Tools To Reverse Engineer Genetic Networks From Microarray Data

Question

[Pradeep]

Please suggest tools, API's/libraries to reverse engineer Gene regulatory networks from transcriptiomic data sets ( microarray / deep sequencing).

Thank you.

Answer 1

[David Quigley]

Here is a list of references, both primary literature and reviews, organized by DREAM. DREAM is a yearly challenge for reverse engineering methods modeled after a similar competition for protein structure prediction. The basic approaches (Mutual Information, Bayesian Networks, Correlation, etc) are represented. Andrea Califano's group at Columbia has been prolific in this area with their ARACHNE algorithm.

[Pradeep]

useful referral thanks David

Answer 2

[Prateek]

check out this paper[?] Bioinformatics applications for pathway analysis of microarray data

http://bit.ly/gqDdGC

[Pradeep]

hi prateek link does not work

Answer 3

[Daniel Standage]

Here is a shameless plug for AIRnet, a piece of software written by a former colleague and friend of mine.

[Pradeep]

will try the tool thanks!