SBIR-STTR Award

A major research focus for gaining insight into the molecular basis for cancer, with the goal of identifying new treatments, is the systematic profiling of cancer cells. This includes the generation of compound potency data and gene/protein expression data. This has led to the generation of massive amounts of disparate data that must be associated in context sensitive ways and collectively data mined in order to reach the goal of finding new treatments. The aim of this project is to develop a new computing platform that will enable researchers throughout the world to interactively collaborate on the analysis of this valuable information. A new web-based platform will be developed that, incorporates recent and emerging Web 2.0 and Enterprise software standards and technologies. This platform will incorporate public cancer cell-based data, including genomics, proteomics, and cytotoxic potency data. It will make possible the systematic exploration of the data through interactive data analysis and visualization tools in order to generate hypotheses. The proposed project will include the development of new statistical methods to identify groups of cells over which selected genes and compounds are highly and significantly correlated. The platform will be used to identify candidate target genes and drugs for cancer chemotherapy, and to determine factors that contribute to chemoresistance and sensitivity.

Public Health Relevance:
Cancer is a major cause of mortality throughout the world. Many types of cancers lack effective treatments, and new treatment approaches have the potential to positively impact large patient populations. This project will build a new data analysis and visualization platform to aid in identifying biomarkers predictive of drug efficacy for optimizing cancer chemotherapy.

Public Health Relevance Statement:
Project Narrative Cancer is a major cause of mortality throughout the world. Many types of cancers lack effective treatments, and new treatment approaches have the potential to positively impact large patient populations. This project will build a new data analysis and visualization platform to aid in identifying biomarkers predictive of drug efficacy for optimizing cancer chemotherapy.

Project Terms:
Analysis, Data; Biology; Businesses; Cancer Treatment; Cancers; Cell Death; Cells; Chemicals; Chemistry; Chemotherapy Protocol; Chemotherapy Regimen; Chemotherapy, Cancer, General; Chemotherapy-Oncologic Procedure; Classification; Code; Coding System; Collaborations; Combination Chemotherapy Regimen; Computer Programs; Computer software; Crossmatching, Tissue; Cytotoxic agent; Cytotoxic drug; Data; Data Analyses; Data Banks; Data Bases; Data Set; Databank, Electronic; Databanks; Database, Electronic; Databases; Dataset; Development; Discipline; Drugs; Environment; Gene Expression; Gene Proteins; Gene Targeting; Generations; Genes; Genomics; Goals; Histocompatibility Testing; Imagery; Information Technology; Institution; Internet; Investigators; Lead; Link; MT-bound tau; Malignant Cell; Malignant Neoplasm Therapy; Malignant Neoplasm Treatment; Malignant Neoplasms; Malignant Tumor; Medication; Methods; Micro RNA; MicroRNAs; Molecular; Mortality; Mortality Vital Statistics; On-Line Systems; Online Systems; Pb element; Pharmaceutic Preparations; Pharmaceutical Preparations; Procedures; Property; Property, LOINC Axis 2; Protein Gene Products; Proteins; Proteomics; Quimioterapia; Research; Research Personnel; Researchers; Science of Chemistry; Software; Statistical Methods; Systematics; Targetings, Gene; Technology; Testing; Tissue Crossmatchings; Tissue Typing; Translating; Translatings; Variant; Variation; Visualization; WWW; Work; analytical method; anticancer therapy; base; biomarker; cancer cell; cancer chemotherapy; cancer therapy; cancer type; clinical data repository; clinical data warehouse; computational tools; computer program/software; computer science; computerized tools; cytotoxic; data mining; data repository; datamining; drug efficacy; drug/agent; effective therapy; gene product; heavy metal Pb; heavy metal lead; histocompatibility typing; insight; interactive computing; language translation; malignancy; miRNA; microtubule associated protein tau; microtubule bound tau; microtubule-associated protein tau; microtubule-bound tau; necrocytosis; neoplasm/cancer; online computer; patient population; protein expression; public health relevance; relational database; response; tau; tau Proteins; tau factor; tool; web; web based; world wide web

