OpenSea specifications

Information


Unique identifier OMICS_14296
Name OpenSea
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Srinivasa Nagalla <>

Publication for OpenSea

OpenSea in publications

 (12)
PMCID: 5902929
PMID: 29686738
DOI: 10.1186/s13148-018-0487-y

[…] dmps identified according to their location relative to cpg islands (cgi) and promoter regions is represented in fig. . the majority of the differentially hypomethylated cpgs in an are located in opensea (78.08%), outside gene promoters, within regions with no enrichment in cpg content followed by cgi-shore (10.23%), cgi-shelf (7.50%), and cgi (4.19%)., dna hypomethylation was the first […]

PMCID: 5478666
PMID: 28634372
DOI: 10.1038/s41598-017-03682-0

[…] to a cpg island (cgi), we used the following categories: island (cgi), s_shore and n_shore (up to 2 kb up- and downstream of the cgi), s_shelf and n_shelf (2–4 kb up- and downstream of the cgi), opensea (all others). when analysing the correlation between dna methylation and gene expression, tss1500, tss200, 5′ utr and first exon were grouped as the ‘5’ region’, whereas gene body and 3′ utr […]

PMCID: 4916993
PMID: 27347385
DOI: 10.5256/f1000research.9514.r14245

[…] na <na> na chr8:61822358-61823028 ## cg25015733 na <na> na chr2:99346882-99348177 ## cg21179654 na <na> na ## relation_to_island ## cg07499259 opensea ## cg26992245 opensea ## cg09747445 n_shore ## cg18808929 s_shelf ## cg25015733 n_shelf ## cg21179654 opensea ## ucsc_refgene_name ## cg07499259 tnfrsf8;tnf […]

PMCID: 5043275
PMID: 27686527
DOI: 10.1038/srep34460

[…] such as cpg island, which is usually more than 200 bp containing >50% gc and observed/expected cpg ratio >60%. a shore is up to 2 kb from cpg island, a shelf is 2–4 kb from cpg island and opensea are isolated cpgs in the genome. dna methylation sites with different genome features can play different roles in gene expression. thus, the genome features of the identified dmps were first […]

PMCID: 5043230
PMID: 27687697
DOI: 10.1038/srep34220

[…] enriched for dmps. we found cgi status of hypermethylated and hypomethylated dmps to be significantly different compared to all cpgs on the array. hypermethylated dmps were more often located in the opensea or the n-shelf region, and the hypomethylated dmps were enriched for the s-shore and n-shore. at present, we do not know if the enrichment can be attributed to the particular design […]


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OpenSea institution(s)
Department of Pediatrics, Department of Public Health & Preventive Medicine, and School of Dentistry, Oregon Health & Sciences University, Portland, OR, USA; Oregon National Primate Research Center, Oregon Health & Sciences University, Beaverton, OR, USA
OpenSea funding source(s)
This work was supported by National Institute of Health Grants U19ES11384 and U24DK5870.

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