Related Experiment Video

Updated: Aug 1, 2025

In Vivo Modeling of the Morbid Human Genome using Danio rerio
12:31

In Vivo Modeling of the Morbid Human Genome using Danio rerio

Published on: August 24, 2013

20.8K

CanIsoNet: a database to study the functional impact of isoform switching events in diseases

Tülay Karakulak1,2,3, Damian Szklarczyk1,3, Cemil Can Saylan4

  • 1Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland.

Bioinformatics Advances
|May 1, 2023
PubMed
Abstract

Insights

CanIsoNet is a new database that tracks changes in alternative splicing (isoform switching) linked to diseases. It integrates gene expression, protein interactions, and clinical data to predict the impact of these switches on disease progression.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Alternative splicing is a key regulatory mechanism in mammalian cells.
  • Dysregulation of alternative splicing is implicated in cancer and other diseases.
  • Isoform switching can alter protein interaction networks, driving disease development.

Purpose of the Study:

  • To introduce CanIsoNet, a novel database for exploring isoform switching events in diseases.
  • To provide a platform for viewing, browsing, and searching disease-associated isoform data.
  • To integrate diverse biological datasets for predicting the pathogenic impact of isoform switching.

Main Methods:

  • Developed CanIsoNet, a web server incorporating isoform expression data.
  • Integrated STRING interaction networks and ClinVar annotations.
  • Enabled browsing by disease and searching by genes or isoforms.

Main Results:

  • CanIsoNet contains data for 11,811 isoforms and 14,357 isoform switching events across 31 diseases.
  • Provides network density scores, PFAM domain IDs, transcript structure visualization, and sample-specific expression data.
  • Highlights ClinVar-annotated genes within interactive networks.

Conclusions:

  • CanIsoNet is a valuable resource for studying the role of alternative splicing in disease.
  • The database facilitates the prediction of pathogenic impacts of isoform switching events.
  • Enables comprehensive analysis of isoform dynamics in various disease contexts.

More Related Videos

Highly Sensitive and Quantitative Detection of Proteins and Their Isoforms by Capillary Isoelectric Focusing Method07:58

Highly Sensitive and Quantitative Detection of Proteins and Their Isoforms by Capillary Isoelectric Focusing Method

Published on: September 19, 2018

6.7K
Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets11:19

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets

Published on: July 7, 2010

14.6K

Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
10.0K
NF-κB-dependent Signaling Pathway02:26

NF-κB-dependent Signaling Pathway

The transcription factor NF-κB was discovered in 1986 in the lab of Nobel laureate Professor David Baltimore, for its interaction with the immunoglobulin light chain enhancer in B-cells. After more than three decades of study, it is now evident that NF-κB regulates the expression of over 100 genes. Most of these genes play an essential role in the innate and adaptive immune responses as well as the inflammatory responses of animals.
NF-κB-dependent Signaling Mechanism
The...
7.6K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
15.4K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
4.8K
RNA Splicing01:32

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
56.6K
The Ras Gene02:38

The Ras Gene

The Ras-gene-encoded proteins are regulators of signaling pathways controlling cell proliferation, differentiation, or cell survival. The Ras-gene family in humans constitutes three primary members—the HRas, NRas, and KRas. These genes code for four functionally distinct yet closely related proteins—the HRas, NRas, KRas4A, and KRas4B. The involvement of mutant Ras genes in human cancer was first discovered in 1982 and is among the most common causes of human tumorigenesis.
Ras is a...
6.3K