Abstract:
Alternative splicing is a process by which the same DNA sequence is used to assemble different proteins, called protein isoforms. Alternative splicing works by selectivel...Show MoreMetadata
Abstract:
Alternative splicing is a process by which the same DNA sequence is used to assemble different proteins, called protein isoforms. Alternative splicing works by selectively omitting some of the coding regions (exons) typically associated with a gene. Detection of alternative splicing is difficult and uses a combination of advanced data acquisition methods and statistical inference. Knowledge about the abundance of isoforms is important for understanding both normal processes and diseases and to eventually improve treatment through targeted therapies. The data, however, is complex and current visualizations for isoforms are neither perceptually efficient nor scalable. To remedy this, we developed Vials, a novel visual analysis tool that enables analysts to explore the various datasets that scientists use to make judgments about isoforms: the abundance of reads associated with the coding regions of the gene, evidence for junctions, i.e., edges connecting the coding regions, and predictions of isoform frequencies. Vials is scalable as it allows for the simultaneous analysis of many samples in multiple groups. Our tool thus enables experts to (a) identify patterns of isoform abundance in groups of samples and (b) evaluate the quality of the data. We demonstrate the value of our tool in case studies using publicly available datasets.
Published in: IEEE Transactions on Visualization and Computer Graphics ( Volume: 22, Issue: 1, 31 January 2016)
Funding Agency:
Keywords assist with retrieval of results and provide a means to discovering other relevant content. Learn more.
- IEEE Keywords
- Junctions ,
- Bioinformatics ,
- Genomics ,
- Splicing ,
- Data visualization ,
- DNA ,
- Encoding
- Index Terms
- Alternative Splicing ,
- Data Quality ,
- Sample Groups ,
- Edge Connectivity ,
- Boxplots ,
- The Cancer Genome Atlas ,
- Biological Data ,
- Edge Weights ,
- Dot Plots ,
- Output Of Algorithm ,
- Exonic Variants ,
- Exon Inclusion ,
- Hundreds Of Samples ,
- Functions Of Gene Products ,
- Exon Expression ,
- Junction Reads ,
- Edge Width ,
- Visual Encoding ,
- Fit For Use ,
- Reading Direction ,
- Parallel Coordinates ,
- Expression Of Isoforms ,
- Start Of Exon ,
- Adjacent Exons ,
- Opposite Strand ,
- Exon Junction ,
- End Sites
- Author Keywords
- MeSH Terms
- Author Free Keywords
Keywords assist with retrieval of results and provide a means to discovering other relevant content. Learn more.
- IEEE Keywords
- Junctions ,
- Bioinformatics ,
- Genomics ,
- Splicing ,
- Data visualization ,
- DNA ,
- Encoding
- Index Terms
- Alternative Splicing ,
- Data Quality ,
- Sample Groups ,
- Edge Connectivity ,
- Boxplots ,
- The Cancer Genome Atlas ,
- Biological Data ,
- Edge Weights ,
- Dot Plots ,
- Output Of Algorithm ,
- Exonic Variants ,
- Exon Inclusion ,
- Hundreds Of Samples ,
- Functions Of Gene Products ,
- Exon Expression ,
- Junction Reads ,
- Edge Width ,
- Visual Encoding ,
- Fit For Use ,
- Reading Direction ,
- Parallel Coordinates ,
- Expression Of Isoforms ,
- Start Of Exon ,
- Adjacent Exons ,
- Opposite Strand ,
- Exon Junction ,
- End Sites
- Author Keywords
- MeSH Terms
- Author Free Keywords