Innovative data visualization for gene-related research

A biomedical engineering Ph.D. student at the University of California, Davis, Yongheng Wang had a problem: He wanted to identify the top 10 targets from thousands of genes affected by a drug he developed. The process to mine and extract information would normally take a huge investment of time and effort, switching back and forth between different programming languages and software packages. Wang was delighted to learn of a solution: an innovative data visualization system called “Dr. Tom” from BGI Genomics, a leading global provider of genomic sequencing and proteomics services, headquartered in Shenzhen, China.

Developed by a team of expert scientists and bioinformaticians at BGI Genomics, Dr. Tom is a powerful tool for analysis, visualization, and interpretation of many types of data, including RNA sequencing (RNA-Seq), long noncoding RNA-Seq, micro RNA-Seq, whole-genome bisulfite sequencing, single-cell RNA-Seq, and proteomics data.

Having an easy learning curve, Dr. Tom is also versatile, and most importantly, allows researchers without backgrounds in bioinformatics to quickly, efficiently, and reliably create meaningful visualizations. "The intuitive interface allows us to select genes of interest and rank differentially expressed genes based on their fold changes," says Wang. "Dr. Tom covers all the practical functionalities. I think a high school student could do it."

Designed by scientists for scientists

Dr. Tom is a project fueled by the passion of Chong Tang, deputy director of research and development at BGI Tech. A biochemist and molecular biologist with expertise in software engineering, Tang's extensive experience helped him uncover the specific pain point experienced by his research colleagues around the world: Given the tsunami of omics data, there is a critical need for a flexible, easy, and turnkey data analysis program. "I designed it in such a way that scientists will like it," he says.

Dr. Tom is designed to be flexible and simple for users with limited computing knowledge, notes Margot Maurer, research associate in the Wolfson Centre for Age-Related Diseases at King's College London. Maurer uses Dr. Tom to analyze the transcriptomics differences in sensory ganglia to help her investigate RNA and age-related diseases. “I don't need to go through all the calculations,” she explains. “Dr. Tom is the bridge. With just a couple of clicks, I can see the graphs, which are easy to read.” No programming skills are needed for analyzing these genetic sequences, she adds. “I really like this very visual Venn diagram comparing the different gene expressions in samples.”

This visualization feature is designed to be interactive so it is easier to bounce ideas around the team, Tang says. He spent 5 years designing, testing, and fine- tuning Dr. Tom to serve his community, and now Dr. Tom's web-based interface is inspiring innovative research and reducing researchers' headaches.

“The BGI culture is a culture of scientists and for scientists.” Tang says. The organization considers it so vital to advance scientific discovery that it is gifting this software to the world.

Making a mark

Relying on cutting-edge sequencing and bioinformatics technology, BGI Genomics has provided scientists and researchers in 100 countries and regions with integrated solutions across a broad range of applications spanning basic life sciences research, clinical research in human health, and agriculture and biodiversity preservation and sustainability.

Since its launch in 2018, Dr. Tom has enchanted more than 15,000 users from over 20 countries and regions. “More than 60 published papers in the field of disease treatment, developmental regulation, immunity, and environmental adaptation have shown Dr. Tom to be a valuable and important tool in addition to any institution's own internal data curation and analysis efforts,” says Tang.

BGI Genomics has partnered with academic institutions to offer workshops on leveraging this system effectively, and will be expanding these opportunities to more countries and regions in the future. 

About BGI Genomics

BGI Genomics, headquartered in Shenzhen China, is the world's leading provider of genomic sequencing and proteomic services. We enable scientists and researchers to reach their full potential by providing them with fully integrated genomic sequencing, proteomic services, and high-quality solutions across a range of applications. Our services cover more than 100 countries and regions, involving more than 2,300 medical institutions.