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Using Datascape for Visualising Genetic Regulatory Codes

Case Study from The University of Warwick on their experiences of using Datascape:

“We have used Datascape to visualise hundreds of short regions of non-protein-coding DNA sequences which are evolutionarily conserved across distant plant species.

The sequences contain short sequence patterns (called “motifs”) and we are interested to see whether there are specific combinations or arrangements of motifs that we can link to particular biological functions. To do so, we first selected a subset of DNA sequences (sequences that are likely to be involved in defence against fungal infection) so we can compare this subset vs the set of remaining sequences.

We displayed each DNA sequence by a black rectangle with its length representing the length of the sequence. We then show triangles to represent motifs where triangle positions correspond to the position of motifs within a sequence. Different types of motifs are represented by different colours. The height of each triangle represents the statistical significance of the motif, i.e. how well does the DNA sequence match the known motif sequence.

Datascape allows us to browse this large data set – hundreds of sequences containing about a thousand motif occurrences – easily so we can study what sort of combinations occurs in what sort of functional sequence. We can also change the grouping of sequences easily (for example, salt stress instead of fungal infection) and analyse our data for links to various different potential biological functions. In addition, Datascape provides a great way for us to present our data and publicise our results.”

The DNA sequences studied here can be found in this publication:
http://www.plantcell.org/content/24/10/3949.abstract

Watch the video

Using Datascape for Visualising Regulatory Codes from DadenMedia on Vimeo.