2005
DOI: 10.1038/nsmb891
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Exploring functional relationships between components of the gene expression machinery

Abstract: Eukaryotic gene expression requires the coordinated activity of many macromolecular machines including transcription factors and RNA polymerase, the spliceosome, mRNA export factors, the nuclear pore, the ribosome and decay machineries. Yeast carrying mutations in genes encoding components of these machineries were examined using microarrays to measure changes in both pre-mRNA and mRNA levels. We used these measurements as a quantitative phenotype to ask how steps in the gene expression pathway are functionall… Show more

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Cited by 92 publications
(103 citation statements)
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“…Both Npl3 ) and Sac3 (Lei et al 2003) were also obtained as interactors with TAF9, suggesting that transcription is coupled to mRNA processing and mRNA export, consistent with current notions of nuclear organization and function (Maniatis and Reed 2002). On the basis of the regulatory integration predicted (Maniatis and Reed 2002), and the large number of proteins known to be involved in both mRNA processing and mRNA export (Burckin et al 2005), we might have imagined more hits between TAF9 and genes in these categories. Nevertheless, four hits were obtained in genes encoding proteins with functions involved in nuclear transport, including Mog1, Soy1, Msn5, and Nup188.…”
Section: Caf40 Cdc40 Loc1mentioning
confidence: 56%
“…Both Npl3 ) and Sac3 (Lei et al 2003) were also obtained as interactors with TAF9, suggesting that transcription is coupled to mRNA processing and mRNA export, consistent with current notions of nuclear organization and function (Maniatis and Reed 2002). On the basis of the regulatory integration predicted (Maniatis and Reed 2002), and the large number of proteins known to be involved in both mRNA processing and mRNA export (Burckin et al 2005), we might have imagined more hits between TAF9 and genes in these categories. Nevertheless, four hits were obtained in genes encoding proteins with functions involved in nuclear transport, including Mog1, Soy1, Msn5, and Nup188.…”
Section: Caf40 Cdc40 Loc1mentioning
confidence: 56%
“…4 and 5) (21)(22)(23)(24)(25). This observation may explain in part why microarray data combined with SVM analysis recognized an rrp6⌬ phenotype consistent with transcriptional defects, rather than decay (8).…”
Section: A New Class Of Rna Transcripts With An Uncertain Relationshimentioning
confidence: 85%
“…Gaussian processes are examples of kernel machines (28). These methods have been used successfully in a variety of applications (29)(30)(31), including prediction on MR images (32), using application-specific kernels. A gaussian process is defined by a mean function, m : P1R, and a covariance or kernel function, k : P · P1R.…”
Section: Pattern Recognition With Gaussian Processesmentioning
confidence: 99%