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Prognostic gene expression biomarker validation software tools | Gene expression data analysis

Survival analysis using gene expression to derive predictive gene signatures is a commonly used feature in research studies employing high throughput genomic data. Gene signatures predictive of overall, relapse free or metastasis free survival are…
cBioPortal
Web

cBioPortal

Provides a web resource for exploring, visualizing, and analyzing…

Provides a web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. cBioPortal reduces molecular profiling data from cancer tissues and cell lines into readily…

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survcomp
Desktop

survcomp

Provides functions to assess and statistically compare the performance of…

Provides functions to assess and statistically compare the performance of survival/risk prediction models. survcomp implements state-of-the-art statistics to (i) measure the performance of risk…

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TIMER
Web

TIMER Tumor IMmune Estimation Resource

Allows explorations of the disease-specific clinical impact of different immune…

Allows explorations of the disease-specific clinical impact of different immune infiltrates in the tumor microenvironment. TIMER was developed to estimate the abundance of six tumor-infiltrating…

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Genefu
Desktop

Genefu

A multi-tiered compendium of bioinformatics algorithms and gene signatures for…

A multi-tiered compendium of bioinformatics algorithms and gene signatures for molecular subtyping and prognostication in breast cancer. Genefu provides bioinformatics implementations of…

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shinyGEO
Web

shinyGEO

A web application that allows a user to download gene expression data sets…

A web application that allows a user to download gene expression data sets directly from GEO in order to perform differential expression and survival analysis for a gene of interest. In addition,…

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RCASPAR
Desktop

RCASPAR

A package that predicts true survival times for the individual patient based on…

A package that predicts true survival times for the individual patient based on microarray measurements. RCASPAR is based on a multivariate Cox regression model that is embedded in a Bayesian…

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LR-Rules
Desktop

LR-Rules

Allows rule induction from survival data. LR-Rules is an algorithm that…

Allows rule induction from survival data. LR-Rules is an algorithm that generates a set of survival rules, following the separate-and-conquer heuristics, in which each rule can be considered…

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miRNA Cancer…
Web
Desktop

miRNA Cancer Analyzer

Provides a machine-learning based system developed to help physicians to…

Provides a machine-learning based system developed to help physicians to diagnose and recommend treatments for 21 different types of cancer. miRNA Cancer Analyzer, to analyze patient’s results,…

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p53MutaGene
Web

p53MutaGene

An online tool for statistical validation of hypotheses regarding the effect of…

An online tool for statistical validation of hypotheses regarding the effect of p53 mutational status on gene regulation in cancer. p53MutaGene is based on several large-scale clinical gene…

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CoxBoost
Desktop

CoxBoost

Builds a risk prediction signature for a specific stratum by down-weighting the…

Builds a risk prediction signature for a specific stratum by down-weighting the observations from the other strata using a range of weights. CoxBoost actively controls the extent to which each…

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CPR
Desktop

CPR Clustering and PageRank

Identifies prognostic genes in the form of networks that provide rich…

Identifies prognostic genes in the form of networks that provide rich information about molecular functions related to cancer development. CPR can identify different prognostic gene networks for…

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blkbox
Desktop

blkbox

Integrates nine machine learning (ML) algorithms to select the best performing…

Integrates nine machine learning (ML) algorithms to select the best performing classifier for a specific dataset and provides an interface for their exploration. blkbox is a software package,…

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QPATH
Desktop

QPATH Quantitative methods for pathology

Predicts the molecular subtypes of colorectal cancer from the routine histology…

Predicts the molecular subtypes of colorectal cancer from the routine histology images. QPATH uses neural networks for extracting local descriptors which were then used for constructing a…

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NetNorM
Desktop

NetNorM

Allows users to schematize whole-exome somatic mutation data. NetNorM…

Allows users to schematize whole-exome somatic mutation data. NetNorM transforms mutation data using gene networks so as to make mutation profiles more amenable to statistical learning. It conserves…

