A flexible representation of omic knowledge for thorough analysis of microarray data

Plant Methods
Yoshikazu HasegawaTetsuro Toyoda

Abstract

In order to understand microarray data reasonably in the context of other existing biological knowledge, it is necessary to conduct a thorough examination of the data utilizing every aspect of available omic knowledge libraries. So far, a number of bioinformatics tools have been developed. However, each of them is restricted to deal with one type of omic knowledge, e.g., pathways, interactions or gene ontology. Now that the varieties of omic knowledge are expanding, analysis tools need a way to deal with any type of omic knowledge. Hence, we have designed the Omic Space Markup Language (OSML) that can represent a wide range of omic knowledge, and also, we have developed a tool named GSCope3, which can statistically analyze microarray data in comparison with the OSML-formatted omic knowledge data. In order to test the applicability of OSML to represent a variety of omic knowledge specifically useful for analysis of Arabidopsis thaliana microarray data, we have constructed a Biological Knowledge Library (BiKLi) by converting eight different types of omic knowledge into OSML-formatted datasets. We applied GSCope3 and BiKLi to previously reported A. thaliana microarray data, so as to extract any additional insights from the data. A...Continue Reading

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Citations

Jul 18, 2008·Briefings in Functional Genomics & Proteomics·Arjun Krishnan, Andy Pereira
Jun 27, 2020·International Journal of Molecular Sciences·Hui WangPeisheng Mao

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Methods Mentioned

BETA
comprehensive

Software Mentioned

OSML Editor
Omic Space Markup Language ( OSML )
AraCyc
OSML
BL
Genome Superhighway ( GPS )
SOM
TraitMap
TraitMap system
JAVA

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