MATSE: Information Visualisation of Microarray Time-course Data

01/11/2007 - 31/10/2009

project image

Microarray Time-series Explorer (MaTSE) is a software application developed to improve the analysis of microarray data by allowing the user to explore their data using a unique visual interface.  Throughout the project we focused on engaging potential end-users in academia and industry toward developing functionality relevant to their needs and producing software that is of a standard that would attract the interest of potential investors or licensors.  In conjunction with this we worked toward amassing commercial know-how across the project team and building a commercialisation plan that can be used to exploit the software and further guide development.

Consultation with our collaborating biologists has allowed us to define three main unique selling points for the MaTSE software. These are:
  • The ability to easily discover patterns in data not possible with other visualisation tools: The primary USP of MaTSE is that it allows users to explore their data in a way that allows them to find patterns of correlated gene activity occur over shorter intervals of time in the data. These patterns often relate to biological phenomena of genuine interest to biologists and they cannot be found using more traditional analysis techniques. MaTSE also allows users to find more dominant trends in recorded gene activity and allows users to cross reference their findings with stored gene groupings.
  • Rapid feedback and easy interpretation of results: The MaTSE software displays microarray data without any type of complex algorithmic preprocessing such as that applied by traditional analysis techniques such as clustering, principle component analysis or self organising maps. While traditional techniques attempt to summarise the data by displaying an abstraction of that data, the only processing of the data involved in MaTSE is the calculation of straight-forward mean and change values in the scatter-plot. This makes the display closer to the actual recorded data and allows users to gain a better understanding of their data during analysis without having to take time to comprehend algorithms which might have applied to the data.
  • The ability to store and recall patterns: The unique scatter-plot layout in MaTSE is such that user selections are measurable (based on activity, change in activity and mean activity) and are meaningful when recalled. These selections, and combinations of selections, are recorded so they can be stored, annotated and shared with other users.
MATSE: Information Visualisation of Microarray Time-course Data is a Proof of Concept Fund project funded by Scottish Enterprise. Carried out in collaboration with and others. For further information please refer to
[Read More]

Resources link icon

  • Combining Queries (Video)
    Each query is stored in a list in the pattern browser component. Superfluous selections are removed after a query that replaces the previous result Brower can be used to restore and adjust parameters with continuous feedback of results
  • TSExplorer
    Genes are segments of DNA that carry the genetic or inherited information within all living organisms and interact with each other to influence the organism's physical development and behavior. Gene expression is a key indicator of gene activity and can be measured in microarray experiments.
next prev

Related Projects

  • BioVisNet
    Biology is a visually grounded scientific discipline-from the way data is collected and analysed to the manner in which the results are communicated to others. Traditionally pictures in scientific publications were hand-drawn; however they are now almost exclusively computer-generated.
  • Scottish Woodlands KTP
    Scottish Woodlands Ltd is Scotland's leading independent full-service forest management company. It is also the second largest operator in the UK, with a network of 17 offices operating throughout Scotland, England, Wales and Northern Ireland.
  • Research Activities I/Net
    Information Management and Presentation for Research Activity and Related Data. A linked intranet and internet solution for the managing and presentation of data concerning the research related activties of university researchers.
  • Future Energy
    Future energy management for buildings.
  • ASD Database Replacement for NHS Lothian
    Build a replacement system for managing purchase approvals and authorised signatories within a large complex organisation.
next prev

Areas of Expertise link icon

  • Information Visualisation
    Information visualisation is the use of enhanced Graphical User Interfaces (GUIs) to communicate and interact with complex data sets such as social networks, multiattribute tables, and financial data. Pages of text and numbers are not the most effective way to communicate or understand information.
next prev

Project Team

Alan Cannon
Research Fellow
+44 131 455 2437
Jessie Kennedy
Dean of Research and Innovation
+44 131 455 2772
Dr Paul Craig
(not currently an institute member)
Robert Kukla
Senior Research Fellow
+44 131 455 2738

Associated Publications

Craig, P., Cannon, A., Kukla, R., Kennedy, J. (2013). MaTSE: the gene expression time-series explorer. BMC Bioinformatics, 14(Suppl 19), (S1), .

Craig, P., Cannon, A., Kukla, R., Kennedy, J. (2012). MaTSE: The Microarray Time-Series Explorer. In: Roerdink, J., Hibbs, M. (Eds.) Proceedings of IEEE Symposium on Biological Data Visualization (BioVis), 2012 , , () ( ed.). (pp. 41-48). : . IEEE.

Craig, P., Kennedy, J., Kukla, R., Cannon, A. (2010). Pattern Browsing and Query Adjustment for the Exploratory Analysis and Cooperative Visualisation of Microarray Time-course Data. In: Luo, Y. (Ed.) Proceedings of the 7th International Conference on Cooperative Design, Visualisation and Engineering, 6240/2010, () ( ed.). (pp. 199-206). Mallorca, Spain: . Lecture Notes in Computer Science.

Craig, P., Kennedy, J., Cumming, A. (2005). Animated Interval Scatter-plot Views for the Exploratory Analysis of Large Scale Microarray Time-course Data. Information Visualization, 4, (3), 149-163.

Craig, P., Kennedy, J., Cumming, A. (2005). Coordinated Parallel Views for the Exploratory Analysis of Microarray Time-course Data. In: (Ed.) Proceedings of 3rd International Conference on Coordinated & Multiple Views in Exploratory Visualization, , () ( ed.). (pp. 3-14). London: . IEEE Computer Society Press.

Craig, P., Kennedy, J., Cumming, A. (2005). Time-series Explorer: An Animated Information Visualisation for Microarray Time-course Data. BMC Bioinformatics 2005, 6, (3), P8.

See all publications