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Candidate gene identification software tools | Genome annotation

Gene prioritization refers to a family of computational techniques for inferring disease genes through a set of training genes and carefully chosen similarity criteria. Test genes are scored based on their average similarity to the training set, and…
ToppGene
Web

ToppGene

A one-stop portal for (i) gene list functional enrichment, (ii) candidate gene…

A one-stop portal for (i) gene list functional enrichment, (ii) candidate gene prioritization using either functional annotations or network analysis and (iii) identification and prioritization of…

Phenolyzer
Desktop
Web

Phenolyzer Phenotype Based Gene Analyzer

A tool focusing on discovering genes based on user-specific disease/phenotype…

A tool focusing on discovering genes based on user-specific disease/phenotype terms. Phenolyzer exhibits superior performance over competing methods for prioritizing Mendelian and complex disease…

POCUS
Desktop

POCUS Prioritization Of Candidate genes Using Statistics

Prioritizes candidate disease genes. POCUS is based on over-representation of…

Prioritizes candidate disease genes. POCUS is based on over-representation of functional annotation between loci for the same disease. It is able to suggest counter intuitive candidates. The tool…

ProGENI
Desktop

ProGENI Prioritization of Genes Enhanced with Network Information

Finds relationship between basal gene expression and drug response. ProGENI…

Finds relationship between basal gene expression and drug response. ProGENI incorporates prior knowledge in the form of an experimentally verified network of protein–protein interactions (PPIs) and…

FlyNet
Web

FlyNet

A network prioritization server dedicated to Drosophila that covers…

A network prioritization server dedicated to Drosophila that covers approximately 95% of the coding genome. FlyNet has several distinctive features, including (i) prioritization for both genes and…

A A A
Lynx
Web

Lynx

A web-based database and a knowledge extraction engine. Lynx supports…

A web-based database and a knowledge extraction engine. Lynx supports annotation and analysis of high-throughput experimental data and generation of weighted hypotheses regarding genes and molecular…

LoFtool
Desktop

LoFtool

Provides a gene score method based on the mutation patterns in the exomes of 60…

Provides a gene score method based on the mutation patterns in the exomes of 60 706 unrelated individuals from the Exome Aggregation Consortium (ExAC) dataset. LoFtool uses ratio of loss-of-function…

Syndrome to…
Web

Syndrome to Gene

Allows efficient searches for candidate genes in a genomic locus. S2G uses…

Allows efficient searches for candidate genes in a genomic locus. S2G uses known genes whose defects cause phenotypically similar syndromes. It can be used to identify molecules that interact with or…

G T A T C G C T A
QueryOR
Web

QueryOR

Helps users to search genes. QueryOR combines different features in order to…

Helps users to search genes. QueryOR combines different features in order to make this platform easy to use. It works about the analysis of human variants from exome and genome sequencing. This tool…

DAWN
Algorithm

DAWN Detecting Association With Networks

Offers a general approach to gene discovery, which can be applied to many…

Offers a general approach to gene discovery, which can be applied to many complex disorders. DAWN is an algorithm that leverages genetic and gene expression data effectively to predict probable risk…

MetaRanker
Web

MetaRanker

Prioritizes the protein-coding part of the human genome to shortlist candidate…

Prioritizes the protein-coding part of the human genome to shortlist candidate genes for targeted follow-up studies. MetaRanker 2.0 allows user to upload lists of genes and their scores, which can…

Beegle
Web

Beegle

An online search and discovery engine that attempts to simplify disease-gene…

An online search and discovery engine that attempts to simplify disease-gene identification by automating the typical approaches. Beegle starts by mining the literature to quickly extract a set of…

HGPEC
Desktop

HGPEC

Prioritizes candidate genes and diseases by employing a heterogeneous method…

Prioritizes candidate genes and diseases by employing a heterogeneous method consisting of a network of genes/proteins and a phenotypic disease similarity system. HGPEC is a Cytoscape app based on a…

G T A T C G C T A
VCF.Filter
Desktop

VCF.Filter

Provides broad support for the VCF format, custom annotations, large VCF files,…

Provides broad support for the VCF format, custom annotations, large VCF files, and flexible analysis types. VCF.Filter is an easy-to-use, standalone, graphical software that allows the user to…

