Editing
Dinh/Dinh 2014/NOTES/2014-4-1
(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!
===Results=== *MOABS calculated DMRs using 3 methods. *GREAT analysis on DMRs using single gene per region association within 10kb extended from midpoint of regulatory domain. *Method #1, # DMRs ** call Dmc and Dmr according to method 1: Fisher Exact Test ** Dmc is defined as depth >= minDepth(suggest 10), p<p_fet_cut(suggest 0.05), nMethDif > nominalMethDifCutoff(0.3333) ** Dmr is defined as minC >=3, maxDist 300, p<p_fet_cut(suggest 0.05), nMethDif > nominalMethDifCutoff(0.3333) 22,125 esc_vs_ips [[File:dmr_M1_esc_vs_ips.txt]] (Pathways common/BioCyc pathways) protein citrullination - 5 genes/15 regions: Padi1, Padi2, Padi3, Padi4, Padi6 22,135 esc_vs_scnt [[File:dmr_M1_esc_vs_scnt.txt]] (Pathways common/BioCyc pathways) protein citrullination - 5 genes/15 regions: Padi1, Padi2, Padi3, Padi4, Padi6 708 ips_vs_scnt [[File:dmr_M1_ips_vs_scnt.txt]] No pathway, but there were 11 significant terms for Mouse Phenotype: [[File:dmr_M1_ips_vs_scnt_mousephenotype.png | 300px]] *Method #2, # DMRs **call Dmc and Dmr according to method 2: Using the credible methylation difference metric (beta-binomial) distribution. **Dmc is defined as cMethDif > credibleMethDifCutoff(0.2) **Dmr is defined as minC >=3, maxDist 300, cMethDif > credibleMethDifCutoff(0.2) 19,799 esc_vs_ips [[File:dmr_M2_esc_vs_ips.txt]] GO Molecular Function protein-arginine deiminase activity, hydrolase activity (acting on carbon-nitrogen) but not peptide bonds IgG binding (Pathways common/BioCyc pathways) protein citrullination - 5 genes/13 regions: Padi1, Padi2, Padi3, Padi4, Padi6 15,318 esc_vs_scnt [[File:dmr_M2_esc_vs_scnt.txt]] GO Molecular function protein-arginine deiminase activity GO Biological process peptidyl-citrulline biosynthetic process from peptidyl-arginine (Pathways common/BioCyc pathways) protein citrullination - 5 genes/12 regions: Padi1, Padi2, Padi3, Padi4, Padi6 BioCyc pathways phosphate acquisition II 52 ips_vc_scnt [[File:dmr_M2_ips_vs_scnt.txt]] No term *Method #3, # DMRs **call Dmc according to hidden markov model with 3 hidden states: hyper/hypo/no_diff. **the states are determined by the difference of true methylation ratios bigger than some value. The default value is 0.2 20,124 esc_vs_ips [[File:dmr_M3_esc_vs_ips.txt]] GO Molecular function protein-arginine deiminase activity (Pathways common/BioCyc pathways) protein citrullination - 5 genes/11 regions: Padi1, Padi2, Padi3, Padi4, Padi6 15,550 esc_vs_scnt [[File:dmr_M3_esc_vs_scnt.txt]] GO Molecular function protein-arginine deiminase activity GO Biological process peptidyl-citrulline biosynthetic process from peptidyl-arginine (Pathways common/BioCyc pathways) protein citrullination - 5 genes/13 regions: Padi1, Padi2, Padi3, Padi4, Padi6 21 ips_vc_scnt [[File:dmr_M3_ips_vs_scnt.txt]] GO Biological Process negative regulation of vascular endothelial growth factor receptor signaling pathway negative regulation of cellular response to growth factor stimulus * The SCNTs appear to be more similar epigenetically to iPSCs than to ESCs. * I converted the DMR files to bed format and uploaded them to GREAT for enrichment analysis. For both sets of DMRs between esc and ips/scnt, the pathway that comes up is '''protein citrullination'''. * I looked up the term and found an interesting excerpt from Wikipedia: ** Citrullination is important because it controls the expression of genes, particularly in the developing embryo, and because the immune system often attacks citrullinated proteins, leading to autoimmune diseases such as rheumatoid arthritis and multiple sclerosis.
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