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Syn-lethality: an integrative knowledge base of synthetic lethality towards discovery of selective anticancer therapies.

Li XJ, Mishra SK, Wu M, Zhang F, Zheng J - Biomed Res Int (2014)

Bottom Line: It integrates experimentally discovered and verified human SL gene pairs into a network, associated with annotations of gene function, pathway, and molecular mechanisms.Such an integrative knowledge base, organized as a relational database with user interface for searching and network visualization, will greatly expedite the discovery of novel anticancer drug targets based on synthetic lethality interactions.The database can be downloaded as a stand-alone Java application.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Research Centre (BIRC), School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798.

ABSTRACT
Synthetic lethality (SL) is a novel strategy for anticancer therapies, whereby mutations of two genes will kill a cell but mutation of a single gene will not. Therefore, a cancer-specific mutation combined with a drug-induced mutation, if they have SL interactions, will selectively kill cancer cells. While numerous SL interactions have been identified in yeast, only a few have been known in human. There is a pressing need to systematically discover and understand SL interactions specific to human cancer. In this paper, we present Syn-Lethality, the first integrative knowledge base of SL that is dedicated to human cancer. It integrates experimentally discovered and verified human SL gene pairs into a network, associated with annotations of gene function, pathway, and molecular mechanisms. It also includes yeast SL genes from high-throughput screenings which are mapped to orthologous human genes. Such an integrative knowledge base, organized as a relational database with user interface for searching and network visualization, will greatly expedite the discovery of novel anticancer drug targets based on synthetic lethality interactions. The database can be downloaded as a stand-alone Java application.

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Related in: MedlinePlus

SL query interface.
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fig4: SL query interface.

Mentions: Our synthetic lethality database contains SL gene pairs in organised form and provides interface to perform query in the database. Our preliminary database is available in the downloadable form from http://www.ntu.edu.sg/home/zhengjie/software/Syn-Lethality/. This software is a Java executable file and requires the installation of Java. The required version 10 of Java (free) and it can be installed from http://www.java.com/en/download/index.jsp. Once the Java is installed on local machine, just double clicking on the Java executable file will launch the database interface. Since the database is available in the single setup file, the database can be used simultaneously by many end users for performing the query (Figure 4). The database includes information such as synthetic lethal gene pairs, type of lethality, type of gene alteration, and target genes for synthetic lethality.


Syn-lethality: an integrative knowledge base of synthetic lethality towards discovery of selective anticancer therapies.

Li XJ, Mishra SK, Wu M, Zhang F, Zheng J - Biomed Res Int (2014)

SL query interface.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4016865&req=5

fig4: SL query interface.
Mentions: Our synthetic lethality database contains SL gene pairs in organised form and provides interface to perform query in the database. Our preliminary database is available in the downloadable form from http://www.ntu.edu.sg/home/zhengjie/software/Syn-Lethality/. This software is a Java executable file and requires the installation of Java. The required version 10 of Java (free) and it can be installed from http://www.java.com/en/download/index.jsp. Once the Java is installed on local machine, just double clicking on the Java executable file will launch the database interface. Since the database is available in the single setup file, the database can be used simultaneously by many end users for performing the query (Figure 4). The database includes information such as synthetic lethal gene pairs, type of lethality, type of gene alteration, and target genes for synthetic lethality.

Bottom Line: It integrates experimentally discovered and verified human SL gene pairs into a network, associated with annotations of gene function, pathway, and molecular mechanisms.Such an integrative knowledge base, organized as a relational database with user interface for searching and network visualization, will greatly expedite the discovery of novel anticancer drug targets based on synthetic lethality interactions.The database can be downloaded as a stand-alone Java application.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Research Centre (BIRC), School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798.

ABSTRACT
Synthetic lethality (SL) is a novel strategy for anticancer therapies, whereby mutations of two genes will kill a cell but mutation of a single gene will not. Therefore, a cancer-specific mutation combined with a drug-induced mutation, if they have SL interactions, will selectively kill cancer cells. While numerous SL interactions have been identified in yeast, only a few have been known in human. There is a pressing need to systematically discover and understand SL interactions specific to human cancer. In this paper, we present Syn-Lethality, the first integrative knowledge base of SL that is dedicated to human cancer. It integrates experimentally discovered and verified human SL gene pairs into a network, associated with annotations of gene function, pathway, and molecular mechanisms. It also includes yeast SL genes from high-throughput screenings which are mapped to orthologous human genes. Such an integrative knowledge base, organized as a relational database with user interface for searching and network visualization, will greatly expedite the discovery of novel anticancer drug targets based on synthetic lethality interactions. The database can be downloaded as a stand-alone Java application.

Show MeSH
Related in: MedlinePlus