Transcription Visualization

Question

[alex]

Hi all,

I am trying to create a visualizer to visualize transcriptome data. I am traditionally a C#/.net programmer.

1. What language would be best for creating a tool to do this?
2. Are there any suggested APIs or current projects that already do something similar to this?

Thanks again!

Answer 1

[Zev.Kronenberg]

I think you might be trying to re-invent the wheel here. There are many good tools for visualizing these sorts of data.

1. IGV
2. Apollo
3. UCSC genome browser's custom tracks
4. [R] transcript clustering heatmaps

Of course I can only speculate since I can't see your data.

Answer 2

[Chris Evelo]

Agree with Zev, you really need to look around first and have a clear picture of what you need.

There are also many tools that help to visualize transcriptomics (and other -omics) results in their biological context. For instance by showing mapping of results on the gene ontology or by facilitating pathway mapping. Our own PathVisio does a fair job at the latter and is open source project. New visualizations can be coded as plugins in Java.

What is it exactly what you want to visualize?

[alex]

I want to visualize two files of omics data against each other. Other than that the exact specifications are still unclear at this point.

[Chris Evelo]

OK, assuming you want to see the biological overlap (are the same processes affected in both data sets) you might indeed want to pathway or GO tree visualization. If the two sets affect the same pathway you can use the visual representation to decide whether the effects would be comparable on a biological level even if they do not affect the same genes.