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Jun
29
awarded  Commentator
Jun
29
comment Deciding a reasonable threshold for copy number variation in a CNV (SNP array) TCGA dataset
Hmm, okay, I think I see. No, you don't want to compare the intensity of the tumor at any one position against the 5-95% distribution of the normal across the whole array. You want to compare the intensity of the tumor at one position against the normal at that position. This will normalize for sequence-specific binding differences.
Jun
26
awarded  Informed
Jun
26
answered Deciding a reasonable threshold for copy number variation in a CNV (SNP array) TCGA dataset
Jun
22
awarded  Editor
Jun
22
revised What does it mean to “map the human genome”
added 47 characters in body
Jun
22
comment What does it mean to “map the human genome”
Good point, I'll edit. I was thinking of the Celera DNA, which I thought was Venter's, but it turns out that they were using a pool, too. (Venter was just in the pool.)
Jun
22
awarded  Yearling
Jun
22
answered What does it mean to “map the human genome”
May
13
comment Downstream analysis after in vivo pathogen RNAseq
Right. The main thing is that you want your groups in an RNA-Seq experiment to focus as cleanly as possible on the difference you want to investigate. If you're interested in antibiotic resistance, use a resistant and a non-resistant strain. If you're interested in immune evasion, use samples in the presence and absence of an immune response. You expect many differences between cultured and in vivo samples-- you've already mentioned metabolism, antibiotic resistance, and immune evasion, and I'm sure there are lots more. So it's hard to relate any given gene expression change to a phenotype.
May
12
comment Downstream analysis after in vivo pathogen RNAseq
The reason I say it's not the clearest model, especially for antibiotic design, is that you're investigating the difference between bacteria in the host and bacteria on the plate. An antibiotic in particular probably isn't going to care about that-- it should kill in both situations, right? And for a vaccine, there are so many differences between culture and in vivo that I'm not sure that you can attribute differences you see to immune evasion. Are there immune-compromised pig models? In vivo samples from those would be a much cleaner control for immune evasion.
May
12
comment Downstream analysis after in vivo pathogen RNAseq
Okay, that does make experimental design much easier.
May
11
answered Downstream analysis after in vivo pathogen RNAseq
May
11
comment Downstream analysis after in vivo pathogen RNAseq
You're going to need to be a lot more specific. To start with, when you say a pathway is up or down-regulated, what comparison are you making? Is there a treatment and you're comparing treated versus control? Are there different populations and you're comparing to each other?
May
2
awarded  Yearling
May
24
answered Databases for gene regulatory network graphs?
May
21
awarded  Critic
May
11
comment Do gene expression levels necessarily correspond to levels of protein activation?
I think you'll find very few papers that demonstrate changes in mRNA levels by microarray, claim that an increase in the gene product's activity is responsible for the biological effect, and then stop. mRNA data is complicated, not useless. Almost anywhere that mRNA upregulation is reported, it will be followed by a measurement of the protein levels and other follow-on experiments to confirm the protein's involvement.
May
10
answered How similar are Circulating Tumor Cells and Cancer Stem Cells?
May
5
awarded  Necromancer