FUSE: a profit maximization approach for functional summarization of biological networks.

PubMed

Seah, Boon-Siew; Bhowmick, Sourav S; Dewey, C Forbes; Yu, Hanry

2012-03-21

The availability of large-scale curated protein interaction datasets has given rise to the opportunity to investigate higher level organization and modularity within the protein interaction network (PPI) using graph theoretic analysis. Despite the recent progress, systems level analysis of PPIS remains a daunting task as it is challenging to make sense out of the deluge of high-dimensional interaction data. Specifically, techniques that automatically abstract and summarize PPIS at multiple resolutions to provide high level views of its functional landscape are still lacking. We present a novel data-driven and generic algorithm called FUSE (Functional Summary Generator) that generates functional maps of a PPI at different levels of organization, from broad process-process level interactions to in-depth complex-complex level interactions, through a pro t maximization approach that exploits Minimum Description Length (MDL) principle to maximize information gain of the summary graph while satisfying the level of detail constraint. We evaluate the performance of FUSE on several real-world PPIS. We also compare FUSE to state-of-the-art graph clustering methods with GO term enrichment by constructing the biological process landscape of the PPIS. Using AD network as our case study, we further demonstrate the ability of FUSE to quickly summarize the network and identify many different processes and complexes that regulate it. Finally, we study the higher-order connectivity of the human PPI. By simultaneously evaluating interaction and annotation data, FUSE abstracts higher-order interaction maps by reducing the details of the underlying PPI to form a functional summary graph of interconnected functional clusters. Our results demonstrate its effectiveness and superiority over state-of-the-art graph clustering methods with GO term enrichment.

How do Kakortokites form? Additional evidence from the Ilimaussaq Complex, S. Greenland

NASA Astrophysics Data System (ADS)

Hunt, E. J.; Finch, A. A.; Donaldson, C. H.

2012-04-01

The Ilímaussaq Complex, South Greenland, contains some of the most evolved igneous rocks in the world and is widely considered to represent one of the largest deposits of rare-earth elements, Ta, Nb and Zr. Our work is focused on the kakortokite layered series at the base of the complex. The layered series is composed of 29 repetitive 3-layer units (named -11 to +17, Bohse et al. 1971), successively enriched in arfvedsonite, eudialyte and nepheline. Despite a large body of work on the development of the kakortokite series, no consensus on the process/processes that produced the layering has been forthcoming. We present the preliminary findings of a combined petrographical, quantitative textural and geochemical analysis on the kakortokite series, initially focused on layer 0. Although many of the hypotheses for the formation of these rocks invoke a pressure change, the enrichment of the series in volatile constituents (CH4 and H; Konnerup-Madsen, 2001) has led many authors to suggest crystallisation occurred in a closed system, with processes of gravitational settling formed the layering. Crystal size distribution (CSD) analysis, performed on hand-digitised photomicrographs, provides insight into processes of crystal nucleation and growth. The results indicate that simple cumulate settling is untenable for layer 0. Instead the plot gradients indicate that the arfvedsonite in the black kakortokite crystallised in situ above a sharp boundary to the white kakortokite. The CSD plots for the alkali feldspars indicate secondary nucleation occurred, with the small crystal size fraction forming in situ. The feldspar phenocrysts also exhibit embayment textures indicating partial resorption. These graphs are consistent with a model whereby an influx of hotter magma results in the partial thermal erosion of the underlying white kakortokite, followed by in situ crystallisation of arfvedsonite above the melt infiltration boundary, followed by in situ crystallisation of eudialyte. Then nepheline and alkali feldspar crystallised through multiple modes of nucleation, developing the characteristic layering. Geochemical trends described by Pfaff et al. (2008) support an open system replenishment model during the formation of layer 0, and potentially also layers +4 and +8. To further this work we intend to apply this combined approach to investigate the formation of individual layers, scaling these processes into a model for the development of the Ilímaussaq complex. Bohse et al. (1971). Rapport Grønlands Geologiske Undergesølgelse, 36, 43 pp. Konnerup-Madsen (2001). Geology Greenland Surv. Bull., 190, 159-166. Pfaff et al. (2008). Lithos, 106, 280-296.