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UALCAN
Web

UALCAN

Enables researchers to study the expression level of genes to compare primary…

Enables researchers to study the expression level of genes to compare primary tumor with normal tissue samples. UALCAN is an interactive web resource that provides critical information and graphic…

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KM plotter
Web

KM plotter Kaplan-Meier plotter

A web application for assessing the effect of 54,675 genes on survival using…

A web application for assessing the effect of 54,675 genes on survival using 10,188 cancer samples. These include 4,142 breast, 1,648 ovarian, 2,437 lung and 1,065 gastric cancer patients. Primary…

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CyNetSVM
Desktop

CyNetSVM

Detects network biomarkers using network-constrained support vector machines…

Detects network biomarkers using network-constrained support vector machines (NetSVM). CyNetSVM predicts clinical outcome of patients and identifies biologically meaningful networks. It includes a…

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hdnom
Web
Desktop

hdnom

Offers a freely available R package, a web application, and an online…

Offers a freely available R package, a web application, and an online prediction tool maker. hdnom is an open-source software package which streamlined the workflow of high-dimensional Cox model…

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MM2S
Desktop

MM2S Medullo-Model to Subtypes

Classifies individual gene expression profiles from Medulloblastoma (MB)…

Classifies individual gene expression profiles from Medulloblastoma (MB) samples. MM2S permits to obtain graphical and tabular summaries of MB subtype predictions for single samples and across sample…

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ExSurv
Web

ExSurv

Predictes the survival contribution of all annotated exons in the human genome.…

Predictes the survival contribution of all annotated exons in the human genome. ExSurv uses RNA sequencing-based expression profiles for cancer samples from four cancer types available from The…

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APPEX
Web
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geneSurv
Web
Desktop

geneSurv

Offers survival analysis methods to define right-censored survival data.…

Offers survival analysis methods to define right-censored survival data. geneSurv includes classical methods such as Kaplan-Meier and Cox PH regression, and advanced methods such as penalized Cox…

CoxPath
Algorithm

CoxPath

Generates patient-specific predictions for the time to recurrence and survival,…

Generates patient-specific predictions for the time to recurrence and survival, along with outcome risk predictions. CoxPath model is a path following algorithm for the L1-regularized Cox…

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TNBCtype
Web

TNBCtype Triple-Negative Breast Cancer type

Permits to accelerate genomic research of Triple-negative breast cancer (TNBC)…

Permits to accelerate genomic research of Triple-negative breast cancer (TNBC) to the community. TNBCtype provides a user- friendly interface for TNBC subtype prediction. Users can classify TNBC…

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ENCAPP
Desktop

ENCAPP

Predicts prognostic outcome and identifies biomarkers for different human…

Predicts prognostic outcome and identifies biomarkers for different human cancers. ENCAPP is an elastic-net-based approach that combines the reference human protein interactome network with gene…

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SarneckiEtAl201…
Desktop

SarneckiEtAl2017

Assists users in visualization of meaningful tiles to facilitate better…

Assists users in visualization of meaningful tiles to facilitate better clinical or biological understanding of tissue phenotypes. SarneckiEtAl2017 provides an image analysis workflow that can…

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survivALL
Web
Desktop

survivALL

Calculates and visualizes survival statistics to assess the association between…

Calculates and visualizes survival statistics to assess the association between a continuous measure and outcome in a compositionally agnostic manner. survivALL is available as an R package and a web…

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voomDDA
Web

voomDDA

Facilitates diagnostic biomarker discovery and classification. voomDDA is based…

Facilitates diagnostic biomarker discovery and classification. voomDDA is based on a method that estimates the mean and variance relationship of the log-counts of RNA-Seq data. It displays the…

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M2EFM
Desktop

M2EFM Methylation-to-Expression Feature Model

Builds prognostic models. M2EFM is a data-integrated modeling approach that…

Builds prognostic models. M2EFM is a data-integrated modeling approach that predicts risk based on data integrated from multiple sources, taking advantage of tried-and-true prognostic factors while…

