dictyNews Volume 41 Number 20

Published in

· 10 months ago

dictyNews 
Electronic Edition 
Volume 41, number 20 
September 18, 2015 

Please submit abstracts of your papers as soon as they have been 
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http://dictybase.org/db/cgi-bin/dictyBase/abstract_submit. 

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========= 
Abstracts 
========= 

Gene prioritization by compressive data fusion and chaining 

Marinka Žitnik, Edward A. Nam, Christopher Dinh, Adam Kuspa,  
Gad Shaulsky & Blaž Zupan 

University of Ljubljana, Ljubljana, Slovenia 
Baylor College of Medicine, Houston, TX, USA 

PLoS Comput. Biol. Accepted for publication 

Data integration procedures combine heterogeneous data sets  
into predictive models, but they are limited to data explicitly  
related to the target object type, such as genes. Collage is a  
new data fusion approach to gene prioritization. It considers  
data sets of various association levels with the prediction  
task, utilizes collective matrix factorization to compress the  
data, and chaining to relate different object types contained  
in a data compendium. Collage prioritizes genes based on their  
similarity to several seed genes. We tested Collage by  
prioritizing bacterial response genes in Dictyostelium as a  
novel model system for prokaryote-eukaryote interactions.  
Using 4 seed genes and 14 data sets, only one of which was  
directly related to the bacterial response, Collage proposed  
8 candidate genes that were readily validated as necessary  
for the response of Dictyostelium to Gram-negative bacteria.  
These findings establish Collage as a method for inferring  
biological knowledge from the integration of heterogeneous  
and coarsely related data sets. 

Submitted by Gad Shaulsky [gadi@bcm.edu]    
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[End dictyNews, volume 41, number 20]