Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting

By P. Cliften, P. Sudarsanam, Ashwin Desikan, L. Fulton, B. Fulton, J. Majors, R. Waterston, B. Cohen, M. Johnston. Science, 2003

917 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/33acb5e7fca584398c5398aad735089868c318a9

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Citations in the corpus

The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. (2005, background): “For the moment we have excluded the four other sequenced Saccharomyces sensu stricto species (Cliften et al. 2003; Kellis et al. 2003) because their gene orders are almost completely collinear with S. cerevisiae .”
Identification and distinct regulation of yeast TATA box-containing genes. (2004, methodology): “S. kudriavzevii, and S. mikatae were from Cliften et al. (2003).”
Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms (2004, methodology): “The genomes of S.mikatae , S.bayanus , S.kudriavzevii , S.castellii and S.kluyveri were sequenced at 2–4 3 coverage by Mark Johnston’s group at Washington University (3).”
Exploring genetic interactions and networks with yeast (2007, background): “As the roster of ORFs has been revised, largely through sequencing of evolutionarily related yeast specie”
Comparative Genomics in Eukaryotes (2005, methodology): “The second method is ‘phylogenetic footprinting’, in which conserved sequences among multiple species in noncoding DNA can indicate regulatory sites (Cliften et al., 2003).”
CYGD: the Comprehensive Yeast Genome Database (2004, background): “All these data as well as results from comparative analysis of completely sequenced genomes are used to reﬁne the gene calls on S.cerevisiae in the CYGD database (4,5,28,29).”
Genome evolution in yeasts (2004, background): “cerevisiae (the sensu stricto group), plus one more distant species, Saccharomyces kluyveri , in order to identify conserved regulatory element”
From signatures to models: understanding cancer using microarrays (2005, background): “…overexpressed when Jun-B is underexpressed, consistent with reports suggesting that loss of Jun-B activity enabled epithelial mesenchymal transition in tumors 66 . promoter sequences, on the basis of experimentally determined sites 16 , de novo identification or evolutionary conservation 17,18 .”
Plant cytochrome P450s from moss to poplar (2006, background): “Fungal genomes are also accumulating with the goal of comparative genomics of highly similar genomes, as in six species of Saccharomyces: S. cerevisiae, S. mikatae, S. kudriavzevii, S. bayanus, S. castellii, and S. kluyveri (Kellis et al. 2003; Cliften et al. 2003).”
Estimating the tempo and mode of gene family evolution from comparative genomic data. (2005, background): “Of the 1254 gene families that differed in number between genomes, 58 had P -values 0.01 (35 are expected).”
Global analysis of protein localization in budding yeast (2003, background): “Subcellular localization of yeast proteins The 4,156 proteins for which we defined subcellular localizations in the GFP library represent 75% of the yeast proteom”
PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny (2005, methodology): “kudriavzevii we used data from the Washington University group [15].”
Computational prediction of transcription-factor binding site locations (2003, methodology): “They limited themselves to comparing four sensu stricto species: S. cerevisiae, S. para-doxus , S. mikatae , and S. bayanus ; there was an overlap of three species with the eight species examined by the John-ston group [97].”