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Pancancer…
Web
Desktop

Pancancer cluster assignment

Serves for studying tumour mutational profiles. Pancancer cluster assignment…

Serves for studying tumour mutational profiles. Pancancer cluster assignment infers the dependency structure of mutations and performed fully Bayesian inference to capture the uncertainty in network…

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SVR-LUAD
Algorithm

SVR-LUAD

Allows users to identify the miRNA signature associated with the survival time…

Allows users to identify the miRNA signature associated with the survival time of patients with lung adenocarcinoma. SVR-LUAD is based on support vector regression (SVR) and uses an inheritable…

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PROMISE
Algorithm

PROMISE PRediction-Oriented Marker SElection

Increases prediction accuracy. PROMISE is a general algorithm that can be…

Increases prediction accuracy. PROMISE is a general algorithm that can be applied to any penalization method. It flexibly selects cutoffs of stability selection (SS) based on the prediction accuracy…

BCIP
Dataset

BCIP Breast Cancer Integrative Platform

Maintains multi-omics data selected with strict quality control and processed…

Maintains multi-omics data selected with strict quality control and processed with uniform normalization methods. BCIP is a database that provides a user-friendly interface integrating comprehensive…

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OS-Analyzer
Desktop

OS-Analyzer Overall Survival Analyzer

A software tool able to compute the overall survival and progression-free…

A software tool able to compute the overall survival and progression-free survival (PFS). OS-Analyzer is able to perform an automatic analysis of data avoiding wasting time on the manual analysis.…

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NCC-AUC
Desktop

NCC-AUC Nearest Centriod Classifier for AUC valuation

An area under curve (AUC) optimization method for multi-biomarker panel…

An area under curve (AUC) optimization method for multi-biomarker panel identification. NCC-AUC provides a rigorous optimization framework to systematically reveal multi-biomarker panel from genomic…

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MIRUMIR
Web

MIRUMIR

Performs survival analyses and draws Kaplan–Meier (KM) plots for submitted…

Performs survival analyses and draws Kaplan–Meier (KM) plots for submitted ‘microRNA' across several available data sets, which cover more than 800 patients. A robust statistical procedure…

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RSF
Desktop

RSF Random Survival Forests

A unified treatment of Breiman's random forests for survival, regression…

A unified treatment of Breiman's random forests for survival, regression and classification problems. RSF provides a unified treatment of Breiman’s random forests for a variety of data…

InSilico DB
Web

InSilico DB

A collaborative platform that allows users to share genomic datasets. Dataset…

A collaborative platform that allows users to share genomic datasets. Dataset administrators can add/remove collaborators or groups of collaborators through a dedicated sharing interface. It is…

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PPISURV
Web

PPISURV

Automatically derives the currently known interactome for a gene of interest…

Automatically derives the currently known interactome for a gene of interest and correlates expression levels of its interactome, with survival outcome in multiple publicly available clinical…

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LRAcluster
Desktop

LRAcluster

Low rank approximation based multi-omics data clustering (LRAcluster) is a new…

Low rank approximation based multi-omics data clustering (LRAcluster) is a new method to discover molecular subtypes by detecting the low-dimensional intrinsic space of high-dimensional cancer…

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PROGgene
Web

PROGgene

A web application that can be used for studying prognostic implications of mRNA…

A web application that can be used for studying prognostic implications of mRNA biomarkers in a variety of cancers. We have compiled data from public repositories such as GEO, EBI Array Express and…

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BioProfiling.de
Web

BioProfiling.de

Provides experimentalists a comprehensive toolkit for gene/protein list…

Provides experimentalists a comprehensive toolkit for gene/protein list interpretation. In one submission, the gene list is profiled with respect to the most information available regarding gene…

ITTACA
Dataset

ITTACA Integrated Tumor Transcriptome Array and Clinical data Analysis

A public database that gathers published clinical and transcriptomic datasets…

A public database that gathers published clinical and transcriptomic datasets for bladder and breast carcinomas, and uveal melanoma. These data are made available on the Internet for users to…