A major research focus for gaining insight into the molecular basis for cancer, with the goal of identifying new treatments, is the systematic profiling of cancer cells. It has resulted in large volumes of data that include the compound potency and gene expression data. To more effectively find treatments, the data must be integrated and associated in context sensitive ways. The overall objective of this project is to create a web-based, high-performance visual analytics platform for the exploration of compound activity and molecular profile data, through interactive visualization that supports human analytical reasoning. The platform will demonstrate how visual exploration of cancer cell-based data that include genomics, proteomics, cytotoxic potency, and other research data can be used to identify candidate targets and drugs for cancer chemotherapy, and determine factors that contribute to chemoresistance and sensitivity. The specific aims are the following: 1) Improve the ability to navigate, search, and directly explore large data in highly-coordinated multi-view visualizations. The heatmap will incorporate interaction mechanisms from zooming interfaces and animation. A new visualization for results of the Tau Path statistical method will explore pairs of variables, such as compound-gene, where significant associations have been found in some, but not all of the cell lines. 2) Develop a high-performance analytics server for multicore systems. The server will execute concurrent components for significance tests, clustering, correlation, regression, and association analysis. 3) Extend the new Tau Path statistical method. The extensions include improved identification of the subpopulation, conditional testing to identify subpopulations under which associations are significantly greater than for the whole population, and extension to larger populations, such as all compounds of interest, so as to prioritize drug candidates 4) Integrate resources with the platform to enable findings to be rapidly validated and provide additional insights. The resources include biological pathways systems (e.g. KEGG), the Gene Ontology annotations (GO), biological screening databases (e.g. PubChem), and chemoinformatics services (e.g. OpenTox). The impact of the resulting visual analytics platform will be to more rapidly identify hypotheses that lead to the discovery of new cancer treatments. These hypotheses include compounds that may serve as leads in a drug discovery program seeking new chemotherapy and genes that modulate drug potencies in selected cell lines. The project will lead to a visual analytics platform for cancer research and curated public content.

Public Health Relevance:
Cancer is a major cause of mortality throughout the world. Many types of cancers lack effective treatments, and new treatment approaches have the potential to positively impact large patient populations. This project will build a new high-performance visual analytics platform to aid in identifying biomarkers predictive of drug efficacy for optimizing cancer chemotherapy.

Thesaurus Terms:
Algorithms;Architecture;Benchmarking;Best Practice Analysis;Biological;Cancer Treatment;Cancers;Cell Line;Cellline;Cells;Chemotherapy Protocol;Chemotherapy Regimen;Chemotherapy, Cancer, General;Chemotherapy-Oncologic Procedure;Client;Code;Coding System;Color;Combination Chemotherapy Regimen;Data;Data Banks;Data Bases;Data Set;Databanks;Databases;Dataset;Development;Drops;Drug Delivery;Drug Delivery Systems;Drug Targeting;Drugs;Electronic Databank;Electronic Database;Elements;Engineering / Architecture;Expression Profiling;Expression Signature;Gene Expression;Genes;Genomics;Goals;Human;Imagery;Institution;Internet;Journals;Loinc Axis 4 System;Lead;Libraries;Link;Mt-Bound Tau;Magazine;Malignant Cell;Malignant Neoplasm Therapy;Malignant Neoplasm Treatment;Malignant Neoplasms;Malignant Tumor;Man (Taxonomy);Marketing;Medication;Methods;Modeling;Modern Man;Modification;Molecular;Molecular Fingerprinting;Molecular Profiling;Mortality;Mortality Vital Statistics;Noise;On-Line Systems;Online Systems;Ontology;Pathway Interactions;Pb Element;Peer Review;Performance;Pharmaceutic Preparations;Pharmaceutical Preparations;Phase;Population;Probability;Proteomics;Protocol;Protocols Documentation;Pubchem;Publishing;Quimioterapia;Roc Analyses;Roc Curve;Research;Research Resources;Resistance;Resources;Screening Procedure;Series;Services;Specificity;Statistical Methods;Strains Cell Lines;Stream;System;Testing;Translating;Visual;Visualization;Www;Work;Analytical Method;Animation;Anticancer Research;Anticancer Therapy;Base;Biomarker;Cancer Cell;Cancer Chemotherapy;Cancer Research;Cancer Therapy;Cancer Type;Chemotherapy;Clinical Data Repository;Cultured Cell Line;Cytotoxic;Data Repository;Developmental;Drug Candidate;Drug Discovery;Drug Efficacy;Drug/Agent;Effective Therapy;Effective Treatment;Heavy Metal Pb;Heavy Metal Lead;Improved;Innovate;Innovation;Innovative;Insight;Interest;Malignancy;Member;Microtubule Associated Protein Tau;Microtubule Bound Tau;Microtubule-Associated Protein Tau;Microtubule-Bound Tau;Molecuar Profile;Molecular Signature;Neoplasm/Cancer;New Approaches;Novel Approaches;Novel Strategies;Novel Strategy;Online Computer;Parallel Computation;Parallel Computing;Pathway;Patient Population;Pharmacophore;Programs;Resistant;Screening;Screenings;Tau;Tau Proteins;Tau Factor;Visual Performance;Web;Web Based;Web Services;World Wide Web