Distinguishing driver mutations from passenger mutations is critical to the understanding of the molecular mechanisms of carcinogenesis and for identifying prognostic and diagnostic markers as well as therapeutic targets. Source text: Zhang et al., 2014. Approaches to identify…
Desktop app
G T A T C G C T A Mutation Significance Mutation Significance

MutSig Mutation Significance

Analyzes lists of mutations discovered in DNA sequencing, to identify genes…

Analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes. MutSig was originally developed…

Web app
G T A T C G C T A Protein ANalysis… Protein ANalysis THrough Evolutionary…

PANTHER Protein ANalysis THrough Evolutionary Relationships

A widely used online resource for comprehensive protein evolutionary and…

A widely used online resource for comprehensive protein evolutionary and functional classification, and includes tools for large-scale biological data analysis. The latest version of PANTHER, 10.0,…

Desktop app
G T A T C G C T A Introns Vs Exons Introns Vs Exons

InVEx Introns Vs Exons

A permutation-based method for ascertaining genes with a somatic mutation…

A permutation-based method for ascertaining genes with a somatic mutation distribution showing evidence of positive selection for non-silent mutations. The method was developed for use in cancer…

Desktop app
G T A T C G C T A ActiveDriver ActiveDriver

ActiveDriver

A computational method for identifying 'active' sites in proteins…

A computational method for identifying 'active' sites in proteins (signalling sites, protein domains, regulatory motifs) that are specifically and significantly mutated in cancer genomes.…

Web app
G T A T C G C T A CanPredict CanPredict

CanPredict

Allows users to determine if particular changes are likely to be…

Allows users to determine if particular changes are likely to be cancer-associated. The impact of each change is measured using two known methods: Sorting Intolerant From Tolerant (SIFT) and the…

Desktop app
G T A T C G C T A Cancer-specific… Cancer-specific High-throughput Annotation of…

CHASM/SNV-Box Cancer-specific High-throughput Annotation of Somatic Mutations

A software toolkit to prioritize SNVs based on their predicted contribution to…

A software toolkit to prioritize SNVs based on their predicted contribution to tumorigenesis. CHASM includes a database of pre-computed predictive features called SNVBox that facilitates rapid…

Desktop app
G T A T C G C T A Mutational… Mutational Significance In Cancer

MuSiC Mutational Significance In Cancer

A set of tools aimed at determining the significance of somatic mutations…

A set of tools aimed at determining the significance of somatic mutations discovered within a given cohort of cancer samples, incorporating the cohort's alignment data, variant lists and any…

Desktop app
G T A T C G C T A Oncodrive-fm Oncodrive-fm

Oncodrive-fm

An approach to uncover driver genes or gene modules. It computes a metric of…

An approach to uncover driver genes or gene modules. It computes a metric of functional impact using three well-known methods (SIFT, PolyPhen2 and MutationAssessor) and assesses how the functional…

Web app
G T A T C G C T A SNPs3D SNPs3D

SNPs3D

Assigns molecular functional effects of non-synonymous SNPs based on structure…

Assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis. There are three unique features of the SNPs3D resource. First, it is designed specifically for…

Desktop app
Web app
Babelomics Babelomics

Babelomics

A web application for the functional analysis of gene expression and genomic…

A web application for the functional analysis of gene expression and genomic data. Babelomics offers user-friendly access to a full range of methods that cover: (i) primary data analysis, (ii) a…

Web app
G T A T C G C T A nsSNPAnalyzer nsSNPAnalyzer

nsSNPAnalyzer

A tool to predict whether a nonsynonymous single nucleotide polymorphism…

A tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) has a phenotypic effect. nsSNPAnalyzer also provides additional information about the SNP to facilitate the…

Web app
G T A T C G C T A PMut PMut

PMut

A computational approach to the prediction of disease-associated amino acid…

A computational approach to the prediction of disease-associated amino acid mutations, using only sequence-based information (amino acid properties, evolutionary information, secondary structure and…

Web app
G T A T C G C T A Cancer-Related… Cancer-Related Analysis of Variants Toolkit

CRAVAT Cancer-Related Analysis of Variants Toolkit

A web-based application designed with an easy-to-use interface to facilitate…

A web-based application designed with an easy-to-use interface to facilitate the high-throughput assessment and prioritization of genes and missense alterations important for cancer tumorigenesis.…

Desktop app
G T A T C G C T A Driver Genes and… Driver Genes and Pathways

DrGaP Driver Genes and Pathways

A powerful and flexible statistical framework for identifying driver genes and…

A powerful and flexible statistical framework for identifying driver genes and driver signaling pathways in cancer genome-sequencing studies. DrGaP is immediately applicable to cancer…

