Editing
Noi/NOTES/2012-4-26
(section)
Jump to navigation
Jump to search
Warning:
You are not logged in. Your IP address will be publicly visible if you make any edits. If you
log in
or
create an account
, your edits will be attributed to your username, along with other benefits.
Anti-spam check. Do
not
fill this in!
== Comparing no CpG-SNP mQTL to the whole CpG and SNP mQTL result == * Analyzing the association of CpG and SNP with 10%FDR derived from each analysis {| {{table}} | align="center" style="background:#f0f0f0;"|'''''' | align="center" style="background:#f0f0f0;"|'''no CpG-SNP''' | align="center" style="background:#f0f0f0;"|'''SNP-free CpG and CpG-SNP''' | align="center" style="background:#f0f0f0;"|'''% of no CpG-SNP to all significant associations''' |- | # of association (10%FDR)||742||2,788||23.17% |- | significant p-value||1.636E-04||5.448E-04|| |} * From the table above, I could see the different of significant p-value from each test. The reason is that the number of tests were different between the test of the whole methylation matrix and the whose SNPs have been filtered out. Therefore the BH correction which deals with the number of test in calculation provide the q-value with at the different significant p-value. It turned out that the significant p-value of no SNP analysis was lower than the whole CpG. This implied that there might be more no CpG-SNP between 1.636E-04 to 5.448E-04 p-value of the 2MB_UCLA_mQTL_3202_10%FDR.txt file (Total significant CpG-SNP association 3,202 sites, 10%FDR) * I then checked the number of CpG-SNP association with the significant p-value 5.448E-04 in no SNP-CpG file and got total 900 sites (but have ~27.4% FDR by the test with out CpG-SNP. * Note: I can count the # of sites based on p-value because this value was not changed, and just used it as the reference. This account for ~28% of the association I got from all association. * Then, I printed out another files of CpG-SNP association with no CpG-SNP significant p-value 0.0005613 awk '{if ($7<=0.0005613) print $0}' sorted_2MB_mQTL-noSNP_minPVal0.05_QVal.txt.txt > sorted_2MB_mQTL-noSNP_minPVal0.0005613_QVal.txt * I also checked if those sites exit in the 10%FDR mQTL result derived from the previous analysis (on the whole mathylMatrix) ./get_overlapping_CpG_SNP.pl ./2MB_UCLA_mQTL_3202_10%FDR.txt <./sorted_2MB_mQTL-noSNP_minPVal0.0005613_QVal.txt > test_mQTL * I checked the overlapped sites on both files again, and there were consistent. This helped to confirm that the analysis of this time and the previous time were likely to be correct. '''head sorted_2MB_mQTL-noSNP_minPVal''' chr8:17533620 rs17125083 8 17533468 0.8961 1.331e-40 2.262e-39 chr8:17533620 rs2301541 8 17533568 0.9029 3.106e-40 2.64e-39 chr8:17533604 rs17125083 8 17533468 0.8839 1.099e-38 1.867e-37 chr19:58791188 rs260500 19 58791213 0.889 5.069e-38 6.083e-37 chr8:17533604 rs2301541 8 17533568 0.8859 1.473e-37 1.252e-36 chr19:58791159 rs260500 19 58791213 0.8844 2.421e-37 2.906e-36 '''head sorted_2MB_mQTL-noSNP_minPVal0.0005613_QVal.txt''' chr8:17533620 rs17125083 8 17533468 0.8961 1.331e-40 2.262e-39 5.9861604e-34 chr8:17533620 rs2301541 8 17533568 0.9029 3.106e-40 2.64e-39 5.9861604e-34 chr8:17533604 rs17125083 8 17533468 0.8839 1.099e-38 1.867e-37 2.82226299666667e-32 chr19:58791188 rs260500 19 58791213 0.889 5.069e-38 6.083e-37 6.8965556275e-32 chr8:17533604 rs2301541 8 17533568 0.8859 1.473e-37 1.252e-36 1.135556488e-31 chr19:58791159 rs260500 19 58791213 0.8844 2.421e-37 2.906e-36 2.19643713666667e-31 * Also break down CpG-SNP distance not only at equal length, but also at a very short distance like within 2kb and 5kb. The table below implied the cis regulation of genetic factor on methylation status especially within 2kb since the number of association not largely increase from 2-5kb (393-327 = 66 association) or 2-10kb (426-327 = 99 association) {| {{table}} | align="center" style="background:#f0f0f0;"|'''CpG-SNP distance''' | align="center" style="background:#f0f0f0;"|'''number of association''' | align="center" style="background:#f0f0f0;"|'''%''' |- | 2kb-noSNP||327||36.33% |- | 5kb-noSNP||393||43.67% |- | 10kb-noSNP||426||47.33% |- | 10-20kb-noSNP||34||3.78% |- | 20-30kb-noSNP||24||2.67% |- | 30-40kb-noSNP||41||4.56% |- | 40-50kb-noSNP||4||0.44% |- | 50kb-2Mb-noSNP||371||41.22% |} * Look at # of associated CpG 900 sorted_2MB_mQTL-noSNP_minPVal0.0005613_QVal.txt awk '{print $1}' sorted_2MB_mQTL-noSNP_minPVal0.0005613_QVal.txt | sort | uniq -u | wc -l --> 361 awk '{print $1}' sorted_2MB_mQTL-noSNP_minPVal0.0005613_QVal.txt | sort | uniq -d | wc -l --> 155 361+155X = 900 --> X ~ (900-361)/155 ~ 3.5 this shows that >1 SNPs associated with the same CpG (155 of individual CpGs associated with more than one SNPs) Total single CpG: 361+155 = 516<br> * Look at # of associated CpG awk '{print $2}' sorted_2MB_mQTL-noSNP_minPVal0.0005613_QVal.txt | sort | uniq -u | wc -l --> 236 awk '{print $2}' sorted_2MB_mQTL-noSNP_minPVal0.0005613_QVal.txt | sort | uniq -d | wc -l --> 134 236+134Y = 900 --> Y ~ (900-236)/134 ~ 5 this suggests that > 1 CpGs associated with the same SNP (134 of individual SNPs associated with more than one CpGs) Total single CpG: 236+134 = 370<br> * Print out the list of unique CpGs and SNPs and duplicated CpGs and SNPs
Summary:
Please note that all contributions to ZhangLabWiki may be edited, altered, or removed by other contributors. If you do not want your writing to be edited mercilessly, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource (see
ZhangLabWiki:Copyrights
for details).
Do not submit copyrighted work without permission!
Cancel
Editing help
(opens in new window)
Navigation menu
Personal tools
Not logged in
Talk
Contributions
Create account
Log in
Namespaces
Page
Discussion
English
Views
Read
Edit
View history
More
Search
Navigation
Main Page
Current events
Recent changes
Random page
Investigators
Matt Cai
Song Chen
Eric Chu
Dinh Diep
Elizabeth Duong
Shicheng Guo
Alan Fung
Daniel Jacobsen
Blue Lake
Huy Lam
Alice Li
Andrew Richards
Brandon Sos
Chris Wei
Yan Wu
Kun Zhang
Tools
What links here
Related changes
Special pages
Page information