About OncoNET ...

OncoNET is an open-access, online resource developed by Kinexus Bioinformatics Corporation to foster cancer-related research in academia and industry. It features comprehensive information on the mutations and mRNA expression levels for about 3,000 genes in diverse types of human cancers. The mRNA expression data used in OncoNET was originally retrieved from the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO), which serves as a repository of experimental gene microarray results submitted by diverse academic and industrial laboratories around the world. With the aid of our academic collaborators, Kinexus has normalized the data from hundreds of different gene microarray studies using a normalization protocol based on the identification of 60 genes that were commonly and highly expressed in all of the biological samples. To explore the mutation of human cancer-related genes, we relied primarily on the collection of data from the Wellcome Trust Sanger Institute’s Catalogue of Somatic Mutations in Cancer (COSMIC) database. Further information on these genes and their encoded proteins was annotated from several other sources, including UniProt and the Atlas of Genetics and Cytogenetics in Oncology and Haematology websites.

OncoNET is a powerful tool to guide cancer researchers in the identification of potential biomarkers and therapeutic targets for cancer diagnosis and treatment. The cancer-related proteins profiled in OncoNET are broadly divided into three categories: those that facilitate cancer, which are known as oncoproteins (OP) or tumour requiring proteins (TRP); and those that inhibit cancer, which are classified as tumour suppressor proteins (TSP). A unique combination of gain-of-function of OP and loss-of-function of TSP underlie each human cancer. By contrast, TRP are rarely mutated. The alterations in the activities of OP and TSP may arise from mutations, altered gene expression, and the actions of environmental agents that directly or indirectly impinge on these proteins. The number of possible combinations of OP and TSP changes that result in the etiology of each individual cancer may actually be in the millions, which means that personalized approaches to diagnose and treat cancer are ultimately needed. Some of the interesting observations that emerge from the careful analysis of the data provided in OncoNET include the finding that the vast majority of mutations found in genes are bystander mutations that have little or no impact on cancer development. Loss of function of TSP such as DNA repair enzymes permit the accumulation of mutations that are not particularly critical. By contrast, driver mutations in OP may occur in higher frequency in many types of cancers, and this can define ideal targets for drug development. Fortunately, amongst the OP, the protein kinases have emerged as very promising targets for therapeutic intervention. Another interesting finding is that gene expression patterns in human cancers are extremely complex and typically involve the induction of TSP and repression of OG. This indicate that the battle for control of cancer cell growth and reproduction lies within individual tumour cells as complex signalling systems use elaborate genomic and proteomic mechanisms to attempt to compensate to prompt these cells act in the best interests of the human body. Cancer therapy will be most effective when it augments these regulatory mechanisms and specifically inactivates those OP that drive individual cancers with a personalized medicine strategy. We also propose that TRP represent another promising class of cancer drug targets.

Instructions ...

OncoNET is designed to be fast and simple to navigate. Just follow the steps outlined in each query. Presently, there are 5 different types of queries that you can perform with OncoNET. You can search for a target gene or protein if you know its UniProt ID, RefSeq ID, or one of its common gene or protein names. A list of possible options for genes/proteins are generated by typing at least three letters of their name or identification number, and waiting for a few moments for a complete list to appear. Pull-down menus list the various types of human cancers profiled in OncoNET. The optimum web browsers for using OncoNET are Internet Explorer, Firefox and Safari.

Other Useful Online Resources From Kinexus ...

Several other useful open-access, online resources are available from Kinexus Bioinformatics Corporation to foster cell signalling research. Direct links to several of our other knowledgebases in the SigNET KnowledgeBank are provided just below the header at the top of each webpage in OncoNET. TranscriptoNET provides additional gene expression information on over 21,000 human genes. PhosphoNET features data on nearly 1 million confirmed or predicted human phosphorylation sites in the proteins encoded by these genes. KinATLAS reveals interactions between these proteins with each other in signalling systems. KinaseNET offers detailed information about human protein kinases, whereas DrugKiNET has data on over 800 known compounds that inhibit protein kinases. Additional knowledgebases are planned for human protein phosphatases, adapter, stress proteins and transcription factors. For semi-quantitative data on actual protein expression in over 10,000 diverse biological specimens, please also visit our open-access KiNET DataBank with immunoblotting and antibody microarray analyses with over 850 pan- and phosphosite-specific antibodies.

Funding, Sponsorship and Advertising Opportunities ...

To develop and sustain this free resource, we are seeking sponsorship from foundations and corporations. We gratefully acknowledge financial assistance for OncoNET from the National Research Council of Canada Industrial Assistance Program and the Natural Sciences and Engineering Research Council of Canada. It is possible for commercial vendors of signal transduction reagents and services to advertise their relevant products and services on this site. Interested parties should contact our Sales and Marketing Department at info@kinexus.ca or call toll free in North America 1-866-KINEXUS.