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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

An example of KRAS related SL pairs (the alteration types refer to the cancer mutated gene).
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fig3: An example of KRAS related SL pairs (the alteration types refer to the cancer mutated gene).

Mentions: Batch Search. User can directly copy and paste names of various genes (separated by space) in each field. Figure 3 shows an example of using KRAS as input to query its related SL pairs. This helps find information simultaneously for various synthetic lethal gene pairs.


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)

An example of KRAS related SL pairs (the alteration types refer to the cancer mutated gene).
© Copyright Policy
Related In: Results  -  Collection

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

fig3: An example of KRAS related SL pairs (the alteration types refer to the cancer mutated gene).
Mentions: Batch Search. User can directly copy and paste names of various genes (separated by space) in each field. Figure 3 shows an example of using KRAS as input to query its related SL pairs. This helps find information simultaneously for various synthetic lethal gene pairs.

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