Cancer research benefits from NodeXL network graph analysis
A diagnosis of cancer can be particularly foreboding for any patient. However, new treatments become possible as we learn more about the disease, and the application of research techniques more commonly found in the social sciences are now providing new insights.
Although medical investigators have been studying cancer for decades, only recently have they focused attention on micro RNAs (miRNAs), small RNA molecules that affect gene regulation and probably many other biological processes. Studies are now underway to learn if alterations in miRNA expression profiles can be used to identify drivers in both colorectal and pancreatic cancers.
To study miRNA expression profiles and their relation to these cancers, researcher Tommaso Mazza in the Bioinformatics research unit at Italy’s Casa Sollievo della Sofferenza Research Hospital and his colleagues paired normal and tumor tissue samples from patients with colorectal or pancreatic cancer and determined the relative levels of miRNA expression in each sample. They then subjected the data to complex statistical analysis to determine which miRNAs appear to be affected in each cancer.
Once the set of miRNAs affected in each cancer type was identified, the researchers applied analyses more commonly seen in the social sciences to construct and analyze the network of interactions between them. To do this, Dr. Mazza and his colleagues built a standalone application in C# utilizing the NodeXL network graph-analysis platform. Analyses of these graphs revealed that each of these cancers is associated with a unique pattern of changes specific to the tissue in which it occurs, and that certain key miRNAs could be tied to biochemical pathways in the cell, some previously known to be associated with cancer—but some that are new discoveries, to be validated in future research. This work also demonstrates the new insights that analytical techniques common in one area of science can bring when applied in a different field.
NodeXL includes an Excel template for easy manipulation of graph data.
NodeXL is a free, open-source template for Microsoft Excel that displays and analyzes graphs by utilizing a custom Windows Presentation Foundation (WPF) control. It can be invaluable whenever you want to explore network graphs. NodeXL can import and export graphs in GraphML, Pajek, UCINET, and matrix formats and can be configured to import and analyze networks from social networking sites, email interactions from Microsoft Exchange, or graphs of web hyperlinks. If you would like to learn more, the NodeXL webpage has a programmer discussion forum and a method to download the latest class libraries.
The research of Dr. Mazza and his colleagues on miRNA expression profiles was published in PLOS ONE (an international, peer-reviewed, open-access, online publication). You can access the paper on the PLOS website.
—Simon Mercer, Director of Health and Wellbeing, Microsoft Research Connections