Dinh/Dinh 2012/NOTES/2012-2-9
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Seminar by Stephen Briggs[edit]
- Development of a highly sensitive and reliable protein quantification by MS.
- System have automated separation of proteins by charge (fewer charge in the machine = higher sensitivity.)
- Current gene annotation are very accurately. However, ~1K proteins needs to be re-annotated (according to MS results.)
- Comparison of protein MS with microarray data shows that most proteins are post-translationally regulated
- Although, a subset of proteins have correlation with microarray data.
- A small subset of proteins have extremely inverse correlation with mRNA levels. What does this mean?
- "if you have a hammer you see the whole full of nails"
Working on 24 ChIP data[edit]
- I'm still analyzing the peak calling results. After normalization and peak calling with MACs, my WIG files did not have the correct number of chromosomes (ie. chr12-19 are often missing). One hypothesis is that the normalization of reads cause MACS to not get any signal from these chromosomes.
- Currently, I will use MACs to generate WIG files for every single ChIP dataset, then I can perform the Fisher Exact Test (2x2 table.)
- I generated some summary statistics from the paired-end mapping.
- Overall, we increased the %mappable reads by PE mapping.
- The increase is up to ~%50 for R.mC and S.mC! PE mapping were able to rescue reads which mapped to repeats.
File:ChIP 24 mapping.png
- After removing PCR duplicates:
File:ChIP 24 PCRdup.png
- I checked the distribution of PE categories
-Proper = properly paired reads - both are in the (->,<-) orientation and within expected length -Diff_chr = both reads are mapped on different chromosomes -Indel = both reads are mapped in (->,<-) orientation but much larger or smaller length than expected. -Inverted = both reads are mapped in (<-,<-) or (->,->) orientation -Tandem = both reads are mapped in (<-,->) orientation, indicating tandem duplication
- Could the "improperly" paired reads be in repeats?
- Can we call peaks on these to see whether some class of repeat is enriched?
File:ChIP 24 PEdist.png