Survival analysis bioinformatics tools | Gene expression analysis

1 - 50 of 107 results

Assesses the effect of genes on survival using cancer samples. KM plotter is a web application, developed for meta-analysis-based biomarker assessment, that can be used for breast, ovarian, lung, gastric, and liver cancer. The software includes patients with a mean follow-up of 69 / 40/ 49 /33 months. The subtool miRpower enables the validation of the prognostic relevance of microRNAs (miRNAs) in breast and liver cancer.

cBioPortal

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 understandable genetic, epigenetic, gene expression, and proteomic events. The query interface, combined with customized data storage, enables researchers to interactively explore genetic alterations across samples, genes, and pathways and, when available in the underlying data, to link these to clinical outcomes.

STROMA4

Allows to estimate generative properties for the Lehmann subtypes, an alternative Triple-Negative Breast Cancer (TNBC) subtyping scheme. STROMA4 can measure four stromal properties identified in TNBC patients in each patient of a gene expression datasets. These four stromal represent the presence of different cells in the stroma: T-cells (T), B-cells (B), stromal infiltrating epithelial cells (E), and desmoplasia (D).

Genefu

A multi-tiered compendium of bioinformatics algorithms and gene signatures for molecular subtyping and prognostication in breast cancer. Genefu provides bioinformatics implementations of classification algorithms to identify molecular subtypes, as well as prognostic predictors along with their published gene signatures. It also includes other functions to facilitate quick manipulation of gene expression datasets, including gene selection and probe-gene mapping across microarray platforms. The genefu package provides a unified framework for integration of molecular subtype and survival analysis of breast cancer. We have demonstrated how the package can be utilized to perform both meta-analyses across datasets and across algorithms, to facilitate integrated analysis of breast cancer gene expression profiles.

RSF / Random Survival Forests

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 settings. Regression and classification forests are grown when the response is numeric or categorical. Multivariate regression and classification responses as well as mixed outcomes are also handled as are unsupervised forests. Different splitting rules invoked under deterministic or random splitting are available for all families. Variable predictiveness can be assessed using variable importance measures for single, as well as grouped variables. Missing data can be imputed on both training and test data.

MIRUMIR

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 is implemented to account for multiple testing. MIRUMIR is incorporated into BioProfiling.de, analytical portal for high-throughput cell biology. MIRUMIR supports the need of biomedical researchers to estimate the power of miR to serve as potential biomarker to predict survival of cancer patients. MIRUMIR provides such analyses based on several publicly available clinical miR data sets annotated with patient survival information.

p53MutaGene

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 expression data sets and currently covers breast, colon and lung cancers. The tool detects differential co-expression patterns in expression data between p53 mutated versus p53 normal samples for the user-specified genes. Statistically significant differential co-expression for a gene pair is indicative that regulation of two genes is sensitive to the presence of p53 mutations. p53MutaGene can be used in 'single mode' where the user can test a specific pair of genes or in 'discovery mode' designed for analysis of several genes.

survcomp

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 prediction models; (ii) combine these statistical estimates from multiple datasets using a meta-analytical framework; and (iii) statistically compare the performance of competitive models.

MultiMed

Determines multiple putative mediators. MultiMed is an R package that supplies a permutation method able to hold specified family-wise error rates (FWER) and false discovery rates (FDR). This approach can be used for estimating high dimensional biomarkers. It was tested on a study that investigates relationships between increased body-mass index (BMI) and an increased risk of breast cancer.

GEMS / Gene Expression Model Selector

Provides gene expression model analyzer. GEMS is a system for automated development and evaluation of cancer diagnostic models and biomarker discovery from microarray gene expression data. It provides an intuitive wizard-like user interface abstracting the microarray data analysis process and not requiring users to be experts in data analysis. This system is informed by a comparative evaluation of many classification and related algorithms.

LyuAndHaque2018

(1)

Assists users in realizing classification on the genomics data. This algorithm is a convolutional neural network that was developed to discover potential biomarkers for each tumor type. It works in several steps: it (i) preprocesses the input data, (ii) makes tumor type classification using a convolutional neural network, (iii) generates the heat map for each class and picks the genes corresponding to top intensities in the heat-maps and (iv) validates the pathways of selected genes.

