دورية أكاديمية
أعرض في EDS

Finding pathway-modulating genes from a novel Ontology Fingerprint-derived gene network.

التفاصيل البيبلوغرافية
العنوان: Finding pathway-modulating genes from a novel Ontology Fingerprint-derived gene network.
المؤلفون: Qin T; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA., Matmati N; The Stony Brook University Cancer Center and the Department of Medicine, Stony Brook, NY 11794, USA., Tsoi LC; Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA., Mohanty BK; Department of Biochemistry & Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA., Gao N; Department of Computer Science and Engineering, University of South Carolina, Columbia, SC 29208, USA., Tang J; Department of Computer Science and Engineering, University of South Carolina, Columbia, SC 29208, USA Tianjin Key Laboratory of Cognitive Computing and Application, Tianjin University, Tianjin, China., Lawson AB; Department of Public Health Science, Medical University of South Carolina, Charleston, SC 29425, USA., Hannun YA; The Stony Brook University Cancer Center and the Department of Medicine, Stony Brook, NY 11794, USA., Zheng WJ; School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA wenjin.j.zheng@uth.tmc.edu.
المصدر: Nucleic acids research [Nucleic Acids Res] 2014 Oct; Vol. 42 (18), pp. e138. Date of Electronic Publication: 2014 Jul 24.
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural
اللغة: English
بيانات الدورية: Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE
أسماء مطبوعة: Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.
مواضيع طبية MeSH: Gene Ontology* , Gene Regulatory Networks*, Bayes Theorem ; Genes, Fungal ; Metabolic Networks and Pathways/genetics ; PubMed ; Sphingolipids/metabolism ; Yeasts/genetics ; Yeasts/metabolism
مستخلص: 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.
(© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.)
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معلومات مُعتمدة: P20 RR017677-10 United States RR NCRR NIH HHS; 1 R56 LM010680 United States LM NLM NIH HHS; R01GM063265-09S1 United States GM NIGMS NIH HHS; 5-T15-LM007438-02 United States LM NLM NIH HHS; 5P20RR017696-05 United States RR NCRR NIH HHS; T32GM074934 07 United States GM NIGMS NIH HHS; R37 GM043825 United States GM NIGMS NIH HHS; R01GM063265 United States GM NIGMS NIH HHS
المشرفين على المادة: 0 (Sphingolipids)
تواريخ الأحداث: Date Created: 20140727 Date Completed: 20150115 Latest Revision: 20211021
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC4191379
DOI: 10.1093/nar/gku678
PMID: 25063300
قاعدة البيانات: MEDLINE
الوصف
تدمد:1362-4962
DOI:10.1093/nar/gku678