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Cox-nnet
Desktop

Cox-nnet

An artificial neural networks (ANN) framework to predict patient prognosis from…

An artificial neural networks (ANN) framework to predict patient prognosis from high throughput transcriptomics data. Cox-nnet utilizes feature importance scores based on the partial derivatives of…

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OvMark
Web

OvMark

A powerful tool for examining putative gene/miRNA prognostic biomarkers in…

A powerful tool for examining putative gene/miRNA prognostic biomarkers in ovarian cancer. OvMark combines 14 datasets from 7 different array platforms measuring the expression of ~17,000 genes and…

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más-o-menos
Desktop

más-o-menos

A simple algorithm for classification and discrimination. One reason why…

A simple algorithm for classification and discrimination. One reason why más-o-menos is comparable with more sophisticated methods such as penalized regression may be that we often use a prediction…

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BioPlat
Desktop

BioPlat Biomarkers Platform

A user-friendly open-source bioinformatic resource, which provides a set of…

A user-friendly open-source bioinformatic resource, which provides a set of analytic tools for the discovery and in silico evaluation of novel prognostic and predictive cancer biomarkers based on…

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BC-BET
Web

BC-BET Bladder Cancer Biomarker Evaluation Tool

A web application for evaluating candidate diagnostic and prognostic gene…

A web application for evaluating candidate diagnostic and prognostic gene expression biomarkers in bladder cancer. Specifically, BC-BET calculates how strongly a gene's expression is associated…

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Oncomine
Web

Oncomine

Provides solutions for individual researchers and multinational companies, with…

Provides solutions for individual researchers and multinational companies, with robust, peer-reviewed analysis methods and a powerful set of analysis functions that compute gene expression…

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GOBO
Web

GOBO Gene expression-based Outcome for Breast cancer Online

A user-friendly online tool that allows rapid assessment of gene expression…

A user-friendly online tool that allows rapid assessment of gene expression levels, identification of co-expressed genes and association with outcome for single genes, gene sets or gene signatures in…

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inSilicoDb
Desktop

inSilicoDb

A command-line front-end to the InSilico DB, a web-based database currently…

A command-line front-end to the InSilico DB, a web-based database currently containing 86 104 expert-curated human Affymetrix expression profiles compiled from 1937 GEO repository series. The use of…

Network…
Desktop

Network regularised Cox

Measures the disease comorbidities and to predict survival of the cancer…

Measures the disease comorbidities and to predict survival of the cancer patient. Network regularised Cox was applied to analyse seven microarray cancer gene expression datasets: breast cancer,…

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GliomaPredict
Web

GliomaPredict

Predicts the subtype of a new glioma patient utilizing his/her tumor gene…

Predicts the subtype of a new glioma patient utilizing his/her tumor gene expression profile. GliomaPredict can easily be used by physicians and clinicians, as well as laboratory researchers,…

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biospear
Desktop

biospear

Allows users to develop, validate prediction model, estimate expected survival…

Allows users to develop, validate prediction model, estimate expected survival of patients and visualize them graphically. biospear is an R package that implements approaches to develop and evaluate…

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GSF
Desktop

GSF Gene Signature Finder

Discovers gene-signatures. GSF is an R package that uses survival time data to…

Discovers gene-signatures. GSF is an R package that uses survival time data to find prognostic gene-signatures.

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rexposome
Desktop

rexposome

Permits to investigate the exposome and to proceed association analyses between…

Permits to investigate the exposome and to proceed association analyses between exposures and health outcomes. rexposome accepts any clustering method that allows to obtain a classification of…

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survminer
Desktop

survminer

Provides functions for facilitating survival analysis and visualization.…

Provides functions for facilitating survival analysis and visualization. survminer is an R package that provides functions to (i) draw survival curves with the ‘number at risk’ table, the…

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RTNsurvival
Desktop

RTNsurvival

Integrates regulons generated by the Reconstruction of Transcriptional Networks…

Integrates regulons generated by the Reconstruction of Transcriptional Networks (RTN) package with survival information. RTNsurvival uses S4 classes and methods for plots and analyses. It can…

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survival
Desktop

survival

Contains the core survival analysis routines, including definition of Surv…

Contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.

