Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters

By Lani F. Wu, Timothy R. Hughes, A. Davierwala, Mark D. Robinson, R. Stoughton, Steven J. Altschuler. Nature Genetics, 2002

373 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1c274fbc84c20ed0246b5b54144678bbfdee55f4

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Citations in the corpus

Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks (2005, background): “Analyses of gene coexpression [3-7] have demonstrated that clusters with similar overall expression are often enriched for genes with similar functions, consistent with the hypothesis of modularly-behaving gene programs, where sets of genes are activated in concert to carry out functions.”
Exploration of essential gene functions via titratable promoter alleles. (2004, neutral): “…that for surveying all relationships among gene classes and have been compiled on a subset of yeast essential genes features in the data set (Wu et al., 2002; Gasch and (Rout et al., 2000; Uetz et al., 2000; Ito et al., 2001; Gavin Eisen, 2002) and it does not automatically determine et…”
Comparative Genomics in Eukaryotes (2005, background): “, 2001) can predict only general functional interactions (Noordewier and Warren, 2001; Wu et al., 2002).”
GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function (2008, methodology): “number of previously uncharacterized genes using the socalled 'guilt-by-association' principle [10-12].”
Topological structure analysis of the protein-protein interaction network in budding yeast. (2003, methodology): “As an isolated quasi-clique may involve different functional categories, P-values (27,28) are used as criteria to assign each quasi-clique a main function.”
Ribosome assembly in eukaryotes. (2003, background): “Depletion of Rrp12 leads to a decrease of the 18S (Wu et al., 2002) suggesting that this protein is essential for the maturation of the small ribosomal subunit.”
Mutations in SBDS are associated with Shwachman–Diamond syndrome (2003, methodology): “YLR022c has been clustered with genes encoding RNA-processing enzymes on the basis of microarray expression profile analysi”
Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors (2003, background): “Results Clustering of genes based on segregating variation Correlation in expression among genes across a set of perturbations is now commonly used to define groups of genes with putative common functio”
FunSpec: a web-based cluster interpreter for yeast (2002, background): “Interpretation of large-scale data types, however, often requires a rapid means to access and present information on large numbers of genes simultaneously [4,5].”
Alternative splicing: new insights from global analyses. (2006, background): “Indeed, this property of transcriptionally coregulated genes has been used to successfully predict the functions of unannotated genes (Wu et al., 2002; Zhang et al., 2004).”
Defining transcription modules using large-scale gene expression data (2004, background): “For example, such data can be used to provide functional links for uncharacterized genes (Hughes et al., 2000b; Ihmels et al., 2002; Tavazoie et al., 1999; Wu et al., 2002), to predict novel cis-regulatory elements (Bussemaker et al.”
Functional Divergence of Duplicated Genes Formed by Polyploidy during Arabidopsis Evolution (2004, background): “Because genes with highly similar expression patterns (r $ 0.7) are probably coregulated, they are likely to be involved in the same biological pathway (Wu et al., 2002).”
Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes (2013, background): “Many successful approaches have been developed for prediction of protein function and pathway membership [1–6], however they rely on prior knowledge in the organism of interest to make new predictions (i.”
Penalized Model-Based Clustering with Application to Variable Selection (2007, background): “Clustering gene expression profiles has become a popular approach for both gene function prediction and discovery (Eisen et al., 1998; Wu et al., 2002; Zhou et al., 2002; Xiao and Pan, 2005).”