Enhanced design allows comparison of side-by-side results from HTSeq/DESeq and Cufflinks
San Mateo CA June 18, 2014:Â Maverix Biomics Inc., a leading genomic analysis software company, today announced improved functionality for RNA-seq differential expression analysis on the Maverix Analytic Platform, an industry leading cloud-based solution that enables life science researchers to directly analyze, visualize, interrogate, and manage biological sequence data in order to accelerate exploration and discovery. The enhancements will enable scientists engaged in RNA-seq studies to better analyze differential expression results through improved visualization for quality assessment of the data and for identifying highly-confident genes uncovered by next generation sequencing of the information-dense transcriptome.
The Maverix Analytic Platform now supports the latest version of Cufflinks, a popular open source software application which assembles transcripts, estimates their quantity, and tests for differential expression and regulation in RNA-seq samples. This new version on the Maverix Analytic Platform allows multiple samples to be compared more efficiently, resulting in enhanced functionality for the platformâ€™s turnkey RNA-seq analysis.
Additionally, inherent in the design of the Maverix Analytic Platform is the ability to easily launch two proven RNA-seq methods, Cufflinks and DESeq, and compare the results side-by-side with the same ease-of-use, cost, flexibility and visualizations to answer the most pressing questions about the transcriptome.
The platform organizes all-vs-all comparisons provided by Cufflinks into a dynamically- controllable heat map, providing researchers an optimal way to select desired sample comparisons, filter and sort by common parameters like p-value, fold-change, and abundance, and quickly zoom in on a shortlist of targeted genes. The Maverix platform also provides seamless integration with a secure, private implementation of the UCSC Genome Browser, enabling alignment and coverage data from user experiments to be viewed in context with hundreds of existing annotation tracks, and public datasets.
Dr. Jeanne Loring, Professor of Developmental Neurobiology, and Director of the Center of Regenerative Medicine at the Scripps Research Institute, is advancing the study of human stem cell research by applying powerful new cutting edge technologies, such as next-generation sequencing.
Dr. Loringâ€™s group, including graduate student Kit Nazor, is building a repository of comprehensive genomic and epigenomic data on human pluripotent stem cells and the wide range of cell types that they can generate. They are focusing on neurological diseases, including Parkinsonâ€™s disease, Alzheimer disease, multiple sclerosis, and autism. The data resulting from these studies is enabling breakthroughs in understanding the molecular basis of human disease and development of safe, effective stem cell-based therapies.
“The Maverix RNA-Seq Analysis Kit provides us with a user-friendly means of quality control and the ability to process data from large RNA sequencing experiments. What really sets Maverix apart is that their platform simultaneously processes the data using not just one but two of the most well accepted methods,â€ť said Nazor. â€śThere is no mystery about how the data is processed, as the underlying code that is being used to process the data is also provided at each stage. This has not only allowed us to understand the intricacies of how the data was analyzed, but also provides a unique opportunity to learn the basics of bioinformatics.â€ť
â€śThe Maverix Analytic Platformâ€™s filtering functions allow for an easy way to reduce the data to a set of genes of interest based on significance and fold change values, and provide contextualization of the identified significant transcripts with previously curated data sets,â€ť said Dr. Loring.
Dr. Jeff Brockman is a Principal Scientist in the commercial animal heath and nutrition field. He has been using cutting edge technologies such as next generation sequencing to understand disease and the aging processes in companion animals, specifically dogs (Canis lupus familiaris). By transitioning his organization from microarray platforms to high throughput sequencing, Dr. Brockman has developed a cutting edge translational genomics program to identify susceptibility biomarkers and candidate genes for therapeutic intervention in multiple areas of animal health and nutrition.
â€śThe increased functionality from both the HTSeq/DESeq and Cufflinks pipelines combined with the ease and convenience of analyzing large data sets in multiple ways is what attracted me to the Maverix Analytic Platform,â€ť said Dr. Brockman. â€śItâ€™s incredibly seamless to identify differentially expressed genes in my canine samples and dynamically compare differential expression results with alternate samples, such as those from time-course studies. Instead of managing a multitude of files required by competitive platforms, I can spend my time where itâ€™s most critical — exploring my results to make new discoveries.â€ť
About the Maverix Analytic Platform
Maverix Analytic Platform is a cloud-based solution designed for use directly by life sciences researchers who may not have software or bioinformatics expertise. It leverages proven, open-source algorithms and applications developed at leading academic and research centers. After loading sequence data from any organism (human, animal, plant, or microbe), researchers are able to immediately perform analysis with reliable, scientifically recommended configurations, as cited in peer- reviewed journal publications. Visualization is provided through a variety of integrated graphical tools, including the UCSC Genome Browser, the worldâ€™s most widely used genome browser.
About Maverix Biomics
Based in San Mateo, CA and backed by leading venture capital firms and Silicon Valley investors, Maverix Biomics, Inc. provides researchers with a cloud-based platform to manage, analyze, and visualize genomic data, build Communities of Discovery, and place their data in context with the latest public data from the full spectrum of life, including human, plant, animal, or microbial organisms. For more information, visit www.maverixbio.com.