Assign gene signature in other cohort

Hi,

Via a GSE dataset, I identify a gene signature of hundred of genes specific to a particular class of samples. Now I want identify another samples (from a distinct cohort) who upregulated my homemade signature. How can i do this in R ? or in another language ? Thanks in advance

Alex

signature rna-seq r

• 765 views • link

updated 5.5 years ago by rpolicastro

• written 5.5 years ago by sunnlife •

1 answer

In R you can take your custom signature and make a two column data.frame with columns 'term' and 'gene', and then pass it to the TERM2GENE argument of the GSEA function from clusterProfiler.

• 0 views • link

written 5.5 years ago by rpolicastro

More posts like this

Close correlation between differentially-expressed genes
written 3.8 years ago by psm

Would really appreciate any thoughts/opinions on what might be going on with my dataset - thanks in advance :) I performed RNA-seq (bulk) of kidney …
Importing data from GEO
written 4.3 years ago by LHA_trash •

Hi everyone, I am struggling since hours to import expression data from GEO. I am trying to work on this dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151095 It is a …
GSEA with normalized protein abundances
written 4.5 years ago by jmFori •

Hi! I am trying to perform a GSEA (Broad Institute) using as input a matrix of normalized protein abundances with 6 conditions (dataset 1) to …
classifying samples by TCGA signature
written 6.1 years ago by garrettbullivant •

Hi all, I have some RNA-seq samples from multiple glioblastoma tumours that I'm now trying to classify according to a specific gene signature (from Verhaak …
NCBI analyze dataset
written 7.7 years ago by lvitale •

I downloaded the following dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68928 and read the file using getGEO function. multicancer <- getGEO(filename='Data/multicancer.soft.gz') like here https://warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/geo/ A this point how I can …
Group/Cluster tumor samples in an RNA-Seq dataset for survival analysis, based on the expression of…
written 7.9 years ago by svlachavas

Dear Community, based on a collaboration project, we have identified a small gene signature, discriminating relatively well control samples from tumor ones, based on an …
Regarding Microarray Platforms
written 8.7 years ago by Arunabh Sharma •

I am trying to subset the samples according to condition type from a particular GSE from Gene Expression Omnibus (GEO). This particular GSE has data …
How to reduce protein sequence dataset size for machine learning?
written 9.7 years ago by rajeshkumar_vinod •

Hello everyone, I have to train neural network for protein class prediction. I am using protein sequences for training and testing of this network. Problem …
What is a microarray "signature" and how can I compare my sample to a known signature?
written 11.1 years ago by JacobS

While reading about molecular subtyping strategies for various cancers, I have come across many papers talk about specific signatures that correlate to particular disease statuses …
Geo Data Matrix Using R
written 14.7 years ago by Yogesh Pandit •

<p>I want something like,</p> <pre><code>ID GB_ACC Gene Title Gene Symbol ENTREZ_GENE_ID GO_BP GO_MF GO_CC Sample1 Sample2...... </code></pre> <p>along with the corresponding values/IDs in the rows …