~8%
http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004525
Posts Tagged ‘encode’
less than 10 percent of the human genome is functional
July 30, 2014Multiscale representation of genomic signals : Nature Methods : Nature Publishing Group
June 14, 2014Interesting but addressing mappability issue is key! Might want to also use a non-analytic stat test….
Compared to wavelets, non-independence betw. scales, perhaps key for allowing pruning.
Multiscale representation of #genomic signals. Fold changes & peaks at different scales; better expression prediction
http://www.nature.com/nmeth/journal/v11/n6/full/nmeth.2924.html
retroelement functional recruitment
May 12, 2014DUX4 binding to #retroelements creates promoters that are active… Highlights #chipseq binding sites in #repeats
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003947 http://www.ncbi.nlm.nih.gov/pubmed/?term=24278031
PLoS Genet. 2013 Nov;9(11):e1003947. doi:
10.1371/journal.pgen.1003947. Epub 2013 Nov 21.
DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis.
Young JM, Whiddon JL, Yao Z, Kasinathan B, Snider L, Geng LN, Balog J, Tawil R, van der Maarel SM, Tapscott SJ.
This synthetic yeast genome may reignite controversy regarding function of non-coding region
March 31, 2014Deletion of introns and other intergenic regions
Total Synthesis of a Functional Designer Eukaryotic Chromosome
http://www.sciencemag.org/content/early/2014/03/26/science.1249252
Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution
December 15, 2013QT:{{”
We found that ~15% of human codons are dual-use codons (“duons”) that simultaneously specify both amino acids and TF recognition sites. Duons are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias.
“}}
http://www.sciencemag.org/content/342/6164/1325.summary
http://www.sciencemag.org/content/342/6164/1367.abstract
Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions
December 6, 2013Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions
L Ward & M Kellis
http://www.sciencemag.org/content/337/6102/1675.abs
In general we know that conservation across species and within humans are correlated. In this paper the authors focus on emphasize the exceptions to this trend. They show that although only ~5% of the human genome is conserved across mammals, regulatory regions in an additional 4% of the genomes are conserved amongst humans. They also show that some elements are conserved across mammals but lack functional activity from ENCODE data and also do not show purifying selection amongst humans. The authors pinpoint regulatory regions near color vision and nerve-growth genes for that show human-specific constraint. This has been criticized in various publications since there are other genes that are higher up in the authors’ list but harder to explain for lineage-specific constraint.
The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line Nature. 2013 – PubMed – NCBI
October 12, 2013http://www.ncbi.nlm.nih.gov/pubmed/23925245
Contains a personal-genome like construction for HeLa
with 100X shotgun and then paired ends used for variant discovery and sequencing of pools of fosmid clones for haplotype resolution. Finally, low-freq. somatic and passage variants layered onto this.
Haplotype-resolved genome… of #HeLa: Has mapping of #ENCODE RNA- & chIP-seq against a personal genome
http://dx.doi.org/10.1038/nature12213 via @aemonten
Systematic identification of trans eQTLs as putative drivers of known disease associations
September 15, 2013http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2756.html
“They found SNPs that regulate one gene (Ikaros) in different cell types, meaning they found different cis-regulatory regions for a single gene, that map to different pathways…. they used the cell-type specific information from ENCODE data.”
FYI: Another Encode Commentary Paper
August 4, 2013Mattick & Dinger
The extent of functionality in the human genome
http://www.thehugojournal.com/content/7/1/2/
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