Quite relevant to #transcriptome changes over #development: Earliest Transcribed… Genes Are Short, Newly Evolved…
http://www.cell.com/cell-reports/fulltext/S2211-1247(13)00788-2
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.
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came across this paper: http://genomebiology.com/content/11/2/R14, which uses GO for RNA-seq data analysis
looks interesting – GoSeq !
The RGASP papers are now out, back-to-back:
http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2722.html http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2714.html A tour de force.
.@markgerstein Both #rnaseq #RGASP papers list the “RGASP Consortium” as an author. But this comprises different people in the 2 papers!
Some notes from a senior author:
* Due to space constraints unfortunately most of the results are in the supplemental data.
* If it is helpful for testing updates to programs, or to compare the results against future methods not yet considered, the analysis code from each study is on GitHub: https://github.com/RGASP-Consortium.
* The papers are not open access, unfortunately.
http://www.nature.com/nsmb/journal/vaop/ncurrent/full/nsmb.2675.html
They say most editing sites identified by modENCODE are technical artifacts !
http://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.”
#Regression Methods for Decoding cis-Regulatory Logic, incl. interaction terms & non-linear sigmoidal relationships
http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000269