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can I get a heat map from two groups of transcriptome data? kurban910 Bioinformatics 0 05-18-2015 04:33 AM

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Old 05-22-2015, 01:08 PM   #1
vectorborne5
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Location: Richland, Washington, USA

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Default Finding Tripartite Data Groups for microRNA-TF-Gene Regulatory Circuits

I'm pretty new to the world of scripting and have a problem in my research lab that, if a script could be written, would have days worth of manual labor and graciously ask for the community's assistance in how I could go about writing a Python or perhaps a Perl script to solve this problem. Any assistance or direction would be GREATLY appreciated!

In the attachment I have a file with four columns as input data, where $1 and $2 essentially come as a pair and $3 and $4 also come as pairs. However, I want to find three-way triplet (tripartite) graph relationships within the data such that there are two main types present:
Type 1) TF --> Gene <-- mir <-- TF
Type 2) miR --> Gene <-- TF <-- miR

This could be broken into two different scripts if need be:

For the first script (Type 1)
Print TF
IF TF present in $TF twice
AND Target present BOTH in one row of $miR and $Gene
THEN print miR and Gene in question as miR and Gene
THEN print 1 in $Type

For the second script (Type 2)
Print miR
IF miR present in $miR twice
AND Gene present BOTH in one row of $TF and $Target
THEN print TF and Target in question as TF and Gene
THEN print 2 in $Type

The attachment has both input and what I hope to receive as output.
Attached Files
File Type: zip Tripartite_input_output.zip (6.4 KB, 1 views)
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correlation, graph, microrna, network, scripting

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