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README.md

IPCT: Integrated Pharmacogenomic Platform of Cancer Cell Lines and Tissues

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 Lines Encyclopedia (CCLE), Cancer Therapeutics Response Portal (CTRP), and The Cancer Genome Atlas (TCGA), it is still challenging for biologists to explore the relationships between drug response and underlying genomic features due to data heterogeneity. The Integrated Pharmacogenomic Database of Cancer Cell Lines and Tissues (IPCT) has been developed to identify new linkages between drug response and genomic features since these findings can lead not only to new biological discoveries but also to new clinical trials. Unfortunately, there is no database in which biologists can address this question in a user-friendly way.

Results

The IPCT platform allows biologists to comparegenomic features of sensitive cell lines [or small molecules with genomic features of tumortissue by integrating CTRP and CCLE databases with TCGA, cBioPortal and ExpressionAtlas databases. The input consists of a list of small molecules or cell lines,and the output is a graph containing data entities connected with smallmolecules and cell lines. The users can apply filters to databases, pathways,and genes and select computed sensitivity values and mutation frequency scoresto focus on their graph of interest. Data entities of different objects aredifferentiated based on different background colors of nodes. In addition, userscan explore shared connections when multiple small molecules or cell lines areused to explore common data entities between two or more than two inputs.Finally, users can view the resulting graphs on screen or download them inGraphML format.


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