BioProfiling.de

Provides a toolkit for gene/protein list interpretation. BioProfiling.de is an analytical web portal that provides a user-friendly dialog-driven web interface and supports gene/protein identifiers. It implements two statistical frameworks which allows implementation of tools capable to explore biological principles to group genes into functional classes or to associate genes by edge into global gene network.

inSilicoDb

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 this package builds on the Bioconductor project's focus on reproducibility by enabling a clear workflow in which not only analysis, but also the retrieval of verified data is supported.

CoxBoost

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 stratum contributes to the variable selection and estimation of regression coefficients. It also focuses on building a risk prediction signature for a specific stratum by down-weighting the observations from the other strata using a range of weights. CoxBoost was designed to identify clusters of variables that either are important only in the stratum of interest or are also important to some extent in the other strata.

GOBO / Gene expression-based Outcome for Breast cancer Online

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 an 1881-sample breast cancer data set. Moreover, GOBO offers the possibility of investigation of gene expression levels in breast cancer subgroups and breast cancer cell lines for gene sets, as well as creation of potential metagenes based on iterative correlation analysis to a prototype gene. The design and implementation of GOBO facilitate easy incorporation of additional query functions and applications, as well as additional data sets irrespective of tumor type and array platform in the form of precompiled R-data sets.

PROGgene

Allows researchers to use publicly available data to study prognostic implications of genes of interest in multiple cancers. PROGgene is a survival analysis tool for performing biomarker identification with a large repository of public datasets. Users can upload their own gene expression datasets. The software can be used to conduct on the fly survival analysis and create survival plots (Kaplan Meier, KM plots) based on gene expression of user input genes in user selected datasets from multiple cancers.

BioPlat / Biomarkers Platform

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 integration and re-use of gene expression signature in the context of follow-up data. The desktop client app is now supported by a dedicated web server for the statistical and computational analysis of very large databases. Furthermore, we have refurbished its graphical interface, added new visualization tools and up-graded the BioPlat data bases. BioPlat facilitates the integration, analysis, validation and feature selection of gene signatures derived from different databases in the context of follow-up data obtained from publicly available gene expression profiling repositories.

PPISURV

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 expression data sets. PPISURV automatically correlates expression of an input gene interactome with survival rates on >40 publicly available clinical expression data sets covering various tumours involving about 8000 patients in total. To derive the query gene interactome, PPISURV employs several public databases including protein-protein interactions, regulatory and signalling pathways and protein post-translational modifications.

SurvBART

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 in high predictive accuracy compared with other methods. In addition, SurvBART provides model-free variable selection of important prognostic markers based on controlling the false discovery rates; thus providing a unified procedure to select relevant genes and predict survivor functions.

SurvMicro

Assesses the performance of prognostic microRNAs (miRNA)-based biomarkers. SurvMicro is a web tool of miRNA expression levels associated with clinical outcome that provides survival analysis and risk assessment in cancer. The software is composed of a database of about 400 cohorts in different tissues and a web tool where survival analysis can be done. It is able to produce information for the validation of miRNA signatures in various cohorts.

RCASPAR

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 framework. A hierarchical prior distribution on the regression parameters is specifically designed to deal with high dimensionality (large number of genes) and low sample size settings, that are typical for microarray measurements. This enables RCASPAR to automatically select small, most informative subsets of genes for prediction.

más-o-menos

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 model trained on one set of patients to discriminate between subgroups in an independent sample, usually collected from a slightly different population and processed in a different laboratory. más-o-menos should be useful for developing prediction models from high-dimensional data in any situation where the covariates are sufficiently correlated and the true effect is roughly linear.

NCC-AUC / Nearest Centriod Classifier for AUC valuation

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 and clinical data. It can serve as a useful tool to identify prognostic biomarkers for survival analysis.

APPEX / Analysis Platform for identification of Prognostic gene EXpression signature in cancer

A web-based software platform to help researchers in the efforts to identify prognostic signatures from genomics data. APPEX is designed to be easy to use and flexible, and it is freely available for advanced statistical survival analyses. A user-friendly graphical interface similar to a desktop application is provided so that users can easily handle their own data on APPEX even if they are not familiar with statistical analysis packages. In addition, APPEX contains >200 publicly available datasets directly applicable on the system so that users can easily validate newly identified signatures in independent patient cohorts.

