Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Cancer-Critical Genes II: Tumor Suppressor Genes01:05

Cancer-Critical Genes II: Tumor Suppressor Genes

10.4K
Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
10.4K
Cancer-Critical Genes II: Tumor Suppressor Genes01:05

Cancer-Critical Genes II: Tumor Suppressor Genes

3.1K
3.1K
Cancer-Critical Genes I: Proto-oncogenes01:33

Cancer-Critical Genes I: Proto-oncogenes

12.2K
Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
12.2K
Cancer-Critical Genes I: Proto-oncogenes01:33

Cancer-Critical Genes I: Proto-oncogenes

6.6K
6.6K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

19.4K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
19.4K
Mouse Models of Cancer Study02:43

Mouse Models of Cancer Study

6.8K
Mice have long served as models for studying human biology and pathology because of their phylogenetic and physiological similarity with humans. They are also easy to maintain and breed in the laboratory, and hence, many inbred strains are now available for research. Studies on mice have contributed immeasurably to our understanding of cancer biology.
The development of transgenic, knockout, and knock-in mice has led to an exponential increase in their use as model organisms in research,...
6.8K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

ESR1 mutations and CDK4/6 inhibitor choice shape clonal selection and adaptive cell states during acquired resistance.

Genome medicine·2026
Same author

Publisher Correction: Tumor transcriptional state predicts survival in immune-checkpoint-blockade-treated glioblastoma.

Nature cancer·2026
Same author

Tumor transcriptional state predicts survival in immune-checkpoint-blockade-treated glioblastoma.

Nature cancer·2026
Same author

Systematic common and rare variant association testing in 392,030 whole genomes in <i>All of Us</i>.

medRxiv : the preprint server for health sciences·2026
Same author

Myeloma Precursors Erode Durable Immunity: Results of the IMPACT study.

Research square·2026
Same author

A 15-layer multi-omics analysis of gastric cancer ecotypes provides therapeutic insights.

Cell reports. Medicine·2026
Same journal

Diagnostic Yield of Genome Sequencing in an Iranian Exome-Negative Autosomal-Recessive Intellectual Disability Cohort.

Human mutation·2026
Same journal

Exploring the Functional Impact of Individual <i>DDX41</i> Variants With a Fast and Robust Cell-Based Method.

Human mutation·2026
Same journal

Modeling the Effects of Single Nucleotide Polymorphisms (SNPs) on the Structure and Function of the Human <i>RET</i> Gene: An In Silico Study.

Human mutation·2026
Same journal

Driver Mutation Subtypes Differentially Shape Immune Evasion Landscapes in Melanoma: An AI-Driven Inflammatory Pathway Model Implicating CCNE1.

Human mutation·2026
Same journal

Comment on "When the Outcome Contains the Exposure: Methodological Limits of a Genome-Wide Cross-Trait Analysis of Type 2 Diabetes and MASLD".

Human mutation·2026
Same journal

AI-Augmented Hematological Signatures for Equitable Detection of Hereditary Hemolytic Anemia Carriers: A Global Systematic Review and Meta-Analysis.

Human mutation·2026
See all related articles

Related Experiment Video

Updated: Apr 17, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

35.1K

Oncotator: cancer variant annotation tool.

Alex H Ramos1, Lee Lichtenstein, Manaswi Gupta

  • 1Cancer Program, Broad Institute, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA; Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA.

Human Mutation
|February 24, 2015
PubMed
Summary
This summary is machine-generated.

Oncotator annotates cancer genomic mutations using data from 14 resources, providing variant and gene information. This tool aids cancer researchers by integrating diverse datasets for comprehensive analysis.

Keywords:
TCGAannotationcancerdatabaseoncotator

More Related Videos

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
11:02

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Published on: October 18, 2013

20.1K
Author Spotlight: Finding New Therapeutic Targets for Malignant Peripheral Nerve Sheath Tumor Through Genome-Scale shRNA Screens
09:33

Author Spotlight: Finding New Therapeutic Targets for Malignant Peripheral Nerve Sheath Tumor Through Genome-Scale shRNA Screens

Published on: August 25, 2023

1.9K

Related Experiment Videos

Last Updated: Apr 17, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

35.1K
Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
11:02

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Published on: October 18, 2013

20.1K
Author Spotlight: Finding New Therapeutic Targets for Malignant Peripheral Nerve Sheath Tumor Through Genome-Scale shRNA Screens
09:33

Author Spotlight: Finding New Therapeutic Targets for Malignant Peripheral Nerve Sheath Tumor Through Genome-Scale shRNA Screens

Published on: August 25, 2023

1.9K

Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Research

Background:

  • Genomic mutations are key drivers of cancer.
  • Integrating diverse mutation data is challenging for researchers.
  • Existing tools lack comprehensive, centralized annotation.

Purpose of the Study:

  • To develop Oncotator, a tool for annotating genomic point mutations and indels.
  • To provide cancer researchers with variant- and gene-centric information.
  • To create an extensible framework for incorporating additional data sources.

Main Methods:

  • Oncotator pools and indexes data from 14 public resources.
  • It provides an extensible framework for adding new data sources.
  • Annotations include gene names, functional classification, and cancer-specific data (COSMIC, Cancer Gene Census, TCGA).

Main Results:

  • Oncotator successfully annotates genomic point mutations and indels.
  • It integrates information from multiple cancer genomics databases.
  • The tool offers both local (Python module) and web-based access.

Conclusions:

  • Oncotator provides a valuable, centralized resource for cancer genomic mutation annotation.
  • The tool enhances cancer research by simplifying data integration and analysis.
  • Its flexible design supports future expansion with new data sources.