Web app
G T A T C G C T A Chromatin Modified… Chromatin Modified SNPs

ChroMoS Chromatin Modified SNPs

Combines genetic and epigenetic data with the goal of facilitating SNPs'…

Combines genetic and epigenetic data with the goal of facilitating SNPs' classification, prioritization and prediction of their functional consequences. ChroMoS uses a large database of SNPs and…

Web app
G T A T C G C T A SAP… SAP Disease-Association Predictor

SAPRED SAP Disease-Association Predictor

Offers the researchers an automatic pipeline to predict the disease-association…

Offers the researchers an automatic pipeline to predict the disease-association of single amino acid polymorphisms (SAPs). Through a strict protein-level 5-fold cross-validation, SAPRED attained an…

Web app
G T A T C G C T A transformed… transformed Functional Impact score for Cancer

transFIC transformed Functional Impact score for Cancer

A method to transform functional impact scores taking into account the…

A method to transform functional impact scores taking into account the differences in basal tolerance to germline SNVs of genes that belong to different functional classes. This transformation allows…

Desktop app
G T A T C G C T A Driver Mutation… Driver Mutation Identification

DMI Driver Mutation Identification

Helps identify cancer-associated ‘driver' mutations from ‘passenger’…

Helps identify cancer-associated ‘driver' mutations from ‘passenger’ ones in a cancer genome. Generally, given a set of mutations, the DMI system could identify which of them are drivers,…

Desktop app
G T A T C G C T A Quaternary Protein… Quaternary Protein Amino acid Clustering

QuartPAC Quaternary Protein Amino acid Clustering

Provides a unique tool to identify mutational clustering while accounting for…

Provides a unique tool to identify mutational clustering while accounting for the complete folded protein quaternary structure. QuartPAC identifies non-random mutational clustering while utilizing…

Desktop app
G T A T C G C T A Graph Protein Amino… Graph Protein Amino acid Clustering

GraphPAC Graph Protein Amino acid Clustering

Identifies mutational clusters of amino acids in a protein while utilizing the…

Identifies mutational clusters of amino acids in a protein while utilizing the proteins tertiary structure via a graph theoretical model. Using GraphPAC, we are able to detect novel clusters in…

Desktop app
G T A T C G C T A identification of… identification of Protein Amino acid Clustering

iPAC identification of Protein Amino acid Clustering

Identifies non-random somatic mutations in proteins while taking into account…

Identifies non-random somatic mutations in proteins while taking into account the three dimensional protein structure. By using the tertiary information, we are able to detect both novel clusters in…

Desktop app
G T A T C G C T A CancerMutationAnalysis CancerMutationAnalysis

CancerMutationAnalysis

Implements gene and gene-set level analysis methods for somatic mutation…

Implements gene and gene-set level analysis methods for somatic mutation studies of cancer. The gene-level methods distinguish between driver genes (which play an active role in tumorigenesis) and…

Web app
Desktop app
G T A T C G C T A integrated CAncer… integrated CAncer GEnome Score

iCAGES integrated CAncer GEnome Score

Solves real-life problems by using patient’s genomic information. iCAGES…

Solves real-life problems by using patient’s genomic information. iCAGES comes up with a list of genes that are responsible for this particular patient, shedding light into personalized cancer…

Desktop app
G T A T C G C T A Low frequency… Low frequency Mutation Analysis via Consensus…

LowMACA Low frequency Mutation Analysis via Consensus Alignment

A software for the identification of gain-of-function mutations in putative…

A software for the identification of gain-of-function mutations in putative oncogenic families, increasing the amount of information on functional domains and their possible role in cancer. In this…

G T A T C G C T A MutPrior MutPrior

MutPrior

An approach to prioritize genes in a given caner. We hypothesize that a gene is…

An approach to prioritize genes in a given caner. We hypothesize that a gene is important for cancer if it has high functional impact mutations, is strategically important for network stability and…

Desktop app
G T A T C G C T A Ensemble classifier Ensemble classifier

Ensemble classifier

An ensemble classifier (EC) machine learning method applied to the discovery of…

An ensemble classifier (EC) machine learning method applied to the discovery of driver candidates in breast and ovarian cancer samples from the Cancer Genome Atlas. EC integrates 10 classifiers that…

Desktop app
G T A T C G C T A EnsembleGASVR EnsembleGASVR

EnsembleGASVR

An embedded classification technique, which combines an adaptive genetic…

An embedded classification technique, which combines an adaptive genetic algorithm (GA) with nu-support vector regression (nu-SVR), through an ensemble algorithmic framework. EnsembleGASVR predicts…

Desktop app
Web app
G T A T C G C T A CanBind CanBind

CanBind

A computational pipeline for mapping large-scale cancer exome data across…

A computational pipeline for mapping large-scale cancer exome data across patients onto protein structures, and automatically extracting proteins with an enriched number of mutations affecting their…

