User: CY

gravatar for CY
CY200
Reputation:
200
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Trusted
Location:
United States
Website:
https://www.dna-ghost....
Last seen:
43 minutes ago
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3 years ago
Email:
c********@hotmail.com

Posts by CY

<prev • 152 results • page 1 of 16 • next >
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Comment: C: Gene expression distribution (non-DE and DE)
... You have already clearified a lot. Really helpful for me! Thanks a lot! ...
written 5 days ago by CY200
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Comment: C: Gene expression distribution (non-DE and DE)
... Yes, the distribution of normal sample pool follows negative binomial distribution. But what about the distribution of tumor sample pool? I imagine there will be no pattern to follow since each tumor sample may have its own disturbed / distrinct expression pattern, right? ...
written 5 days ago by CY200
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Shannon index vs Simpson index in evaluating TCR diversity
... From what I have heard about the difference between Shannon and Simpson index: Shannon index puts more weights on richness (how many different species are there including the very rare one). Simpson put more attentions on dominant species (rare species don't make much difference) From the TCR dive ...
tcr-seq tcr diversity written 5 days ago by CY200
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Gene expression distribution (non-DE and DE)
... I know there are lots of discussion about this. But all sorts of distributions were mention regarding both differential expression gene and non-differential expression gene. I have not found anything conclusive. Maybe this is still an unsettled issue. But here is what I thought: I have been under t ...
rna-seq differential expression written 6 days ago by CY200 • updated 5 days ago by Kevin Blighe30k
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Answer: A: Correcting for tumor purity in tumor evolution analysis
... I have two hypothesis on such case. Not sure if it is logically sound... Maybe more than one tumorigenesis network / pathway being activated in your sample and not all these mutants contribute to single one pathway. Maybe only one oncogenic pathway being activated but different mutants on differen ...
written 11 days ago by CY200
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Comment: C: Low VAF (around 7%) mutated gene prevalent in cancer patient (3/4), driver?
... I think the logic is reasonable. Anyway, it turns out that all samples are primary. We still can't believe it is a drive with such low VAF. Guess only way to confirm is validating the variant on more sample. ...
written 11 days ago by CY200
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Comment: C: Low VAF (around 7%) mutated gene prevalent in cancer patient (3/4), driver?
... Other genes does not seem to be interesting based on their VAF and population frequency. Only this gene looks weird based on its situation above. Why do you think whether it is primary or metastatic makes such difference in terms of VAF? What I thought is just the opposite: The variant in primary ...
written 11 days ago by CY200
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Low VAF (around 7%) mutated gene prevalent in cancer patient (3/4), driver?
... We found a gene (TSC2) mutated with low VAF (around 7%) in 3/4 brain tumor patients. Although the sample size is limited, 3/4 patients is hard to be concidence. Besides, this gene is known to be a tumor suppressor preventing cells from growing too fast. However, the low VAF makes it less unlikely ...
mutation driver gene vaf written 11 days ago by CY200
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Comment: C: What kind of distribution to you expect to see for RNA-Seq expression levels?
... Could you elaborate in more details regard the cases you mentioned? I have been under the impression that not differentially expressed gene would follow negative binomial distribution due to biological / technical variation. In the cancer sample pool, over / under expressed genes would follow negat ...
written 11 days ago by CY200
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Comment: C: Would different enrichment tools result differently by defining pathway differen
... Very informative clarification. Thx :) ...
written 13 days ago by CY200

Latest awards to CY

Popular Question 4 days ago, created a question with more than 1,000 views. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Popular Question 23 days ago, created a question with more than 1,000 views. For STAR genomeLoad issue
Popular Question 5 weeks ago, created a question with more than 1,000 views. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Appreciated 3 months ago, created a post with more than 5 votes. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Good Question 3 months ago, asked a question that was upvoted at least 5 times. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Student 5 months ago, asked a question with at least 3 up-votes. For why PCA for RNA-Seq but tSNE for scRNA-seq?
Centurion 7 months ago, created 100 posts.
Supporter 10 months ago, voted at least 25 times.
Popular Question 11 months ago, created a question with more than 1,000 views. For Call variant from RNA-Seq data using Haplotypecaller

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