PERCH
Desktop

PERCH Polymorphism Evaluation Ranking and Classification for Heritable traits

Studies disease genes by quantitatively unifying a new deleteriousness measure…

Studies disease genes by quantitatively unifying a new deleteriousness measure called BayesDel, an improved assessment of biological relevance of genes to the disease of interest (BayesGBA), a…

GenRank
Desktop

GenRank

Provides methods that are based on convergent evidence obtained from multiple…

Provides methods that are based on convergent evidence obtained from multiple independent evidence layers. GenRank adapts three methods that are popular for meta-analysis. The package facilitates an…

Arete
Desktop

Arete

Combines network analysis capabilities with integrative analysis. Arete allows…

Combines network analysis capabilities with integrative analysis. Arete allows users to further enrich these results with their own information of different types. It offers two modern prioritization…

G T A T C G C T A
VarElect
Web

VarElect

A free web-based phenotype-dependent NGS variant prioritizer, which leverages…

A free web-based phenotype-dependent NGS variant prioritizer, which leverages the wealth of information in GeneCards and its affiliated databases. VarElect employs GeneCards’ powerful search and…

OncoScore
Web
Desktop

OncoScore

Ranks genes according to their association with cancer, based on available…

Ranks genes according to their association with cancer, based on available biomedical literature. OncoScore is a bioinformatics text-mining tool capable of automatically scanning the biomedical…

GoD
Desktop

GoD Gene ranking based on Diseases

Enables the prioritization of a list of input genes with respect to a selected…

Enables the prioritization of a list of input genes with respect to a selected disease. GoD is based on HPO ontology and GO ontology for the calculation of ranking. It ranks a given set of genes…

staRank
Desktop

staRank

Improves the stability of any given base ranking method. staRank applied the…

Improves the stability of any given base ranking method. staRank applied the concept of stability selection to gene rankings to generate more reproducible ordered hit lists for data generated from…

RobustRankAggre…
Desktop

RobustRankAggreg

Detects genes that are ranked consistently better than expected under null…

Detects genes that are ranked consistently better than expected under null hypothesis of uncorrelated inputs and assigns a significance score for each gene. RobustRankAggreg is a rank aggregation…

FUN-L
Web

FUN-L Functional Lists

A tool for target prioritization for experimentalists. Fun-L carries out the…

A tool for target prioritization for experimentalists. Fun-L carries out the following: given a set of query genes known to be involved in the pathway of interest the remainder of the genome is…

HyDRA
Desktop

HyDRA Hybrid Distance-score Rank Aggregation

Combines the advantages of score-based and combinatorial aggregation…

Combines the advantages of score-based and combinatorial aggregation techniques. HyDRA was tested on a number of gene sets, including Autism, Breast cancer, Colorectal cancer, Endometriosis,…

AGP
Web

AGP Age related disorders Gene Prediction

A machine learning based prediction tool that calculates the probability of…

A machine learning based prediction tool that calculates the probability of association for each gene with age-related disorders in humans. AGP achieved an overall accuracy in terms of precision 75%,…

ProDiGe
Desktop

ProDiGe Prioritization of Disease Genes

Prioritizes disease genes. ProDiGe uses a machine learning method based on…

Prioritizes disease genes. ProDiGe uses a machine learning method based on learning from positive and unlabeled examples. It shares information about known disease genes across diseases by…

Phenomantics
Desktop

Phenomantics

Ranks a given set of genes relative to patient phenotype. Phenomantics orders…

Ranks a given set of genes relative to patient phenotype. Phenomantics orders genes by the semantic similarity computed between phenotypic descriptors associated with each gene and those describing…

HumanNet
Dataset

HumanNet Human gene functional interaction Network

A probabilistic functional gene network of 18,714 validated protein-encoding…

A probabilistic functional gene network of 18,714 validated protein-encoding genes of Homo sapiens, constructed by a modified Bayesian integration of 21 types of 'omics' data from multiple…

PINTA
Web

PINTA

A web resource for the prioritization of candidate genes based on the…

A web resource for the prioritization of candidate genes based on the differential expression of their neighborhood in a genome-wide protein-protein interaction network. PINTA supports both candidate…

GPSy
Web

GPSy Gene Prioritization System

A cross-species gene prioritization system that facilitates the arduous but…

A cross-species gene prioritization system that facilitates the arduous but critical task of prioritizing genes for follow-up functional analyses. GPSy's modular design with regard to species,…

