Dinh/Dinh 2014/NOTES/2014-4-1: Difference between revisions
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>Dinh (Created page with "=DMR finding with MOdel-based Analysis of Bisulfite Sequencing data (MOABS)= * Using only the mcomp module from the MOABS pipeline requires: 1. setting LC_ALL variable with:...") |
>Dinh mNo edit summary |
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esc versus scnt | esc versus scnt | ||
ipsc versus scnt | ipsc versus scnt | ||
* MOABS commands: | |||
/home/dinh/softwares/moabs-v1.2.7.src.x86_64_Linux.data/bin/mcomp -r merged.esc.$c.G.bed -r merged.scnt.$c.G.bed -c moabs.esc_scnt.$c -l esc.$c scnt.$c | |||
/home/dinh/softwares/moabs-v1.2.7.src.x86_64_Linux.data/bin/mcomp -r merged.esc.$c.G.bed -r merged.ips.$c.G.bed -c moabs.esc_ips.$c -l esc.$c ips.$c | |||
/home/dinh/softwares/moabs-v1.2.7.src.x86_64_Linux.data/bin/mcomp -r merged.ips.$c.G.bed -r merged.scnt.$c.G.bed -c moabs.ips_scnt.$c -l ips.$c scnt.$c | |||
* Results: | |||
Method #1, # DMRs | |||
22,125 esc_vs_ips | |||
22,135 esc_vs_scnt | |||
709 ips_vs_scnt | |||
Method #2, # DMRs | |||
19,799 esc_vs_ips | |||
15,318 esc_vs_scnt | |||
53 ips_vc_scnt | |||
Method #3, # DMRs | |||
20,124 esc_vs_ips | |||
15,550 esc_vs_scnt | |||
21 ips_vc_scnt | |||
* The SCNTs appear to be more similar epigenetically to iPSCs than to ESCs. | |||
* I converted the DMR files to bed format and uploaded them to GREAT for enrichment analysis. For both sets of DMRs between esc and ips/scnt, the pathway that comes up is '''protein citrullination'''. It appears that the DMRs have many overlaps. | |||
* I looked up the term and found an interesting excerpt from Wikipedia: | |||
** Citrullination is important because it controls the expression of genes, particularly in the developing embryo, and because the immune system often attacks citrullinated proteins, leading to autoimmune diseases such as rheumatoid arthritis and multiple sclerosis. |
Revision as of 18:19, 2 April 2014
DMR finding with MOdel-based Analysis of Bisulfite Sequencing data (MOABS)
- Using only the mcomp module from the MOABS pipeline requires:
1. setting LC_ALL variable with: export LC_ALL=C 2. installing RInside for R. Open R and type: install.packages("RInside")
- The input for mcomp is a G.bed file (ie), more detailed explanation see the MOABS documentations.
#chrom start end ratio totalC methC strand next Plus tcP mcP Minus tcM mcM chr5 3009585 3009587 1 1 1 - G + 0 0 - 1 1 chr5 3011471 3011473 0.711 45 32 B G + 28 18 - 17 14
Analysis of mouse WGBS
- Prepare the G.bed files with methylFreq2Gbed.pl (genome-miner)
/home/dinh/scripts/methylFreq2GBED.pl 1 < [methylFreq] > [BED name]
- We perform 3 tests:
esc versus ipsc esc versus scnt ipsc versus scnt
- MOABS commands:
/home/dinh/softwares/moabs-v1.2.7.src.x86_64_Linux.data/bin/mcomp -r merged.esc.$c.G.bed -r merged.scnt.$c.G.bed -c moabs.esc_scnt.$c -l esc.$c scnt.$c /home/dinh/softwares/moabs-v1.2.7.src.x86_64_Linux.data/bin/mcomp -r merged.esc.$c.G.bed -r merged.ips.$c.G.bed -c moabs.esc_ips.$c -l esc.$c ips.$c /home/dinh/softwares/moabs-v1.2.7.src.x86_64_Linux.data/bin/mcomp -r merged.ips.$c.G.bed -r merged.scnt.$c.G.bed -c moabs.ips_scnt.$c -l ips.$c scnt.$c
- Results:
Method #1, # DMRs 22,125 esc_vs_ips 22,135 esc_vs_scnt 709 ips_vs_scnt Method #2, # DMRs 19,799 esc_vs_ips 15,318 esc_vs_scnt 53 ips_vc_scnt
Method #3, # DMRs 20,124 esc_vs_ips 15,550 esc_vs_scnt 21 ips_vc_scnt
- 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. It appears that the DMRs have many overlaps.
- 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.