Tools / Links

Gene set Enrichment analysis (GSEA)

Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).

The Database for Annotation, Visualization and Integrated Discovery (DAVID)

DAVID provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes. For any given gene list, DAVID tools are able to identify enriched biological themes, particularly GO terms, discover enriched functional-related gene groups, cluster redundant annotation terms, visualize genes on BioCarta& KEGG pathway maps, Link gene-disease associations and many more.

Reduce + Visualize Gene ontology (REVIGO)

REVIGO is a Web server that summarizes long, unintelligible lists of GO terms by finding a representative subset of the terms using a simple clustering algorithm that relies on semantic similarity measures. Furthermore, REVIGO visualizes this non-redundant GO term set in multiple ways to assist in interpretation: multidimensional scaling and graph-based visualizations accurately render the subdivisions and the semantic relationships in the data, while treemaps and tag clouds are also offered as alternative views.

KMplotter

The Kaplan Meier plotter is capable to assess 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 with a mean follow-up of 69 / 40 / 49 / 33 months. Primary purpose of the tool is a meta-analysis based biomarker assessment.

cBioportal for cancer genomics

The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal 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. The portal provides graphical summaries of gene-level data from multiple platforms, network visualization and analysis, survival analysis, patient-centric queries, and software programmatic access. The intuitive Web interface of the portal makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries.

References for gene-based studies in cancer

The site is primarily intended for health professionals and researchers. The aim of the site is to provide comprehensive links to reliable information about genes, their associated proteins, and genetic mutations associated with cancer and related disorders. Each gene page includes links to major genetic databases and where possible links to other related web sites, abstracts references, external searches, and summary information. The site is integrated with Guide to Internet Resources for Cancer to provide links to related clinical and research information sources. - See more at: http://www.cancer-genetics.org/#sthash.aEescqXv.dpuf

WebGestalt (WEB-based GEneSeTAnaLysis Toolkit)

WebGestalt is a "WEB-based GEne SeT AnaLysis Toolkit". It is designed for functional genomic, proteomic and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides an easy way for biologists to make sense out of gene lists.