ENDEAVOUR
Web

ENDEAVOUR

A web resource for the prioritization of candidate genes. Using a training set…

A web resource for the prioritization of candidate genes. Using a training set of genes known to be involved in a biological process of interest, this approach consists of (i) inferring several…

GeneSeeker
Web

GeneSeeker

A web server that gathers and combines data from a series of databases. All…

A web server that gathers and combines data from a series of databases. All database searches are performed via the web interfaces provided with the original databases, guaranteeing that the most…

GUILD
Desktop

GUILD Prioritization of Genes Underlying Inheritance Linked Disorders

A framework prioritization of disease candidate genes. GUILD uses a priori…

A framework prioritization of disease candidate genes. GUILD uses a priori gene-disease associations and protein interactions and implementsvarious network-based disease-gene prioritization…

GUILDify
Web

GUILDify

An easy-to-use web server for the phenotypic characterization of genes.…

An easy-to-use web server for the phenotypic characterization of genes. GUILDify offers a prioritization approach based on the protein-protein interaction network where the initial phenotype-gene…

GPEC
Desktop

GPEC

A Cytoscape plug-in to help identify putative genes likely to be associated…

A Cytoscape plug-in to help identify putative genes likely to be associated with specific diseases or pathways. In the plug-in, gene prioritization is performed through a random walk with restart…

SUSPECTS
Web

SUSPECTS

A web-based server which combines annotation and sequence-based approaches to…

A web-based server which combines annotation and sequence-based approaches to prioritize disease candidate genes in large regions of interest. SUSPECTS uses multiple lines of evidence to rank genes…

NetworkPrioriti…
Desktop

NetworkPrioritizer

A Cytoscape plugin that particularly supports the integrative network-based…

A Cytoscape plugin that particularly supports the integrative network-based prioritization of candidate disease genes or other molecules. NetworkPrioritizer computes a number of important centrality…

PULP
Desktop

PULP Positive and Unlabeled Learning for Prioritization

Integrates multiple publicly available genomic data sources in a…

Integrates multiple publicly available genomic data sources in a machine-learning model for the prioritization of candidates identified in patients with retinal disease. PULP calculates probabilities…

PRINCIPLE
Desktop

PRINCIPLE PRINCE Plugin

A Java application implemented as a Cytoscape plug-in, based on a previously…

A Java application implemented as a Cytoscape plug-in, based on a previously published algorithm, PRINCE. Given a query disease, PRINCIPLE prioritizes disease-related genes based on their closeness…

GORBI
Dataset

GORBI

Presents the results of a novel model for computational assignment of gene…

Presents the results of a novel model for computational assignment of gene function using phylogenetic profiling. The predictions for 998 prokaryotic genomes include ~400000 high-confidence…

MimMiner
Web

MimMiner

A text-mining approach to map relationships between more than 5000 human…

A text-mining approach to map relationships between more than 5000 human genetic disease phenotypes from the OMIM database. This interface enables the user to retrieve the similarity ranking for a…

GeneDistiller
Web

GeneDistiller

Provides knowledge-driven, fully interactive and intuitive access to multiple…

Provides knowledge-driven, fully interactive and intuitive access to multiple data sources. GeneDistiller displays maximum relevant information, while saving the user from drowning in the flood of…

Biomine
Web

Biomine

A system that integrates cross-references from several biological databases…

A system that integrates cross-references from several biological databases into a graph model with multiple types of edges, such as protein interactions, gene-disease associations and gene ontology…

BITOLA
Web

BITOLA

An interactive literature-based biomedical discovery support system. The…

An interactive literature-based biomedical discovery support system. The purpose of the system is to help the biomedical researchers make new discoveries by discovering potentially new relations…

DADA
Desktop

DADA Degree-Aware Disease Gene Prioritization

A MATLAB Toolbox used for prioritizing candidate diseases genes with respect to…

A MATLAB Toolbox used for prioritizing candidate diseases genes with respect to a disease of interest. Prioritization is made based on the proximity of candidate genes with disease associated genes…