NBS2 / Network-Based Supervised Stratification

Enables cancer subtype classification. NBS2 is an application which is based on the supervised random walk algorithm with an additional loss function that determines the direction of network propagation. The software was developed to be able to detect how adjusting the weight of each molecular interaction and can assist users in identifying underlying biological pathways. It was tested on both glioblastoma and breast tumors.

QPATH / Quantitative methods for pathology

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 dictionary–based representation of each tumor sample. It is based on support vector machine (SVM) classifiers models, with radial basis functions kernels. The tool can identify with high confidence at least four of five subtypes, the most difficult to recognize is the subtype E.

INFO+

Assists users in pinpointing relevant biomarkers and their effects. INFO+ provides a standalone software dedicated to the captures of the second-order biomarker interactions. This program can be used for classifying biomarkers that include subgroups with an enhanced treatment effect or to explore the ranking of the top-K most influential biomarkers. It aims to be applied even to data including several noisy variables.

biospear

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 a prediction model within a high-dimensional Cox regression setting, and to estimate expected survival at a given time point. The software consists of two core functions: BMsel, that identifies a prediction model, and expSurv, that estimates expected survival. biospear also provides a function for generating survival data.

CancerSubtypes

Offers a method for detecting cancer subtypes from multiple omics data. CancerSubtypes is an R package that gathers six discovery methods: (consensus clustering, consensus non-negative matric factorization, integrative clustering, similarity network fusion, SNF-CC and weighted similarity network fusion) sharing the same input/output requirements. The package also contains functionalities for comparing and visualizing the various results.

CPR / Clustering and PageRank

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 heterogeneous patient sample sets. It allows users to infer different biological processes related to specific groups of samples by analyzing those networks separately. This tool is able to identify heterogeneous prognostic genes.

TomljanovicEtAl2017

Assists users in understanding of the molecular drivers of synaptic and neurophysiologic dysfunction in Alzheimer’s disease (AD). This method allows identification of master regulators of synaptic and neurophysiologic dysfunction in AD, and contains data mining techniques to neuronal RNA expression data from AD brain tissue. It permits users to work on the protein ZCCHC17, also known as pNO40.

ePCR / Ensemble-based Penalized Cox Regression

Serves for survival and time-to-event prediction. The ePCR model makes use of inter-variable interactions and advanced multi-variable machine learning to identify marker combinations. This tool aids users to apply the prognostic model to real-world prostate cancer patient cohorts. Moreover, this program is designed for clinical trial data from docetaxel-treated mCRPC patients, or heterogeneous hospital registry cohorts of advanced prostate cancer patients.

GeneCT / Generalizable Cancerous-status and Tissue-of-origin classifier

Discovers cancerous status and tissue origin of pan-cancer biopsies. GeneCT employs gene expression profiles and exploits deep learning methods. It can be applied to any metastatic cancer cases and for every cancer types. This tool is useful for the investigation of tissue biopsies, especially in molecular cancer studies. It is based on a deep learning approach that requires a high number of training samples.

SigMat

Classifies gene signature matching. SiMat can deduce the class that a given signature belongs to using as input a compendium of gene signatures from a cell line. It is based on a support vector machine (SVM) algorithm and includes a trained model’s prediction based on a simple nearest neighbor classifier. This tool is useful for cross-cell line assessments and improvement of drug signature matching across cell lines.

bc-GenExMiner / Breast Cancer Gene-Expression Miner

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 database. Survival analyses are performed with R statistical software and packages. Molecular subtyping was performed by means of three single sample predictors (SSPs) and three subtype clustering models (SCMs).

OvMark

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 341 miRNAs across 2,129 ovarian cancer samples. The value of OvMark is in the preliminary assessment of biomarkers in ovarian cancer, particularly for research groups with limited bioinformatics facilities.

survminer

(1)

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 cumulative number of events table and the cumulative number of censored subjects table, (ii) arrange multiple ggsurvplots on the same page, (iii) plots the distribution of event’s times, (iv) determine the optimal cut-point for one or multiple continuous variables at once, and others.

BreastMark

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 contain miRNA expression information, and detailed clinical data to correlate outcome with gene/miRNA expression levels. This algorithm integrates gene expression and survival data from 26 datasets on 12 different microarray platforms corresponding to ~17,000 genes in up to 4,738 samples. It also allows us to examine the prognostic potential of 341 microRNAs. The value of BreastMark is both in the simplicity of its design and the robustness of its approach. It is designed with non-bioinformatic research groups in mind and is of great value in the preliminary assessment of putative biomarkers in breast cancer as a whole and within its molecular subtypes.

