User: Stane

gravatar for Stane
Stane50
Reputation:
50
Status:
New User
Location:
Europe
Last seen:
4 months, 1 week ago
Joined:
3 years, 3 months ago
Email:
s*******************@gmail.com

Posts by Stane

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Go annotation reliability ?
... Well I may have add that I looked at mass spec data of cell surface for many cell lines, and didn't find much serpinb2, also for some reason the source of the go annotation can not be verified, the link does not work for me. I am not saying the annotation if false, but in this case I am more likely ...
written 4 months ago by Stane50
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Comment: C: Go annotation reliability ?
... Thank you very much, great answer ...
written 4 months ago by Stane50
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Go annotation reliability ?
... Hey, I have been using Gene Ontology to try to understand some differently express gene and I am now wondering if I should trust the GO annotation. I was looking at serpinb2, for this gene I am getting GO term: GO:0005576 'extracellular region' and GO:0005615 'extracellular space'. However when I ...
go written 4 months ago by Stane50 • updated 4 months ago by Kevin Blighe11k
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Comment: C: Meta analysis of cancer gene expression
... not bad but they want me to use a subset of genes instead of the full 20k , I will check if I can get everything through their R interface ...
written 4 months ago by Stane50
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Meta analysis of cancer gene expression
... Hello, Is there any online website/database with meta analysis of dis-regulated gene expression in cancers. I am not interested in specific cancer, I need something across multiple type of cancer. So far I found a few websites about mutations and some paper that do single cancer type de gene ex ...
database micro array rna-seq written 4 months ago by Stane50
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Comment: C: Go term for cell surface receptors
... I think I found the good go term finally : transmembrane signaling receptor activity GO:0004888 ...
written 4 months ago by Stane50
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Go term for cell surface receptors
... Hello, I am looking at micro-arrays and differently expresse genes and I was wondering if the condition that I am looking at has some enriched cell surface marker/receptor. I have been playing around with go term, making intersection with my DE gene. I try several of them: receptor binding, host ...
gene written 4 months ago by Stane50
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Comment: C: snp frequency with annovar
... The frequency computed in convert2annovar.pl are somehow correct, it divide the snp appearance on the population by 2 times the total number individual which makes sense as 2 alleles per individual, but now my problem is that denominator to be 2 times pop minus the missing call for this snp ...
written 10 months ago by Stane50
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Answer: A: How to interpret snp frequency
... I kinda figure it out the real freq I was interested in is the the snp population freq and it seems to be N_CHR x right part of FREQ / (2 X polution) ...
written 10 months ago by Stane50
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Comment: C: How to interpret snp frequency
... I am not familiar with varScan but I have only access to the variant vcf files not the mpileup ...
written 10 months ago by Stane50

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