Abstract:
:To enhance our knowledge regarding biological pathway regulation, we took an integrated approach, using the biomedical literature, ontologies, network analyses and experimental investigation to infer novel genes that could modulate biological pathways. We first constructed a novel gene network via a pairwise comparison of all yeast genes' Ontology Fingerprints--a set of Gene Ontology terms overrepresented in the PubMed abstracts linked to a gene along with those terms' corresponding enrichment P-values. The network was further refined using a Bayesian hierarchical model to identify novel genes that could potentially influence the pathway activities. We applied this method to the sphingolipid pathway in yeast and found that many top-ranked genes indeed displayed altered sphingolipid pathway functions, initially measured by their sensitivity to myriocin, an inhibitor of de novo sphingolipid biosynthesis. Further experiments confirmed the modulation of the sphingolipid pathway by one of these genes, PFA4, encoding a palmitoyl transferase. Comparative analysis showed that few of these novel genes could be discovered by other existing methods. Our novel gene network provides a unique and comprehensive resource to study pathway modulations and systems biology in general.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Qin T,Matmati N,Tsoi LC,Mohanty BK,Gao N,Tang J,Lawson AB,Hannun YA,Zheng WJdoi
10.1093/nar/gku678subject
Has Abstractpub_date
2014-10-01 00:00:00pages
e138issue
18eissn
0305-1048issn
1362-4962pii
gku678journal_volume
42pub_type
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