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
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.
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.
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.
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.