CTD² Data Portal

Last Updated: July 14, 2017

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Note: Users must use data with discretion and acknowledge the CTD² Network

Project Title	Experimental Approaches	Data	Principal Investigator	Contact Name	Submission Date
The Broad Institute : Identifying and Targeting Cancer Dependencies with Small Molecules
Cancer Therapeutics Response Portal (CTRP v1, 2013) dataset Basu, Bodycombe, Cheah et al. (Cell)	informer set assembly cell-line selection small-molecule sensitivity profiling ACME analysis correlation analysis	Dashboard Submission(s) Raw/Analyzed Data (DCC)	Stuart L. Schreiber, Ph.D.	Paul Clemons	2015-10-14
Cancer Therapeutics Response Portal (CTRP v2, 2015) dataset Adams et al. (ACS Chem Biol)		Raw/Analyzed Data (DCC)			2015-10-14
Annotated Cluster Multidimensional Enrichment (ACME) analysis Seashore-Ludlow et al. (Cancer Discov)		Analyzed Data (DCC)			2015-10-14
Basal Gene-Expression and Copy-Number Correlation analysis Rees et al. (Nature Chem Biol)		Analyzed Data (DCC)			2015-12-16
Columbia University : Systems Biology of Tumor Progression and Drug Resistance
Computational Human High-Grade Glioblastoma Multiform (GBM) Interactome - miRNA (Post-Transcriptional) Layer Sumazin et al. (Cell, 2011)	miRNA network reverse engineering (Hermes)	Raw/Analyzed Data (DCC) Dashboard Submission(s)	Andrea Califano, Ph.D.	Kenneth Smith	2015-03-17
Direct Reversal of Glucocorticoid Resistance by AKT Inhibition in Acute Lymphoblastic Leukemia (T-ALL) Piovan et al. (Cancer Cell, 2013)	transcriptional-level signal transduction network reverse engineering (ARACNe) master regulator analysis (MARINa)	Raw/Analyzed Data (GEO) Analyzed Data (DCC) Dashboard Submission(s)	Andrea Califano, Ph.D.	Kenneth Smith	2014-08-14
Dana-Farber Cancer Institute (DFCI) : Functional Annotation of Cancer Genomes
Mapping the Function of Rare Oncogenic Variants Kim et al. (Cancer Discov, 2016)	mutant allele tumorigenicity and expression screening	Raw/Analyzed Data (DCC) Dashboard Submission(s)	William C. Hahn, M.D., Ph.D.	Joshua Dempster	2016-09-29
Discovery of Resistance Mechanisms Moody et al. (Oncogene) Shao et al. (Cell)	ORF library screening	Raw/Analyzed Data (DCC) Dashboard Submission(s)			2016-02-01
Discovery of Novel Oncogenes Dunn et al. (PNAS, 2014) Hagerstrand et al. (Cancer Discovery, 2013) Luo et al. (Molecular Cancer Research, 2014)	multiplexed in vivo transformation assay targeted loss- and gain-of-function (shRNA and ORF) studies cancer genome analysis and analysis of pooled shRNA screening data	Raw/Analyzed Data (DCC) Dashboard Submission(s)			2016-02-01
Identification of Therapeutic Targets Across Cancer Types Cheung et al. (PNAS) Cowley et al. (Nature) Shao et al. (Genome Res) Nijhawan, Zack et al. (Cell) Aguirre et al. (Cancer Discov, 2016)	pooled shRNA screening, deconvolution by Affymetrix custom barcode microarrays pooled shRNA screening, deconvolution by next-generation sequencing CRISPR screening, deconvolution by next-generation sequencing	Raw/Analyzed Data (DCC) Dashboard Submission(s)			2016-07-29
Identification of Therapeutic Targets in KRAS Driven Lung Cancer Barbie et al. (Nature)	shRNA screening	Raw/Analyzed Data (DCC) Dashboard Submission(s)			2015-10-21
