SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Calculating PSI values for rat RNA-seq kajot Bioinformatics 1 10-08-2015 10:13 PM
Values to use for hierarchical clustering of RNA-seq data with outliers cjsifuen Bioinformatics 3 01-08-2015 10:49 AM
zero rna-seq values AFTER normalisation in edgeR feralBiologist Bioinformatics 9 08-19-2014 02:49 PM
pattern of p-values for DE testing for RNA-Seq data alittleboy Bioinformatics 4 07-24-2013 08:42 AM
Cut-off values for fold change in RNA seq smalan RNA Sequencing 1 07-12-2012 10:10 AM

Reply
 
Thread Tools
Old 01-21-2015, 04:02 AM   #1
priya
Member
 
Location: sweden

Join Date: Apr 2013
Posts: 57
Question Similar trends from RNA-Seq values

Hi,

I have time-series RNA-Seq data . Both FPKM and counts values are available. Especially for the DE analysis, Counts are transformed to voomed values and all the DE-tests are performed. I would like to find out the group of genes that are having similar trend over time.

Eg, I would like to pick the genes that are showing similar trend like GeneA

Gene A :
T0 T1 T2 T3 T4 T5
10 20 30 25 10 2

Is there any proper approach to categorize the genes .
Any method or papers or suggestions will of great help.
priya is offline   Reply With Quote
Old 01-21-2015, 06:17 PM   #2
mattanswers
Member
 
Location: Boston

Join Date: Oct 2009
Posts: 65
Default supervised clustering

I would suggest supervised clustering. You can input a given gene's expression pattern and the rest of the genes will be clustered by what genes show the most similar patterns.

Class Neighbors and/or Gene Neighbors in GenePattern, http://http://www.broadinstitute.org...re/genepattern, will do what you want.

There is also STEM,http://http://www.cs.cmu.edu/~jernst/stem/, and some publications that you can get by googling 'gene expression time series'.
mattanswers is offline   Reply With Quote
Old 01-22-2015, 04:24 AM   #3
priya
Member
 
Location: sweden

Join Date: Apr 2013
Posts: 57
Default

Quote:
Originally Posted by mattanswers View Post
I would suggest supervised clustering. You can input a given gene's expression pattern and the rest of the genes will be clustered by what genes show the most similar patterns.

Class Neighbors and/or Gene Neighbors in GenePattern, http://http://www.broadinstitute.org...re/genepattern, will do what you want.

There is also STEM,http://http://www.cs.cmu.edu/~jernst/stem/, and some publications that you can get by googling 'gene expression time series'.
Thank you for your suggestions and links. It is exactly what I was looking for,
priya is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:33 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO