linkstream2 microblog

#Network Legos: Building Blocks of Cellular Wiring Diagrams
http://online.liebertpub.com/doi/abs/10.1089/cmb.2007.0139 Active subnets from protein interactions & co-expression

This paper describes a top-down, set-theoretic approach to comparing gene expression network dynamics under multiple conditions. The method takes an input “wiring diagram” of gene interactions as well as gene expression datasets, which are used to derive interaction profiles composed of enriched genes. Sets of these interaction profiles are used to identify statistically significant “network blocks”
representing network modules underlying the various enriched profiles. These blocks are then organized in a directed acyclic graph in order to identify “network legos”, which represent the most fundamental building blocks of the enriched gene expression networks. The authors demonstrate the utility of the method by identifying a differentially enriched pathway in various forms of leukemia and finding common network modules activated by two human cell types in response to different cellular stresses.

http://online.liebertpub.com/doi/abs/10.1089/cmb.2007.0139

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://arxiv.org/abs/1309.6001

Structural networks of signaling pathways
http://www.sciencedirect.com/science/article/pii/S0959440X1200070X Prism on IL10 #networks, mapping on Cosmic, disrupting mutations as drivers

Target Essentiality… Characterizes Drug Side Effects – much more so than the total number of targets for a #drug
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.100311

Pavlidis mentions: …Multifunctional Genes…
http://www.plosone.org/article/info%253Adoi%252F10.1371%252Fjournal.pone.0017258 … hubbiness predicts these better than more complex methods #ismb #afp14

Rosvall, Martin, and Carl T. Bergstrom. “An information-theoretic framework for resolving community structure in complex networks.” Proceedings of the National Academy of Sciences 104.18 (2007): 7327-7331.

Info-theoretic framework for… community structure in complex #networks. Compression v modularity, former better?
http://www.pnas.org/content/104/18/7327.short

Inferring… #Networks Using Probabilistic Graphical Models. Nice intro to #Bayesian methods, useful for #teaching
http://www.sciencemag.org/content/303/5659/799.abs

Citi #Bike Rides 9/17/2013. Great #visualization of daily #network dynamics. Neat if applicable to cellular networks
http://vimeo.com/89305412

PARADIGM-SHIFT predicts… function of mutations in… #cancers using pathway[s]. #Network-based gene prioritization
http://bioinformatics.oxfordjournals.org/content/28/18/i640