significance of more than 600000 annotated exons in Ensembl using survival package in R. We stored the TCGA clinical data, exon survival p-values and the expression of the significant exons for visualizing the survival curves in a MySQL database. We developed an integrated backend using PHP and R and used JavaScript in the frontend. The PHP/R backend is reponsible for querying the MySQL database upon user input, calling R to visualize the corresponding database results (using survival package) and returning these results to the frontend. In the frontend, the results are shown to the users in an organized way as a table where each row corresponds to an exon in the queried gene symbol or Ensembl gene ID. It is possible to export the survival plots in SVG (scalable vector graphics) format and the raw data used to generate the plot in TSV (tab-separated values) format.
Seten: Gene set enrichment on CLIP-seq RNA-binding protein binding signals datasets
Seten is a tool for systematic identification and comparison of processes, phenotypes and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles. Seten is a web-based as well as a command line tool which can identify and compare processes, phenotypes and diseases associated with RBPs from condition-specific CLIP-seq profiles. Seten currently provides precomputed results for more than 150 CLIP-seq datasets and can be used to analyze other kinds of binding profile data such as ChIP-seq data.
OperomeDB: Operon prediction for bacterial genomes
In prokaryotic organisms, a substantial fraction of adjacent genes are related functionally and most of these are organized into operons. Operons are a group of co-directionally organized genes in prokaryotic genomes with the presence of a common promoter and terminator. Operons provide insight into the cellular functions and also help in determining distinct experimental designs. It is now clear that the structure of an operon is not static but rather changes with environmental conditions in bacterial species.
READDB: RNA-binding protein expression and disease dynamics database
RNA-binding Protein Expression and Disease Dynamics database is a non-redundant, curated database of human RNA-binding proteins (RBPs). We collected RBPs data from multiple experimental studies and reported their annotation, tissue expression, microRNA predictions, disease associations, protein-protein interactions and their sequence motifs.