CircNetVis: an interactive web application for visualizing interaction networks of circular RNAs
Thi-Hau Nguyen1, Ha-Nam Nguyen1,2, Trung Nghia Vu3
1University of Engineering and Technology, Vietnam National University in Hanoi, Hanoi, 84024, Vietnam.
BMC Bioinformatics
|January 17, 2024
Summary
CircNetVis is a new web tool for visualizing circular RNA (circRNA) interactions. It helps researchers explore circRNA networks, including unknown ones, through an easy-to-use online platform.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Circular RNAs (circRNAs) play vital roles, and understanding their interactions is key to their functional analysis.
- Existing circRNA interaction visualization tools are limited to known circRNAs and require complex installations.
- There is a need for a user-friendly web application for interactive circRNA network exploration.
Purpose of the Study:
- To develop an interactive web application, CircNetVis, for analyzing human and mouse circRNA interactions.
- To provide a user-friendly platform for visualizing circRNA networks, including those of previously unknown circRNAs.
- To facilitate the investigation of complex interactions between circRNAs, microRNAs, mRNAs, and RNA-binding proteins.
Main Methods:
- CircNetVis accepts circRNA data via IDs (CircBase), genomic coordinates, or FASTA sequences.
- The tool integrates multiple interaction networks for comprehensive analysis.
- It is implemented as a web application using R-shiny for accessibility.
Main Results:
- CircNetVis enables interactive visualization and exploration of circRNA interaction networks.
- Users can analyze interactions involving both known and unknown circRNAs.
- The application supports multiple input formats and generates interactive plots with downloadable results.
Conclusions:
- CircNetVis offers a valuable, accessible resource for researchers studying circRNA functions.
- The web application simplifies the analysis of circRNA interactions, overcoming limitations of existing tools.
- It promotes broader investigation into the roles of circRNAs in biological processes.
Related Concept Videos
01:23RNA Interference
26.0K
RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
26.0K
03:21RNA-seq
10.0K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.0K
02:26Protein Networks
4.0K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.0K
02:15Experimental RNAi
6.1K
RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
6.1K
01:19RNA Structure
4.8K
The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
4.8K