Biomarker, what is the best bioinformatics platform to determine cancer biomarkers

The discovery of molecular biomarkers is important for human cancer diagnosis, treatment, and prognosis. Cancer treatment and prognosis have been hampered by tumour molecular heterogeneity and a lack of appropriate biomarkers. The public cancer transcriptome databases, such as The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), have increased due to recent advances in high-throughput microarray and sequencing technology. Additional tools and opportunities for biomarker development and validation can be found in these databases. Unfortunately, those tools are underutilized, and doctors and basic researchers without a strong bioinformatics background will struggle to translate stored high-dimensional data into practical usage. KM plotter, GEPIA (Gene Expression Profiling Interactive Analysis), Oncomine, and TIMER (Tumor Immune Estimation Resource) are just a few of the powerful bioinformatics webservers/tools that have been developed to analyze public transcriptome datasets alongside clinical data for oncology research. However, these web servers/tools still have restrictions, such as a time-consuming registration process or a single data source. As a result, researchers urgently want user-friendly online web servers/tools. They gathered several original research articles and reviews on this Research Topic and valuable web resources and tools. These tools will aid in the more accurate and timely discovery of cancer biomarkers and their clinical translation.

            The treatment of biomarker genes discovered has a vital role in tumour growth and metastasis. These biomarker genes are linked to the cell cycle, which makes sense given their involvement in reducing genomic instability. Tumorigenesis is caused by the deletion or mutation of these genes. The biomarker genes discovered in treatment research have been linked to ubiquitination and stress response. Ubiquitination is a multi-step process that regulates the function and signalling of cellular pathways, which cancer cells use for survival and spread. A deeper knowledge of the ubiquitination process and its underlying pathways could aid in the development of improved cancer therapy possibilities.

Reference

  1. Longxiang Xie1, Liuyang Wang2, Wan Zhu3, Jing Zhao4 and Xiangqian Guo1*; Editorial: Bioinformatics Tools (and Web Server) for Cancer Biomarker Development; Front. Oncol., 20 October 2020 |