linkstream2 microblog

Gene-gene & gene-env interactions…by #transcriptome…in twins by @dermitzakis lab
http://www.nature.com/ng/journal/v47/n1/full/ng.3162.html Nice model for ASE HT @cjieming

Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins
Alfonso Buil, Andrew Anand Brown, Tuuli Lappalainen, Ana Viñuela, Matthew N Davies, Hou-Feng Zheng, J Brent Richards, Daniel Glass, Kerrin S Small, Richard Durbin, Timothy D Spector & Emmanouil T Dermitzakis

http://www.nature.com/ng/journal/v47/n1/full/ng.3162.html

http://www.ncbi.nlm.nih.gov/pubmed/25477383

also
http://www.ncbi.nlm.nih.gov/pubmed/25477383
Nucleic Acids Res. 2015 Feb 27;43(4):e23. doi: 10.1093/nar/gku1252. Epub 2014 Dec 3.
Allele-specific copy number profiling by next-generation DNA sequencing. Chen H1, Bell JM2, Zavala NA2, Ji HP2, Zhang NR3.

perhaps related?

http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3222.html

Nat Genet. 2015 Mar 2. doi: 10.1038/ng.3222. [Epub ahead of print]

Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance.

Crowley JJ1, Zhabotynsky V1, Sun W2, Huang S3, Pakatci IK3, Kim Y1, Wang JR3, Morgan AP4, Calaway JD4, Aylor DL1, Yun Z1, Bell TA4, Buus RJ4, Calaway ME4, Didion JP4, Gooch TJ4, Hansen SD4, Robinson NN4, Shaw GD4, Spence JS1, Quackenbush CR1, Barrick CJ1, Nonneman RJ1, Kim K5, Xenakis J5, Xie Y1,Valdar W6, Lenarcic AB1, Wang W3, Welsh CE3, Fu CP3, Zhang Z3, Holt J3, Guo Z3, Threadgill DW7, Tarantino LM8, Miller DR4, Zou F5, McMillan L3, Sullivan PF9, Pardo-Manuel de Villena F4.

http://www.nature.com/ng/journal/v47/n4/full/ng.3222.html

Carefully controlled allele expt – hets midway in expr betw homs for parents for 76pct (additive model) but 25pct hets diff. from parents

ASE in…divergent mouse crosses identifies pervasive allelic imbalance, 80%, w/ 60% closely following additive model
http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3222.html

Genome sequence-independent identification of #RNA editing
siteshttp://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3314.html GIREMI uses LD to separate edit sites from #SNPs

Qing Zhang
& Xinshu Xiao

Nature Methods (2015) doi:10.1038/nmeth.3314Received

Analysis of high-throughput B-cell sequencing
http://www.pnas.org/content/early/2015/02/05/1417683112.abstract Successful locus-level application of #personalgenome construction

WASP: allele-specific software for robust discovery of molecular quantitative trait loci
Bryce van de Geijn, Graham McVicker, Yoav Gilad, Jonathan Pritchard

doi: http://dx.doi.org/10.1101/011221
http://biorxiv.org/content/early/2014/11/07/011221

QT:{{”
Mapping of reads to a reference genome is biased by sequence polymorphisms6. Reads which contain the non-reference allele may fail to map uniquely or map to a different (incorrect) location in the genome6.
“}}

http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3162.html

Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins

Alfonso Buil,
Andrew Anand Brown,
Tuuli Lappalainen,
Ana Viñuela,
Matthew N Davies,
Hou-Feng Zheng,
J Brent Richards,
Daniel Glass,
Kerrin S Small,
Richard Durbin,
Timothy D Spector
& Emmanouil T Dermitzakis

QT:{{”
We discovered abundant (12 to 24%) monoallelic expression of autosomal genes and that expression of the two alleles occurs independently. The monoallelic expression appeared random and dynamic because there was considerable variation among closely related embryonic cells. “}}

Call for… analysis papers: nice description of hypothesis generation v. validation & 3 types of #network robustness
http://www.nature.com/ng/journal/v46/n3/full/ng.2914.html

Call for data analysis papers
Nature Genetics 46, 213 (2014) doi:10.1038/ng.2914Published online 26 February 2014
Deadline expired but maybe still relevant…

QT:{{”
We discovered abundant (12 to 24%) monoallelic expression of autosomal genes and that expression of the two alleles occurs independently. The monoallelic expression appeared random and dynamic because there was considerable variation among closely related embryonic cells. Similar patterns of monoallelic expression were observed in mature cells. Our allelic expression analysis also demonstrates the de novo inactivation of the paternal X chromosome.
“}}

http://www.sciencemag.org/content/343/6167/193.full