ArticleBMC bioinformatics2013
MaTSE: the gene expression time-series explorer.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
What it found
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Who cites it
2 citing papers in PubMed.
- Development of a Novel Vaccine Candidates againstBioMed research international · 2023Article
- Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHigh throughput gene expression time-course experiments provide a perspective on biological functioning recognized as having huge value for the diagnosis, treatment, and prevention of diseases. There are however significant challenges to properly exploiting this data due to its massive scale and complexity. In particular, existing techniques are found to be ill suited to finding patterns of changing activity over a limited interval of an experiments time frame. The Time-Series Explorer (TSE) was developed to overcome this limitation by allowing users to explore their data by controlling an animated scatter-plot view. MaTSE improves and extends TSE by allowing users to visualize data with missing values, cross reference multiple conditions, highlight gene groupings, and collaborate by sharing their findings.
resultsMaTSE was developed using an iterative software development cycle that involved a high level of user feedback and evaluation. The resulting software combines a variety of visualization and interaction techniques which work together to allow biologists to explore their data and reveal temporal patterns of gene activity. These include a scatter-plot that can be animated to view different temporal intervals of the data, a multiple coordinated view framework to support the cross reference of multiple experimental conditions, a novel method for highlighting overlapping groups in the scatter-plot, and a pattern browser component that can be used with scatter-plot box queries to support cooperative visualization. A final evaluation demonstrated the tools effectiveness in allowing users to find unexpected temporal patterns and the benefits of functionality such as the overlay of gene groupings and the ability to store patterns.
conclusionsWe have developed a new exploratory analysis tool, MaTSE, that allows users to find unexpected patterns of temporal activity in gene expression time-series data. Overall, the study acted well to demonstrate the benefits of an iterative software development life cycle and allowed us to investigate some visualization problems that are likely to be common in the field of bioinformatics. The subjects involved in the final evaluation were positive about the potential of MaTSE to help them find unexpected patterns in their data and characterized MaTSE as an exploratory tool valuable for hypothesis generation and the creation of new biological knowledge.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.