Web app
G T A T C G C T A ContrastRank ContrastRank

ContrastRank

A method for prioritizing putative impaired genes in cancer. ContrastRank is…

A method for prioritizing putative impaired genes in cancer. ContrastRank is based on the comparison of exome sequencing data from different cohorts and can detect putative cancer driver genes. The…

Desktop app
G T A T C G C T A MEGSA MEGSA

MEGSA

A powerful and flexible framework for identifying mutually exclusive gene sets…

A powerful and flexible framework for identifying mutually exclusive gene sets (MEGS). MEGSA outperforms existing methods for de novo analyses and greatly improves the capability of recovering the…

Desktop app
G T A T C G C T A Driver Genes Driver Genes

Driver Genes

Allows integration of mutation, expression and functional data, a weighting…

Allows integration of mutation, expression and functional data, a weighting scheme for counting putative driver genes and a method for identifying drivers in a global and patient-specific manner…

Desktop app
G T A T C G C T A SomInaClust SomInaClust

SomInaClust

A method that identifies cancer driver genes from whole exome/genome somatic…

A method that identifies cancer driver genes from whole exome/genome somatic mutation data. SomInaClust specifically prioritizes genes with a higher than expected number of clustering and/or…

Desktop app
G T A T C G C T A DEOD DEOD

DEOD

A method for uncovering the dominant effects of cancer-driver genes based on a…

A method for uncovering the dominant effects of cancer-driver genes based on a partial covariance selection approach. Inspired by a convex optimization technique, DEOD estimates the dominant effects…

Desktop app
G T A T C G C T A SPARse selected… SPARse selected expRessiOn regulators identified…
Desktop app
G T A T C G C T A Model-based Approach… Model-based Approach for identifying Driver Genes…

MADGiC Model-based Approach for identifying Driver Genes in Cancer

Identifying and prioritizing somatic mutations is an important and challenging…

Identifying and prioritizing somatic mutations is an important and challenging area of cancer research that can provide new insights into gene function as well as new targets for drug development.…

Desktop app
Web app
G T A T C G C T A Polymorphic Rates… Polymorphic Rates Indicate Somatic Mutations As…

PRISMAD Polymorphic Rates Indicate Somatic Mutations As Drives

The catalogue of tumour-specific somatic mutations (SMs) is growing rapidly…

The catalogue of tumour-specific somatic mutations (SMs) is growing rapidly owing to the advent of next-generation sequencing. Identifying those mutations responsible for the development and…

Desktop app
G T A T C G C T A CanDrA CanDrA

CanDrA

Predicts cancer-type specific driver missense mutations based on a set of 95…

Predicts cancer-type specific driver missense mutations based on a set of 95 structural and evolutionary features computed by over 10 functional prediction algorithms such as CHASM, SIFT, and…

Desktop app
Web app
G T A T C G C T A Functional Analysis… Functional Analysis through Hidden Markov Models

FATHMM Functional Analysis through Hidden Markov Models

A high-throughput web-server capable of predicting the functional consequences…

A high-throughput web-server capable of predicting the functional consequences of both coding variants, i.e. non-synonymous single nucleotide variants (nsSNVs), and non-coding variants. To facilitate…

Desktop app
G T A T C G C T A e-Driver e-Driver

e-Driver

A method that exploits the internal distribution of somatic missense mutations…

A method that exploits the internal distribution of somatic missense mutations between the protein’s functional regions (domains or intrinsically disordered regions) to find those that show a bias…

Desktop app
G T A T C G C T A OncodriveCLUST OncodriveCLUST

OncodriveCLUST

A method to identify genes with a significant bias towards mutation clustering…

A method to identify genes with a significant bias towards mutation clustering within the protein sequence. This method constructs the background model by assessing coding-silent mutations, which are…

G T A T C G C T A eFISMIC eFISMIC

eFISMIC

A comprehensive database containing experimental evidence on the functional…

A comprehensive database containing experimental evidence on the functional impacts of somatic mutations detected in human cancer. eFISMIC is a valuable resource for storing and visualizing the…

Desktop app
G T A T C G C T A Mutation Set… Mutation Set Enrichment Analysis

MSEA Mutation Set Enrichment Analysis

By focusing on somatic SNVs and indels, we proposed two novel methods to detect…

By focusing on somatic SNVs and indels, we proposed two novel methods to detect candidate cancer genes whose somatic mutations tend to form mutation hotspot regions. The first method, MSEA-clust,…

Desktop app
Web app
G T A T C G C T A OncodriveROLE OncodriveROLE

OncodriveROLE

A machine learning-based approach that classifies driver genes according to…

A machine learning-based approach that classifies driver genes according to their role, using several properties related to the pattern of alterations across tumors. OncodriveROLE shows an accuracy…

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