linkstream2 microblog

Signaling #hypergraphs
http://www.cell.com/trends/biotechnology/abstract/S0167-7799(14)00071-7 Edges from interactions of 2 sets of nodes. Better representation of assemblies & #complexes.

QT:{{”
each edge is defined not by interaction of 2 nodes (as in graphs), but 2 sets of nodes (known as hypernodes in hypergraphs)……The use of hypernodes also represents three concepts better than directed or non-directed graphs: protein complexes, protein assemblies and regulation (especially involving complexes/assemblies).
“}}

Signaling hypergraphs. Ritz et al. (2014) TIB

This opinion paper advocates the use of hypergraphs to complement graph-based signaling network and pathway analyses, where each edge is defined not by interaction of 2 nodes (as in graphs), but 2 sets of nodes (known as hypernodes in hypergraphs). They argue that
hypergraphs is a set-based method that acts like a more general version of a graph. The use of hypernodes also represents three concepts better than directed or non-directed graphs: protein complexes, protein assemblies and regulation (especially involving complexes/assemblies). They propose that hypergraphs can be very useful in situations where the effects of individual proteins might be neglected in graphs but will have a noticeable effect when these proteins are included in protein complexes as hypernodes. They use 3 applications as examples: pathway enrichment, pathway reconstruction, and pathway crosstalk.

http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3101.html

An interesting report of potential non-coding drivers without actually doing any wet lab work.

“These methods identify recurrent mutations in regulatory elements upstream of PLEKHS1, WDR74 and SDHD, as well as previously identified mutations in the TERT promoter”. In the text they mention “Khurana et al. also reported WDR74 promoter mutations in 2 of the 20 prostate cancer genomes analyzed”.

Nice viz of the quality of a single sequencing run
{Disclaimer I’m a consultant to this company.}

http://help.bina.com/demo/#/quality_report

Splicing changes along the blood lineage, good ex. of the
state-of-the-art in human transcriptomics
http://www.sciencemag.org/content/345/6204/1251033.abstract

Science 26 September 2014:
Vol. 345 no. 6204
DOI: 10.1126/science.1251033

Transcriptional diversity during lineage commitment of human blood progenitors

Chen et al.

They published a paper on a web tool to generate box plots !! http://www.nature.com/nmeth/journal/v11/n2/full/nmeth.2811.html QT:{{”
Despite the obvious advantages of the box plot for simultaneous representation of data set and statistical parameters, this method is not in common use, in part because few available software tools allow the facile generation of box plots. For example, the standard spreadsheet tool Excel is unable to generate box plots.
…
M.S. and J.W. conceived of the box plot tool
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Related:
http://bioinformatics.oxfordjournals.org/content/early/2014/01/21/bioinformatics.btu038.abstract

http://www.nature.com/nature/journal/v505/n7483/full/nature12981.html?WT.ec_id=NATURE-20140116

https://www.23andme.com/researchportal

http://www.npr.org/blogs/health/2014/09/09/342196432/by-the-numbers-search-nih-grant-data-by-institution

http://epigenomesportal.ca/ihec/grid.html

http://www.alivecor.com/home