Identification of genes significant for cancer through analysis of sequence databases and publications
2020
Johns Hopkins University, Baltimore, USA
Sequencing is sufficiently inexpensive and rapid that researchers have at their disposal thousands of tumor tissues with RNA-Seq data, providing unprecedented insight into the transcriptional landscape of cancer. However, the sheer volume of data has proven challenging when it comes to deriving biological meaning. Many types of analysis, rely to some degree on a priori knowledge of the pathways, the biological role, or the molecular function of genes. In the present study, the researchers aimed at drawing attention to the fact that a substantial portion of genes statistically associated with cancer biology lack annotations adequate for understanding their role in cancer pathology. The researchers performed database explorations for genes associated with an unfavourable outcome in cancer using the Human Protein Pathology Atlas which contains a correlation of mRNA and clinical outcome for almost 8,000 cancer patients. The study showed that a range of biologically relevant genes is not associated with known published pathways. They also tend not to be linked with known dominant mutations. Further, the researchers did draw gene network maps to point to biological areas which are generally understudied. Overall, the study concludes that there is little relationship between the relative biological importance of genes and the literature dedicated to specific genes, suggesting instead that most genes, after their initial discovery, attract limited attention, while other genes attract disproportionate attention due, at least in part, to social trends and the tendency of the scientific community to be a “small-world”. In the future, the data-driven analysis should help to pinpoint biological "terra incognita" which should be considered as challenges to tackle.
Functionally enigmatic genes in cancer: using TCGA data to map the limitations of annotations
Channing J. Paller
Added on: 12-22-2021
[1] https://www.nature.com/articles/s41598-020-60456-x
