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Steven Roberts add three multi-oyster DMRs
almost 9 years ago
Commit id: 964a1f6858b2a5e0ce79540a26d174fa8daf19ef
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...
6 | 7645 | 4044 | 53 | 9
In order to examine regions that were differentially methylated
across all three multiple oysters,
features feature were identified where there
were was at least
3 three adjacent
probes with significantly differentially methylated. A total of 111 features
that were
identified as hypomethylated and 54 features as hypermethylated when differentially methylated probe with 100bp were merged. present in at least two individuals. The specific locations are
```
scaffold481 576986 578532 -3
scaffold247 141885 142442 -3
scaffold1518 212680 213736 -3
scaffold853 46186 46496 -2
scaffold406 419330 419384 -2
scaffold406 419005 419060 -2
scaffold406 418360 418767 -2
scaffold394 555813 556224 -2
scaffold247 144031 144583 -2
scaffold242 75918 76344 -2
scaffold142 656144 656735 -2
scaffold12 243960 244376 -2
scaffold257 1235165 1235481 +2
```
With twelve features hypomethylated and one feature hypermethylated.
Going down the list, _scaffold418_576986_ is a feature that overlaps gene EKC36328, [_Bromodomain-containing protein 8_](http://www.uniprot.org/uniprot/K1QRE8). Specifically the location is in the intron between exon 18 and 19 (total of 20 exons). This gene is differentially expressed, that is expressed at an elevated level following heat shock.
"The precise function of the domain is unclear, but it may be involved in protein-protein interactions and may play a role in assembly or activity of multi-component complexes involved in transcriptional activation [PMID: 7580139]."
![scaffold418_576986](./figures/scaffold481_576986.png)
---
Another DMR that is consistent across oysters is located within the intron of [_Homeobox protein LOX2_](http://www.uniprot.org/uniprot/K1RXD0). Homeobox are transcription factors often associated with developmental processes.
![scaffold247_141885](./figures/scaffold247_141885.png)
---
Significant hypomethylation is also present within the intron of [Tenascin](http://www.uniprot.org/uniprot/K1PZ30), a glycoprotein expressed in the extracellular matrix during stress.
![scaffold1518_212680](./figures/scaffold1518_212680.png)