1. TMHRI-LINCS Center: itNETZ

The primary goal of TMHRI每LINCS center is to address the needs of LINCS (Library of Integrated Network每based Cellular Signatures) by developing a signature每oriented software platform, the Integrative and Translational Network每based Cellular Signature Analyzer (itNETZ). This system will enable the following functions: first, the basic analysis and discovery toolkits for processing cellular images, Luminex genomics data, transcriptome sequencing data, and for modeling phosphoproteins signaling pathway; and second, data integration and mining toolkits for mapping genomics and proteomics to cellular phenotypes, for core pathway signature identification on cell lines treated by different inhibitors and drug-induced pathway signature alterations, and for constructing drug kinome landscapes.

The itNETZ system comprises pipelines that load input, analyze images, process genomics and proteomics data, export outputs into a relational database, integrate and mine the data, and generate network每based cellular signatures of interest. XML每based protocols will be used for data exchanging.

LINCS NIH U01 grant: 1 U01 HL111560-01

Title: itNETZ: The Integrative and Translational Network-Based Cellular Signature Analyzer

TMHRI - itNETZ Link:

PI:
Xiaobo Zhou, Ph.D.
Associate Member
The Methodist Hospital Research Institute
-----------------------------------------
Director of Translational Biosystems
Chief of Bioinformatics
Department of Translational Imaging

Houston, TX 77030
Office: (713) 441-8692

Leader of LINCS-TMHRI Working Group:
Jing Su, Ph.D.
Research Associate
The Methodist Hospital Research Institute
Houston, TX 77030
Office: (713)441-8686

Abstract:

There is an urgent need to develop systematic platforms to address the challenges and opportunities introduced by the rapid progress of the Library of Integrated Network-Based Cellular Signatures (LINCS) program. The LINCS program performs cross-cutting high-throughput assays and integrative computational analysis of informative molecular activity and cellular feature signatures generated in response to a variety of agents and drug candidates.

itNETZ Platform: Interface for streamlining different pipelines

The primary goal of the proposed study is to develop a signature-oriented software platform, the Integrative and Translational Network-based Cellular Signature Analyzer (itNETZ). The work flow of the system is: 1) to identify disease- and drug-specific molecular and cellular features, 2) to reveal the mechanismistic associations between components of such features and delineate them as signaling and regulating networks, 3) to present the dynamics of such networks by mathematical models, 4) to construct network-based molecular and cellular signatures, 5) to discover common signatures and networks across cell lines and diseases, 6) to establish and maintain a public resource of the increasing resultant knowledge of therapeutic responses, and 7) to facilitate the research community on querying signatures of interests, exploring correlations among signatures, and generating hypotheses.

This system will enable the following functions: first, the basic analysis and discovery toolkits for processing cellular images, Luminex genomics data, transcriptome sequencing data, and for modeling phosphoproteins signaling pathway; and second, data integration and mining toolkits for mapping genomics and proteomics to cellular phenotypes, for core pathway signature identification on cell lines treated by different inhibitors and drug-induced pathway signature alterations, and for constructing drug kinome landscapes. The itNETZ system comprises pipelines that load input, analyze images, process genomics and proteomics data, export outputs into a relational database, integrate and mine the data, and generate network-based cellular signatures ofinterest. XML-based protocols will be used for data exchanging.





Center Description:
The primary goal of TMHRI-LINCS center is to address the needs of LINCS by developing a signature-oriented software platform, the Integrative and Translational Network-based Cellular Signature Analyzer (itNETZ). This system will enable the following functions: first, the basic analysis and discovery toolkits for processing cellular images, Luminex genomics data, transcriptome sequencing data, and for modeling phosphoproteins signaling pathway; and second, data integration and mining toolkits for mapping genomics and proteomics to cellular phenotypes, for core pathway signature identification on cell lines treated by different inhibitors and drug-induced pathway signature alterations, and for constructing drug kinome landscapes.

The itNETZ system comprises pipelines that load input, analyze images, process genomics and proteomics data, export outputs into a relational database, integrate and mine the data, and generate network-based cellular signatures ofinterest. XML-based protocols will be used for data exchanging.