Identification of Therapeutic Targets in Ovarian Cancer Baratta et al. (PNAS, 2015) Ren, Cheung et al. (Sci Transl Med)	in vivo shRNA screening cancer genome analysis and analysis of pooled shRNA screening data tumor-penetrating siRNA nanocomplexes for validation	Raw/Analyzed Data (DCC) Dashboard Submission(s)			2016-02-01
Emory University : High-Throughput Protein-Protein Interaction Interrogation in Cancer
High-Throughput Protein-Protein Interaction Analysis for Hippo Pathway Profiling Mo et al. (J Mol Cell Biol)	high-throughput orthogonal protein-protein interaction screening	Raw/Analyzed Data (DCC) Dashboard Submission(s)	Haian Fu, Ph.D.	Andrei Ivanov	2015-04-15
LC-MS Analysis of PRAS40 Protein-Protein Interactions Havel et al. (Oncogene 2015)	liquid chromatography-mass spectrometry	Raw/Analyzed Data (DCC) Dashboard Submission(s)			2016-10-28
High-Throughput Protein-Protein Interaction Dataset for Lung Cancer-Associated Genes Li Z, Ivanov AA, Su R, et al. (Nat Commun 2017)	high-throughput orthogonal protein-protein interaction screening	Raw/Analyzed Data (DCC) Dashboard Submission(s)			2016-12-30
MEDICI (Mining Essentiality Data to Identify Critical Interactions) for Cancer Drug Target Discovery and Development Harati, S et al. (PLoS One2017)	mining protein-protein interactions (PPIs)	Raw/Analyzed Data (DCC)			2017-01-23
Discovery of Novel MYC Protein Interactors with NanoPCA High-throughput Protein-protein Interaction Screening Mo, X et al. (Mol Pharmacol. 2017)	NanoPCA high-throughput protein-protein interaction screening	Raw/Analyzed Data (DCC) Dashboard Submission(s)			2017-02-13
Fred Hutchinson Cancer Research Center (FHCRC-1) : An Integrated Functional and Computational Discovery Engine for Preclinically-Validated Cancer Drug Targets
Genetic Disruption of CTCF Destabilizes DNA Methylation Kemp et al. (Cell Rep)	methylation profiling by next-generation sequencing	Raw/Analyzed Data (GEO,SRA)	Christopher Kemp, Ph.D.	Olga Nikolova	2015-08-21
Functional Landscape of the Human Kinome in MYCN Amplified and Non-amplified Neuroblastoma	high-throughput siRNA transfections	Raw/Analyzed Data (DCC)			2017-02-13
Identification of drug targets for combination therapy with Retinoic Acid in Neuroblastoma	high-throughput siRNA transfections	Raw/Analyzed Data (DCC)			2017-02-13
Functional Exploration of the Druggable Genome in MYCN Amplified and Non-amplified Neuroblastoma	high-throughput siRNA transfections	Raw/Analyzed Data (DCC)			2017-02-13
Translational Genomics Research Institute (TGen) : Systematic Development of Novel Druggable Targets in Glioblastoma
Glioblastoma Multiforme (GBM) Orthotopic Xenograft Transcriptome	expression profiling by microarray	Raw/Analyzed Data (GEO) Analyzed Data (DCC)	Michael E. Berens, Ph.D.	Gil Speyer	2013-05-23
Identification of Pathways Enriched with Condition-Specific Statistical Dependencies Across Four Subtypes of Glioblastoma Multiforme (GBM) Jung et al. (Nucleic Acid Res)	Evaluation of Differential DependencY(EDDY)	Raw/Analyzed Data (DCC) Dashboard Submission(s)			2015-08-27
Quantified Cancer Cell Line Encyclopedia (CCLE) RNA-seq Data	expression profiling of mRNA-seq data	Analyzed Data (DCC)			2017-03-24
University of California San Fransisco (UCSF-1) : Identification of Tumor-Specific Vulnerabilities
Chemical-Genetic Interaction Mapping Strategy Martins, Zhou et al. (Cancer Discov)	isogenic cell panel screening	Raw/Analyzed Data (DCC) Dashboard Submission(s)	Frank P. McCormick, Ph.D.	Sourav Bandyopadhyay	2014-03-03