MethSurv

Correlates overall survival with DNA methylation levels. MethSurv allows to investigate methylation biomarkers that associate with the survival of various human cancers. It combines unsupervised hierarchical clustering and principal component analysis (PCA) for any particular gene. This tool can give a graphical overview of methylation differences between the cancer patients as well as gene subregions.

OS-Analyzer / Overall Survival Analyzer

Assists users in interpreting and analyzing the data of observational studies. OS-Analyzer is a software for the automatic association analysis among the genome variants of patients and their clinical condition. This method allows automatic computation of the overall survival (OS) and progression-free survival (PFS) analysis of a whole DMET (Drug Metabolizing Enzymes and Transporters) dataset.

UALCAN

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 ability to make stage, grade, race and other sub status specific expression features from transcriptome sequencing data. This portal can aid in the identification of candidate biomarkers of specific cancer subclasses, with diagnostic, prognostic or therapeutic implications. It can also be used as a platform for in silico validation of target genes.

Cox-nnet

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 gene features selected by the model, so that the relative importance of the genes to prognosis outcome can be directly assessed. The hidden layer node structure in ANN can be harnessed to reveal much richer information of featuring genes and biological pathways, compared to other methods. Cox-nnet is a desirable survival analysis method with both excellent predictive power and usage to gain biological functions related to prognosis.

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 useful information regarding both the total mutational burden of a patient and the distribution of the mutations on the gene network. The tool does not integrate further information about mutations such as their predicted functional impact.

PatkarEtAl2017

Offers an approach for characterize sample-specific function of a gene. The algorithm aims to investigate molecular changes related with cancer thanks to a network-based featuring. It uses guilt-by-association for increasing previous annotations. This method can be used for determining gained or lost functions in cancer relative to normal tissues as well as for investigating the gain or loss of a specific function in a gene.

SVR-LUAD

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 bi-objective combinatorial genetic algorithm (IBCGA) to identify informative miRNAs associated with the estimation of lung adenocarcinoma survival time. The algorithm was tested using lung adenocarcinoma patients obtained from the TCGA database.

sPAGM / subPathway Activity by integrating Gene and MiRNA

Deduces subpathway functional activity for single samples. sPAGM provides a method that determines subPathway Activity (sPA) scores from the expression levels of genes and miRNAs in corresponding subpathway graphs. It can be used for featuring biological mechanisms at the subpathway level and for detecting and characterizing functional signatures in the prognoses of cancer patient. Besides, the activity score generated by the method can also be applied to other researches, such as drug action mechanisms for various types of tumors.

LRAcluster

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 multi-omics data. The low-rank constraint is the core to generate the low-dimensional representation of the original data. And the convexity of the regularized likelihood function provides efficient gradient-descent algorithm for optimization. Extensive experiments show that LRAcluster is computationally efficient with high accuracy and thus suitable for large-scale cancer multi-omics studies.

ENCAPP

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 expression data. The software identifies functional modules that are differentially expressed between patients with good and bad prognosis and uses these to fit a regression model that can be used to predict prognosis for breast, colon, rectal, and ovarian cancers. It can also accurately identify genes that can serve as prognostic biomarkers for different cancers.

SurvExpress

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 censored clinical information covering tumors over 20 tissues. We implemented a web interface to perform biomarker validation and comparisons in this database, where a multivariate survival analysis can be accomplished in about one minute. SurvExpress is a valuable and comprehensive web tool and cancer database with clinical outcomes tailored to rapidly evaluate gene expression biomarkers.

PrognoScan

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 annotation, as well as 2) a tool for assessing the biological relationship between gene expression and prognosis. PrognoScan searches the relation between gene expression and patient prognosis such as overall survival (OS) and disease free survival (DFS) across a large collection of publicly available cancer microarray datasets.

Parent categories

RNA-seq analysis

Transcription analysis

Link to literature

Review of tools

(Klonowska et al., 2016) Oncogenomic portals for the visualization and analysis of genome-wide cancer data. Oncotarget.
PMID: 26484415
(Chen et al., 2014) Survival analysis tools in genomics research. Human genomics.
PMID: 25421963

Related users

Prognostic gene expression biomarker validation software tools | Transcription data analysis