User: CY

gravatar for CY
CY460
Reputation:
460
Status:
Trusted
Location:
United States
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https://www.dna-ghost....
Last seen:
2 hours ago
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4 years, 1 month ago
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Posts by CY

<prev • 242 results • page 1 of 25 • next >
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Comment: C: Arm-level SCNA does not change mRNA expression level?
... Deletion of both local and arm level result in same degree of expression reduction. In another word, deletion does not share the phenomenon we are talking about. ...
written 8 days ago by CY460
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Comment: C: Does variant enrichment analysis make sense?
... One is COBAS ([http://kobas.cbi.pku.edu.cn/][1]). I am not sure if there are others. But this one seems to be frequently used although I don't think this type of analysis make sense. [1]: http://kobas.cbi.pku.edu.cn/ ...
written 8 days ago by CY460
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Does variant enrichment analysis make sense?
... Gene set expression analysis have been wide used in find significantly dis-regulated pathways in given population. We also found some similar enrichment analysis tools using somatic variants. Does this make biological sense. Besides, somatic variants are sparse and I think it would not be able to pr ...
expression enrichment analysis somatic variant written 10 days ago by CY460
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Comment: C: Arm-level SCNA does not change mRNA expression level?
... Not yet. Will try that very soon. ...
written 15 days ago by CY460
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Comment: C: Arm-level SCNA does not change mRNA expression level?
... We have already tested this on a number of gene. It looks like not a gene specific phenomenon. All genes we have tested shown increased expression level in times of local amplification. But in times of arm-level amplification, the expression did not change at all. BTW, this seems to be well accepted ...
written 15 days ago by CY460
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Comment: C: Why can we still be able to continuously discover new cancer driver bioinformati
... Good point. I guess the other angle is to come up with new methods that, within reasonable sample size, discover biological (mutational / expressional / epigenetic) oncogenic pattern. ...
written 16 days ago by CY460
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Comment: C: Why can we still be able to continously discover new cancer driver bioinformatic
... If sample size is the only factors here, does this mean that only large collaborative cancer project (with large sample size) is useful in terms of discovering new driver event, and study with smaller sample size stand few chance for that? ...
written 16 days ago by CY460
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Comment: C: Why can we still be able to continously discover new cancer driver bioinformatic
... What do you mean by "far from 80 percents for many cancer types"? Can you point me to a reference paper? Also, I did not find the PanCancer Atlas (Cell 2018) paper. Do you mind share some details, like PubMed ID or the title? Thanks ...
written 16 days ago by CY460
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Arm-level SCNA does not change mRNA expression level?
... It is almost common sense that local amplification of gene increase the its mRNA expression. I recently heard that large scale SCNA (such as arm-level amplification) does not increase the mRNA expression level of gene within the region. I did some analysis (SCNA is determined by SNP array and NGS, m ...
scna expression cnv written 16 days ago by CY460
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Why can we still be able to continuously discover new cancer driver bioinformatically these days?
... This question may stray to focus of Biostar a little bit. Still, I believe this regards both cancer research as well as technical bioinformatics. There are numerous cancer driver genes / mutations that, by definition, frequently appear in certain cancer types and drive tumorigenesis. Many of them ...
driver gene cancer written 16 days ago by CY460

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