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rbsurv
Desktop

rbsurv

Selects survival-associated genes based on the partial likelihood of the Cox…

Selects survival-associated genes based on the partial likelihood of the Cox model and separates training and validation sets of samples for robustness. rbsurv can discover multiple sets of genes by…

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iterativeBMAsur…
Desktop

iterativeBMAsurv

A variable selection method for applying survival analysis to microarray data.

A variable selection method for applying survival analysis to microarray data.

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SurvBART
Desktop

SurvBART

A Bayesian ensemble method for survival prediction in high-dimensional gene…

A Bayesian ensemble method for survival prediction in high-dimensional gene expression data. This non-parametric method incorporates both additive and interaction effects between genes, which results…

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BreastMark
Web

BreastMark

A simple user-friendly tool for examining putative gene/miRNA prognostic…

A simple user-friendly tool for examining putative gene/miRNA prognostic markers in breast cancer. BreastMark combines gene expression data from multiple microarray experiments which frequently also…

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bc-GenExMiner
Web

bc-GenExMiner Breast Cancer Gene-Expression Miner

A user-friendly, web-based application, based on DNA microarrays results to…

A user-friendly, web-based application, based on DNA microarrays results to improve gene prognostic analysis performance. bc-GenExMiner was developed as a web-based tool including a MySQL relational…

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SurvExpress
Web

SurvExpress

A versatile free tool to perform validation of multi-gene biomarkers for gene…

A versatile free tool to perform validation of multi-gene biomarkers for gene expression in human cancers. We generated a cancer database collecting more than 20,000 samples and 130 datasets with…

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PrognoScan
Web

PrognoScan

Provides a powerful platform for evaluating potential tumor markers and…

Provides a powerful platform for evaluating potential tumor markers and therapeutic targets. PrognoScan is 1) a large collection of publicly available cancer microarray datasets with clinical…

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MICA-SVM
Web
NSLR
Desktop

NSLR Network-regularized Sparse Logistic Regression

Incorporates clinical binary outcome, gene expression data, and normalized…

Incorporates clinical binary outcome, gene expression data, and normalized Laplacian matrix that encode protein-protein interaction (PPI) network. NSLR helps user to make biomarker discovery and…

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BayesMP
Desktop

BayesMP

Combines multiple transcriptomic studies by Bayesian modeling on p-values.…

Combines multiple transcriptomic studies by Bayesian modeling on p-values. BayesMP is a two-stage approach to model directly on p-values, compared to the unified model in BayesMetaSeq and CBM. This…

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Recurrence…
Web

Recurrence Online

An online classification system capable of using common genome-wide microarrays…

An online classification system capable of using common genome-wide microarrays to assess hormone receptor status and to compute the risk of recurrence. The system performs all bioinformatic steps…

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PROGmiR
Web

PROGmiR

Allows users to study prognostic properties of miRNAs in several cancer types,…

Allows users to study prognostic properties of miRNAs in several cancer types, using publicly available data. We have compiled data from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas…

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PrognoWeb
Web

PrognoWeb

A survival prediction model (termed RS for risk score) built on gene expression…

A survival prediction model (termed RS for risk score) built on gene expression profiles of patients suffering from multiple myeloma (MM) (n = 551), breast cancer (n = 602) or glioma (n = 460).…

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Survival Online
Web

Survival Online

A web-based system that allows for the analysis of Affymetrix GeneChip…

A web-based system that allows for the analysis of Affymetrix GeneChip microarrays by using a parallel version of dChip. The user is first enabled to select pre-loaded datasets or single samples…

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