Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

This article is part of the supplement: Highlights from the 2nd IEEE Symposium on Biological Data Visualization

Open Access Highly Accessed Research

MaTSE: the gene expression time-series explorer

Paul Craig1*, Alan Cannon2, Robert Kukla2 and Jessie Kennedy2

Author Affiliations

1 Universidad Tecnológica de la Mixteca, Carretera a Acatlima Km. 2.5 Huajuapan de León, Oaxaca., C.P. 69000, México

2 Edinburgh Napier University, School of Computing, Merchiston Campus, Edinburgh Napier University, 10 Colinton Road, Edinburgh, EH10 5DT, UK

For all author emails, please log on.

BMC Bioinformatics 2013, 14(Suppl 19):S1  doi:10.1186/1471-2105-14-S19-S1

Published: 12 November 2013

Abstract

Background

High 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.

Results

MaTSE 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.

Conclusions

We 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.

Keywords:
Information Visualization; Animation; Bioinformatics; Gene Expression; Time-course