MaTSE: The Gene Expression Time-series Explorer
pattern

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 visualise data with missing values, cross reference multiple conditions, highlight gene groupings, and collaborate by sharing their findings.

gene groupings

Methods available for displaying gene groupings in the scatter-plot. a) color coding, b) outlined color, c) symbols, d) areas with texture and color, and e) smoothed outline shapes with transparent shading.

multiple conditions

Display of multiple conditions using a different set of linked scatter-plot and line-chart views for each condition.

coop'erative vis

Cooperative visualization in MaTSE: a) Cross-hair positioned at a rounded-value approximation of the mouse cursor position. The coordinates of the cursor are used to when forming queries. Bold font labels on the axes describe the cross-hair position to inform the user before and during query specification.  b) A users attempt to specify a threshold on the value of a single axis by dragging a box query. The user clicks on point I and drags to point II to form the box-query illustrated with dotted lines. c) The dotted line indicates the threshold the user wants to set and the threshold sent to the MaTSE pattern browser as the recorded query. This is also what the user sees when they elect to refine this query.

pattern

Animating the scatter-plot to view patterns of activity among gene groupings.

screenshot

A screenshot of the MaTSE interface. Labeled components are I) the pattern-browser, II) scatter-plot and III) line-chart. The current pattern is the result of two queries.

)

The video demo.

Publications

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

Craig, P., Cannon, A., Kukla, R., Kennedy, J. (2012, October). MaTSE: The Microarray Time-Series Explorer. Paper presented at 2nd IEEE Symposium on Biological Data Visualization, Seattle, WA.

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. (pp. 199-206). Mallorca, Spain: Lecture Notes in Computer Science.

fp – PCraigGB-1

About

Leave a Reply

Your email address will not be published. Required fields are marked *