Question: K-means clustering of differentially expressed genes based on GO
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gravatar for Atefeh Mahdavi
5.2 years ago by
Bangi, Malaysia
Atefeh Mahdavi10 wrote:

Hi everybody!

I have transcript clusters (hierarchical clustering) of differentially expressed genes generated by Trinity pipeline. But, I don't have any information about the GO of genes in each cluster or even knowing how many genes belong to every cluster.

Therefore, I wonder if anybody has idea how can I do K-means clustering based on GO of differentially expressed genes.

Really appreciate your help. 

rna-seq next-gen • 2.8k views
ADD COMMENTlink modified 2.7 years ago by Biostar ♦♦ 20 • written 5.2 years ago by Atefeh Mahdavi10
1

Do you have go annotation of your transcriptome assembly at all? If not, you need to run an annotation pipeline first. See A: Annotating sequences after de-novo Trinity assembly and RSEM analysis...there mu or maybe A: Transcriptome Analysis with only a fasta file  about GO annotation first.

You can't do k-means clustering of go terms, because there is no euclidean metric for go terms (DAG is not a vector space, what's the centroid of "hydrolysis" and "DNA-repair"?).

See instead: Clustering Go Terms? or Clustering Genes Based On Gene Ontology and ftp://ftp.geneontology.org/go/www/GO.tools.microarray.shtml

 

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by Michael Dondrup47k
2
gravatar for Michael Dondrup
5.2 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

The Bioconductor package GOsim contains methods for comparing sets of genes based on their functional annotation

e.g. getGeneSim to calculate distance of gene sets based on their functional annotation or clusterEvaluation to compute cluster quality scores for existing clusters (e.g. from k-means). 

ADD COMMENTlink written 5.2 years ago by Michael Dondrup47k
0
gravatar for Atefeh Mahdavi
5.2 years ago by
Bangi, Malaysia
Atefeh Mahdavi10 wrote:

Thanks indeed for your reply and help Michael!

I have GO annotation results generated through Trinitate. However, I am also running Blast2Go now.

Is there any other easier bioconductor ! I don't know anything about R programming... I found DNAstar software quite friendly for those who doesn't know programming but we should buy it.

Merry Christmas and happy new year!

 

 

 

 

 

ADD COMMENTlink written 5.2 years ago by Atefeh Mahdavi10
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