Question: Enrichment analysis on TCGA data
gravatar for david.tieri
2.2 years ago by
david.tieri0 wrote:


I have a list of differentially expressed genes between tumor and normal samples determined from TCGA data (BRCA). I am trying to cluster the genes into related groups and determine gene annotations for each cluster. The clustering is no problem, but annotating the clusters is proving to be difficult. I have tried using the TCGA_Biolinks function TCGAanalyze_EAcomplete, however I do not know how to make sense out of the output of this function. I have followed the tcgabiolinks vignette, and made the EABarplot (I could only get this to work for the dataset provided, not for a different dataset downloaded from the gdc), however I dont know how to get access to the genes that make up the different bars in the plot. I would like to find, for instance, a set of genes that are related to T-cell activity.

Thank you, David

rna-seq tcgabiolinks • 1.0k views
ADD COMMENTlink modified 22 months ago by Biostar ♦♦ 20 • written 2.2 years ago by david.tieri0

how to download tumor and normal samples from TCGA database?

ADD REPLYlink written 2.2 years ago by Ben50

Hi Ben,

If the query is not related to the main topic discussed, please make a separate post to discuss.

Tip: Also check previous posts before making redundant queries, Example: TCGA: how to download matched normal and tumor samples from TCGA website.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by EagleEye6.4k
gravatar for EagleEye
2.2 years ago by
EagleEye6.4k wrote:

Method 1:

1) Use GeneSCF to extract complete Gene Ontology as simple text (tab separated) format.

./prepare_database -db=GO_all -org=goa_human

2) Extract the genes related to you keyword 'T cell'

grep "T cell" geneSCF-master-source-v1.1-p2/class/lib/db/goa_human/GO_all_sym.txt | cut -f2 | sed s'/.$//' | sed 's/,/\n/g' | awk '!x[$0]++'

3) Overlap those genes with your list of genes

Method 2:

If you are confident that the genes you have, are related to 'T cell', try simple gene enrichment analysis with GeneSCF and check if the 'T cell activity' terms pops up.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by EagleEye6.4k

Hi EagleEye,

Thank you very much for your response. That seems to be what I am trying to do, however I would like to keep my analysis in R. Is there a tool that works in R that does a similar task?

Thank you, David

ADD REPLYlink written 2.2 years ago by david.tieri0

I do not know if this task can be easily done with R. Alternatively you can import the table/TEXT file obtained with GeneSCF ('geneSCF-master-source-v1.1-p2/class/lib/db/goa_human/GO_all_sym.txt') into R and match your gene list.

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by EagleEye6.4k
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