ArticleNucleic acids research2014
Finding pathway-modulating genes from a novel Ontology Fingerprint-derived gene network.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
8 citing papers in PubMed, 16 citations in OpenAlex.
- A knowledge empowered explainable gene ontology fingerprint approach to improve gene functional explication and prediction.iScience · 2023Article
- Evidence for craniofacial enhancer variation underlying nonsyndromic cleft lip and palate.Human genetics · 2020Article
- Article
- Gene fingerprint model for literature based detection of the associations among complex diseases: a case study of COPD.BMC medical informatics and decision making · 2019Article
- Article
- A Multi-Parameter Analysis of Cellular Coordination of Major Transcriptome Regulation Mechanisms.Scientific reports · 2018Article
- A statistical framework for biomedical literature mining.Statistics in medicine · 2017Article
- Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature.Database : the journal of biological databases and curation · 2015Article
Corrections and comments
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Authors and funding
9 authors at 6 institutions in 2 countries.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.