University of California San Fransisco (UCSF-2) : Genetic Network Analysis to Discover Cancer Targets
Integrative Genomic Approaches in Neuroblastoma (NBL) Chen J et al. (Cancer Discov)	splicing QTL analysis of backcrossed transgenic NBL mice	Raw/Analyzed Data (GEO) Analyzed Data (DCC) Dashboard Submission(s)	William A. Weiss, M.D., Ph.D.	David Quigley	2015-04-03
Expression Analysis of Superior Cervical Ganglion from Backcrossed TH-MYCN Transgenic Mice Hackett et al. (Cell Rep)	expression profiling by microarray	Raw/Analyzed Data (GEO)			2015-08-31
Gene Expression Profiling of Normal Mouse Skin, Hras WT and Hras -/-	gene expression microarrays	Raw/Analyzed Data (DCC) Dashboard Submission(s)			2016-11-14
University of Texas MD Anderson Medical Center (UTMDA) : Biological Annotation of Data from Large-Scale Cancer Genomic Initiatives
Characterization of PIK3R1 Neomorphic Mutations Cheung et al. (Cancer Cell)	cytotoxicity screening reverse-phase protein lysate microarrays (RPPA) viability, functional and tumorigenicity assays	Raw/Analyzed Data (DCC) Dashboard Submission(s)	Gordon B. Mills, M.D., Ph.D.	Sahil Seth	2014-12-18
High-Throughput Screening Identifying Driving Mutations in Endometrial Cancer Liang et al. (Genome Res)	whole exome sequencing (WXS) shRNA high-throughput screening viability assays	Raw/Analyzed Data (DCC) Dashboard Submission(s)			2014-12-08
Phenotypic Examination of PIK3CA Allelic Series Using MCF10A Cell Sensor Platform Dogruluk et al. (Cancer Res)	allelic series construction and cell line production anchorage-independent growth assays proliferation assays	Raw/Analyzed Data (DCC) Dashboard Submission(s)			2015-09-02
University of Texas Southwestern Medical Center (UTSW) : A Concerted Attack on Patient-Specific Oncogenic Vulnerabilities in Lung Cancer
Lung Cancer Oncogenotype-Selective Drug Target Discovery (Natural Products Focus)	siRNA library screening small molecule screening	Raw/Analyzed Data (DCC) Dashboard Submission(s)	Michael Roth, Ph.D.	Bruce Posner Anwu Zhou	2012-04-12
Functional Signature Ontology Tool: Triplicate Measurements of Reporter Gene Expression in Response to Individual Genetic and Chemical Perturbations in HCT116 Cells (Colon Cancer) Potts, Kim, Fisher, Hu et al. (Sci Signal)	QuantiGene Plex 2.0 assays	Raw/Analyzed Data (DCC)			2014-05-01
U01 Natural Products Screening	small molecule screening	Raw/Analyzed Data (DCC)			2014-05-07
High-Throughput siRNA Screening of a Non-Small Cell Lung Cancer (NSCLC) Cell Line Panel	siRNA library screening	Raw/Analyzed Data (DCC) Dashboard Submission(s)			2014-09-02
Identification of ASCL1 as a Therapeutic Target for High-Grade Neuroendocrine Lung Cancers Augustyn et al. (PNAS)	expression profiling by microarray ChIP-seq	Raw/Analyzed Data (GEO) Raw/Analyzed Data (GEO,SRA)			2015-08-07
SW04428 is a Novel Topoisomerase 1 Inhibitor Zubovych et al. (Mol Cancer Ther. 2016) Kim et al. (Cell 2013)	RNA-seq analysis	Raw/Analyzed Data (DCC) Dashboard Submission(s)			2017-01-10
NSCLC Cell Lines with Loss of SMARCA4 Expression are Hypersensitive to Inhibitors of Aurora Kinase A Tagal et al (Nature Communications, 2017)	RNAi depletion & chemical inhibition	Raw/Analyzed Data (DCC) Dashboard Submission(s)			2017-05-11