Analytical Tools

The CTD2 Network develops new approaches to identify novel targets and functionally validate discoveries made from large-scale genomic initiatives, such as The Cancer Genome Atlas (TCGA), Therapeutically Applicable Research to Generate Effective Treatments (TARGET), and the Cancer Genome Characterization Initiative (CGCI), and advance them toward precision medicine. Through robust cross-Network collaborations, CTD2 (1) mines data to find alterations that potentially influence tumor biology, (2) characterizes the functional roles of candidate alterations in cancers, and (3) identifies novel approaches that target causative alterations either directly or indirectly. Methodologies include bioinformatics, genome-wide gain- and loss-of-function screening, and small molecule high-throughput screening, among others.

Part of the CTD2 mission is to make data and tools available and accessible to the greater research community to accelerate the discovery process. Bioinformatics support is often required for analyses of the massive datasets used and generated through experimental pipelines employed by the Network Centers. To facilitate the processes of mining, visualizing, analyzing, and using such datasets, OCG has curated this collection of analytical tools. OCG/CTD2 does not endorse any specific tool. However, this list gives researchers a gateway to access many tools that are useful for analyzing and/or visualizing large-scale genomic and/or complex datasets generated through high-throughput screens and other assays.

2 Analytical Tools
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F

Functional Annotation of Somatic Mutations in Cancer (FASMIC) (University of Texas MD Anderson Cancer Center)

FASMIC is an interactive and open-access web portal for comprehensively querying and visualizing mutation-associated data. The queried gene is displayed in a tabular view with basic information for each mutation and details like summary (gene name, mutation, etc.), 3D structure, literature, mutation frequency etc. under the table.

For questions, please contact Han Liang: (hliang1@mdanderson.org)
Functional Signature Ontology (FuSiOn) (University of Texas Southwestern Medical Center)

FuSiOn is an ontology map built from gene expression data resulting from human kinome perturbation screens using miRNA mimics, shRNAs, and natural products. These maps link bioactive molecules to the proteins and biological processes that they engage in cells. This tool can be used to search for chemical or genetical perturbagens that behave functionally similarly to target a gene of interest.

For questions, please contact John MacMillan: (john.macmillan@utsouthwestern.edu)