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Kellis M, et al.  (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423(6937):241-54

Abstract: Identifying the functional elements encoded in a genome is one of the principal challenges in modern biology. Comparative genomics should offer a powerful, general approach. Here, we present a comparative analysis of the yeast Saccharomyces cerevisiae based on high-quality draft sequences of three related species (S. paradoxus, S. mikatae and S. bayanus). We first aligned the genomes and characterized their evolution, defining the regions and mechanisms of change. We then developed methods for direct identification of genes and regulatory motifs. The gene analysis yielded a major revision to the yeast gene catalogue, affecting approximately 15% of all genes and reducing the total count by about 500 genes. The motif analysis automatically identified 72 genome-wide elements, including most known regulatory motifs and numerous new motifs. We inferred a putative function for most of these motifs, and provided insights into their combinatorial interactions. The results have implications for genome analysis of diverse organisms, including the human.

Status: Published Type: Journal Article PubMed ID: 12748633

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Number of different genes curated to this paper: 127

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AAT2 API2 ASA1 ASR1 ATG4 AUA1 AVT5 BLM10 BUD19 CAT5
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CBS1 CIN8 COG2 COQ3 CWC23 CYC2 DOC1 DPB2 ESS1 FIR1
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FOL1 FUN19 FUR1 FYV1 FYV12 FYV5 GAL1 GAL10 GCV3 GET2
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Topics Genes linked to topics (#31 - 40 )
GUS1 GWT1 HSP12 ICS3 INO1 ITR2 JIP4 KAE1 LSM8 LST7
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MDJ1 MDL2 MIA40 MPS3 MRPL13 MRPL36 MRPL49 MSC2 MSF1 NIT1
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NKP1 NPR2 OST2 PAN6 PDA1 PFF1 PGD1 PHA2 PML39 PPT2
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Topics Genes linked to topics (#61 - 70 )
PRS4 PSF3 PTK1 RDH54 RIM8 RMR1 RRP3 RRP46 RRP8 RTT102
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RXT2 SAF1 SCJ1 SCM3 SDL1 SEA4 SHM1 SMY2 SPG5 SRO9
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SRP72 SSZ1 STB1 STP1 SWC3 SWH1 TMA23 TSR2 UBP14 URH1
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Topics Genes linked to topics (#91 - 100 )
UTR5 VPS60 VPS61 VPS65 VPS69 VPS72 YAR044W YBL103C-A YBR075W YBR184W
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YCL007C YDL144C YDR474C YFL006W YFL042C YFL043C YGL046W YGR201C YIL165C YIL168W
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Topics Genes linked to topics (#111 - 120 )
YIM2 YIR014W YJL016W YJL017W YJL018W YKL199C YKR045C YLR012C YMR084W YMR085W
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Topics Genes linked to topics (#121 - 127 )
YMR268W-A YOR088W YOR238W YPR089W YPR090W YPT10 YVC1
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