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IPCT: Integrated Pharmacogenomic Platform of Human Cancer Cell Lines and Tissues

1,2,†, 1,2,†, 3,* and 2,4,*
1
Department of Biomedical Engineering, College of Medicine, University of Ulsan, Asan Medical Center, Seoul 100-011, Korea
2
Gachon Institute of Genome Medicine and Sciences, Incheon 400-011, Korea
3
Department of Biosciences, COMSATS University Islamabad, Islamabad 45710, Pakistan
4
Department of Genome Medicine and Science, College of Medicine, Gachon University, Seongnam 461-140, Korea
*
Authors to whom correspondence should be addressed.
These authors equally contributed to this paper.
Genes 2019, 10(2), 171; https://doi.org/10.3390/genes10020171
Received: 21 January 2019 / Revised: 16 February 2019 / Accepted: 18 February 2019 / Published: 22 February 2019
(This article belongs to the Special Issue Systems Analytics and Integration of Big Omics Data)
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Abstract

(1) Motivation: The exponential increase in multilayered data, including omics, pathways, chemicals, and experimental models, requires innovative strategies to identify new linkages between drug response information and omics features. Despite the availability of databases such as the Cancer Cell Line Encyclopedia (CCLE), the Cancer Therapeutics Response Portal (CTRP), and The Cancer Genome Atlas (TCGA), it is still challenging for biologists to explore the relationship between drug response and underlying genomic features due to the heterogeneity of the data. In light of this, the Integrated Pharmacogenomic Database of Cancer Cell Lines and Tissues (IPCT) has been developed as a user-friendly way to identify new linkages between drug responses and genomic features, as these findings can lead not only to new biological discoveries but also to new clinical trials. (2) Results: The IPCT allows biologists to compare the genomic features of sensitive cell lines or small molecules with the genomic features of tumor tissues by integrating the CTRP and CCLE databases with the REACTOME, cBioPortal, and Expression Atlas databases. The input consists of a list of small molecules, cell lines, or genes, and the output is a graph containing data entities connected with the queried input. Users can apply filters to the databases, pathways, and genes as well as select computed sensitivity values and mutation frequency scores to generate a relevant graph. Different objects are differentiated based on the background color of the nodes. Moreover, when multiple small molecules, cell lines, or genes are input, users can see their shared connections to explore the data entities common between them. Finally, users can view the resulting graphs in the online interface or download them in multiple image or graph formats. (3) Availability and Implementation: The IPCT is available as a web application with an integrated MySQL database. The web application was developed using Java and deployed on the Tomcat server. The user interface was developed using HTML5, JQuery v.3.1.0, and the Cytoscape Graph API v.1.0.4. The IPCT web and the source code are available in Sample Availability section. View Full-Text
Keywords: genomics; pharmacogenomics; cell lines; database; drug sensitivity genomics; pharmacogenomics; cell lines; database; drug sensitivity
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Shoaib, M.; Ansari, A.A.; Haq, F.; Ahn, S.M. IPCT: Integrated Pharmacogenomic Platform of Human Cancer Cell Lines and Tissues. Genes 2019, 10, 171.

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