User: banerjeeshayantan
banerjeeshayantan • 110
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Posts by banerjeeshayantan
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C: Estimate gene expression data
... Hi Kevin, I went through your notes and basics of regression analysis. I have a few questions. Firstly, in the above example, you assumed that I have ClinicalParam1, ClinicalParam2, gene1, gene2 data for many patients. That means the clinical data has already been integrated with gene expression dat ...
written 12 weeks ago by
banerjeeshayantan • 110
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C: Estimate gene expression data
... Hi Kevin. I am still in the process of going through recently published materials on the topic (which is quite overwhelming, to say the least :P). I have gone through R packages to both estimate and simulate gene expression data, but I am kind of lost along the way. I feel that there is a significan ...
written 3 months ago by
banerjeeshayantan • 110
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... I have a set of patients who has suffered heart attacks and I have the clinical information already available. Now I want to extract/estimate the gene expression data for the same group of patients. Since I don't have the data for those exact patients, is there any way I can sort of average the expr ...
written 3 months ago by
banerjeeshayantan • 110
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... I am trying to integrate EHR based clinical data for heart attacks with genomics data. Is there a way to do the same? Can I integrate gene expression data with clinical data for heart attack patients in-silico? ...
written 3 months ago by
banerjeeshayantan • 110
• updated
3 months ago by
Kevin Blighe ♦ 43k
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... I am trying to perform a one-class classification of driver vs non-driver mutations. I have a list of experimentally validated driver mutations from a pancancer study. But is it possible to retrieve a list of non-cancerous mutations as well? Since the number of non-cancerous mutations far exceeds th ...
written 3 months ago by
banerjeeshayantan • 110
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... I have a very basic question. So I have downloaded somatic mutation data from the COSMIC database. Each mutation has corresponding strand information associated with them. This usually coincides with the coding strand of the gene in which the mutation is located. The strand information goes like "+" ...
written 4 months ago by
banerjeeshayantan • 110
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... So if I want to extract fasta sequence of the flanking regions around mutations (SNVs), I should just consider all the mutations to be in one particular strand and go ahead with the analysis (bedtools getfasta), right? ...
written 4 months ago by
banerjeeshayantan • 110
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... Thanks for your reply. I have tried something very similar to your first suggestion. I tried finding motifs that are over-represented around disease-causing mutations as compared to non-disease. I also have a list of such motifs with their respective significance values. But the problem is I am unab ...
written 4 months ago by
banerjeeshayantan • 110
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... I have a list of mutations and the motifs are the bases flanking the mutation. I want to check whether over-representation of certain motifs influences the type of mutation. ...
written 4 months ago by
banerjeeshayantan • 110
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... I have a set of di-, tri- and tetra-nucleotide motifs from the coding region of the genome that are over-represented. Is there any way to establish the biological significance of the over-representation? Right now it's just statistically significant with respect to a null model (of random sequences ...
written 4 months ago by
banerjeeshayantan • 110
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