Question: Translation Of Graph Theory Into Experimental Verification
1
gravatar for GreenDiamond
5.7 years ago by
GreenDiamond70
GreenDiamond70 wrote:

Hi BioStars,

Graph theoretical approaches are becoming very common in bioinformatics. Have you ever come across a group that generated a network to construct hypotheses, and then used that information to design follow-up experiments that discovered something new and important?

I am interested to see an example of this translation, regardless of the network generation technique (what represents nodes - genes, etc - and edges), the experimental technique, the organism of study, etc.

Thank you!!

translation graph • 1.5k views
ADD COMMENTlink modified 5.7 years ago by B. Arman Aksoy1.2k • written 5.7 years ago by GreenDiamond70
2
gravatar for donfreed
5.7 years ago by
donfreed1.4k
Mountain View, CA
donfreed1.4k wrote:

The Eichler lab created a network of interacting proteins more likely to harbor de novo [mutations in autism probands: http://www.nature.com/nature/journal/v485/n7397/full/nature10989.html]. They then performed follow-up sequencing to confirm that these genes are more likely to be mutated. I did not see a reference for the follow-up study (it may be unpublished), but [this review: http://www.ncbi.nlm.nih.gov/pubmed/24387789] briefly describes the follow-up (page 100).

I am not sure that their follow-up discovered something 'new and important' but it certainly confirmed that their protein network contained many genes likely to have de novo mutations in sporadic autism populations.

ADD COMMENTlink modified 5.7 years ago by Ashutosh Pandey11k • written 5.7 years ago by donfreed1.4k

Edited as the links were not visible.

ADD REPLYlink written 5.7 years ago by Ashutosh Pandey11k
1
gravatar for B. Arman Aksoy
5.7 years ago by
B. Arman Aksoy1.2k
New York, NY
B. Arman Aksoy1.2k wrote:

Here are two such examples from our lab, where networks are being inferred from the data and then they are being used for further prediction followed by experimental follow-up:

  1. Perturbation Biology: Inferring Signaling Networks in Cellular Systems
  2. Drug Synergy Screen and Network Modeling in Dedifferentiated Liposarcoma Identifies CDK4 and IGF1R as Synergistic Drug Targets
ADD COMMENTlink written 5.7 years ago by B. Arman Aksoy1.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1147 users visited in the last hour