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.

3 Analytical Tools
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Pathway Commons

Pathway Commons is a network biology resource that serves as a convenient access point to biological pathway information collected from public pathway databases, which users can search, visualize, and download.

PiHelper (Cold Spring Harbor Laboratory)

PiHelper integrates drug target and antibody target interactions from publicly available resources to facilitate research in systems pharmacology, perturbation biology, and proteomics. PiHelper can (1) import drug and antibody target information; (2) search the interactions; (3) visualize data interactively in a network; and (4) export interaction data for use in publications or other analysis tools.

For questions, please contact this email: (pihelper@cbio.mskcc.org)
Project Achilles Portal (Dana-Farber Cancer Institute)

Project Achilles uses genome-wide pooled shRNA screens to identify and catalog genetic vulnerabilities associated with genetic or epigenetic changes across hundreds of cancer cell lines. In the Project Achilles portal, genes can be queried for essentiality across all cell lines. Data can be easily downloaded and visualized with GENE-E or the data analysis GenePattern module, PARIS

For questions, please contact For questions, please contact this email:: (depmap@broadinstitute.org)