GeneTIER
Web

GeneTIER Gene TIssue Expression Ranker

A web-based application for candidate gene prioritization. GeneTIER replaces…

A web-based application for candidate gene prioritization. GeneTIER replaces knowledge-based inference traditionally used in candidate disease gene prioritization applications with experimental data…

RiceNet
Dataset

RiceNet

A genome-scale functional network server constructed by integrating diverse…

A genome-scale functional network server constructed by integrating diverse genomics data and demonstrated the use of the network in genetic dissection of rice biotic stress responses and its…

CATAPULT
Web

CATAPULT Combining dATa Across species using Positive-Unlabeled Learning Techniques

A supervised machine learning method that uses a biased support vector machine…

A supervised machine learning method that uses a biased support vector machine where the features are derived from walks in a heterogeneous gene-trait network. Catapult significantly outperforms…

RWRH
Desktop

RWRH Random Walk with Restart on Heterogeneous network

A heterogeneous network by connecting the gene network and phenotype network…

A heterogeneous network by connecting the gene network and phenotype network using the phenotype-gene relationship information from the OMIM database. The RWRH algorithm is inspired by the co-ranking…

CIPHER
Web

CIPHER

Predicts and prioritizes disease genes. CIPHER is applicable to genetically…

Predicts and prioritizes disease genes. CIPHER is applicable to genetically uncharacterized phenotypes, effective in the genome-wide scan of disease genes, and also extendable to explore gene…

Inductive…
Desktop

Inductive Matrix Completion Formulation

An approach based on inductive matrix completion for prioritizing disease…

An approach based on inductive matrix completion for prioritizing disease genes. This approach combines complementary types of evidence which is essential for generalizing to new diseases, as no…

MaxLink
Desktop
Web

MaxLink

A guilt-by-association network search algorithm, has been made available as a…

A guilt-by-association network search algorithm, has been made available as a web resource and a stand-alone version. Based on a user-supplied list of query genes, MaxLink identifies and ranks genes…

pgFusion
Desktop
Web

pgFusion pinpointing disease genes through phenomic and genomic data fusion

A bioinformatics tool for prioritizing candidate genes. pgFusion proposes a…

A bioinformatics tool for prioritizing candidate genes. pgFusion proposes a rigorous statistical model that integrates one type of phenotype similarity and seven types of gene similarities to…

pgWalk
Desktop
Web

pgWalk

Prioritizes candidate genes by integrating multiple phenomic and genomic data.…

Prioritizes candidate genes by integrating multiple phenomic and genomic data. The three types of phenotype similarity data, which covers a total of 7,719 diseases in the OMIM database, are derived…

EvoTol
Web

EvoTol

A framework to identify disease-causing genes using patient sequence data from…

A framework to identify disease-causing genes using patient sequence data from within protein coding-regions. EvoTol quantifies a gene's intolerance to mutation using evolutionary conservation…

DGP
Dataset

DGP Disease Gene Prediction

Provides probability scores for genes being involved in hereditary disease in…

Provides probability scores for genes being involved in hereditary disease in the human genome. DGP can be queried for any of the diseases that have been mapped to a chromosomal region. From this…

BioGraph
Web

BioGraph

A data integration and data mining platform for the exploration and discovery…

A data integration and data mining platform for the exploration and discovery of biomedical information. The platform offers prioritizations of putative disease genes, supported by functional…

NetRanker
Web

NetRanker

Help users to analyze their own microarray experiment data in raw CEL files…

Help users to analyze their own microarray experiment data in raw CEL files along with protein-protein interaction (PPI) network built from user-specified database for disease-related gene…

GIST
Web

GIST Gene Information Search Tool

Allows searching both by genes and by microsatellite markers from multiple…

Allows searching both by genes and by microsatellite markers from multiple information sources. GIST is a one-site query tool for multiple databases. Its frames format has been designed to allow the…

GeneWanderer
Desktop

GeneWanderer

Allows prioritization of candidate genes by use of a global network distance…

Allows prioritization of candidate genes by use of a global network distance measure, random walk analysis, for definition of similarities in protein-protein interaction (PPI) networks. GeneWanderer…

PepPSy
Web

PepPSy

Identifies tissues in which unseen gene products should be looked for. PepPSy…

Identifies tissues in which unseen gene products should be looked for. PepPSy currently embeds eight filtration criteria and seven prioritization modules dedicated to the filtration of protein…

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