Similar trends from RNA-Seq values

priya · 01-21-2015, 05:02 AM

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.

mattanswers · 01-21-2015, 07:17 PM

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'.

priya · 01-22-2015, 05:24 AM

Quote:

Originally Posted by mattanswers

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,

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Calculating PSI values for rat RNA-seq	kajot	Bioinformatics	1	10-08-2015 11:13 PM
Values to use for hierarchical clustering of RNA-seq data with outliers	cjsifuen	Bioinformatics	3	01-08-2015 11:49 AM
zero rna-seq values AFTER normalisation in edgeR	feralBiologist	Bioinformatics	9	08-19-2014 03:49 PM
pattern of p-values for DE testing for RNA-Seq data	alittleboy	Bioinformatics	4	07-24-2013 09:42 AM
Cut-off values for fold change in RNA seq	smalan	RNA Sequencing	1	07-12-2012 11:10 AM

01-21-2015, 05:02 AM	#1
priya Member Location: sweden Join Date: Apr 2013 Posts: 57	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.

01-21-2015, 07:17 PM	#2
mattanswers Member Location: Boston Join Date: Oct 2009 Posts: 65	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'.