SGD: Saccharomyces Genome Database

Cherry, J. Michael; Adler, Caroline; Ball, Catherine A.; Chervitz, Stephen A.; Dwight, Selina S.; Hester, Erich T.; Jia, Yankai; Juvik, Gail; Roe, Taiyun; Schroeder, Mark; Weng, Shuai; Botstein, David

doi:10.1093/nar/26.1.73

Cited by 983 publications

(750 citation statements)

References 24 publications

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“…To directly compare the yeast and human stress response datasets, we used a BLAST-based method to find candidate orthologues between the ENSEMBLpredicted human gene set (Hubbard et al, 2002) and the SGD yeast-predicted protein set (Cherry et al, 1998). We calculated pairwise alignment scores between each yeast-human gene pair by using the WU-BLAST software package (http://blast.wustl.edu) with the options "-postsw -wordmask SEG -W4 -T20 -Z ϭ 1000000000 -lcmask -topcomboN 1."…”

Section: Comparison Of Expression In Yeast-human Homologuesmentioning

confidence: 99%

Diverse and Specific Gene Expression Responses to Stresses in Cultured Human Cells

Murray

Whitfield

Trinklein

et al. 2004

MBoC

275

236

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We used cDNA microarrays in a systematic study of the gene expression responses of HeLa cells and primary human lung fibroblasts to heat shock, endoplasmic reticulum stress, oxidative stress, and crowding. Hierarchical clustering of the data revealed groups of genes with coherent biological themes, including genes that responded to specific stresses and others that responded to multiple types of stress. Fewer genes increased in expression after multiple stresses than in free-living yeasts, which have a large general stress response program. Most of the genes induced by multiple diverse stresses are involved in cell-cell communication and other processes specific to higher organisms. We found substantial differences between the stress responses of HeLa cells and primary fibroblasts. For example, many genes were induced by oxidative stress and dithiothreitol in fibroblasts but not HeLa cells; conversely, a group of transcription factors, including c-fos and c-jun, were induced by heat shock in HeLa cells but not in fibroblasts. The dataset is freely available for search and download at http://microarray-pubs.stanford.edu/human_stress/Home.shtml.

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Section: Comparison Of Expression In Yeast-human Homologuesmentioning

confidence: 99%

Diverse and Specific Gene Expression Responses to Stresses in Cultured Human Cells

Murray

Whitfield

Trinklein

et al. 2004

MBoC

275

236

View full text Add to dashboard Cite

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“…For each subcluster, we searched for cis-regulatory motifs (represented as PSSMs), within 500-bp upstream of each gene in the subcluster (sequences were retrieved from SGD on July 2, 2002; Cherry et al, 1998). We used a discriminative motif finder (Segal et al, 2003), based on Bayesian networks, which attempts to discover motifs that are overrepresented in the upstream sequences of cluster genes compared with the upstream sequences of genes in all other clusters.…”

Section: Promoter and Functional Annotations Analysesmentioning

confidence: 99%

Disruption of Yeast Forkhead-associated Cell Cycle Transcription by Oxidative Stress

Shapira

Segal

Botstein

2004

MBoC

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The effects of oxidative stress on yeast cell cycle depend on the stress-exerting agent. We studied the effects of two oxidative stress agents, hydrogen peroxide (HP) and the superoxide-generating agent menadione (MD). We found that two small coexpressed groups of genes regulated by the Mcm1-Fkh2-Ndd1 transcription regulatory complex are sufficient to account for the difference in the effects of HP and MD on the progress of the cell cycle, namely, G1 arrest with MD and an S phase delay followed by a G2/M arrest with HP. Support for this hypothesis is provided by fkh1fkh2 double mutants, which are affected by MD as we find HP affects wild-type cells. The apparent involvement of a forkhead protein in HP-induced cell cycle arrest, similar to that reported for Caenorhabditis elegans and human, describes a potentially novel stress response pathway in yeast. INTRODUCTIONReactive oxygen species (ROS) are by-products of aerobic metabolism, but are also attributes of the extracellular environment. They pose a threat to organisms by damaging a variety of cellular macromolecules, including DNA, membrane lipids, and proteins and are implicated with carcinogenesis, aging, and numerous degenerative diseases (Finkel and Holbrook, 2000;Neumann et al., 2003). The major ROS derived from oxygen are superoxide ions, hydrogen peroxide (HP), and hydroxy radicals, ordered here by increasing reactivity (reviewed in Shackelford et al., 2000).Oxidative stress in yeast has been studied by exposing cells to agents that are already reactive, typically HP, or drugs that cause the intracellular accumulation of reactive oxygen species (Godon et al., 1998;Dumond et al., 2000;Gasch et al., 2000). Menadione (MD) is such a drug, generating reactive superoxide ions, which can be further oxidized to give HP (Monks et al., 1992;Shackelford et al., 2000). It has been previously reported that exposure to HP or MD results in a cell cycle arrest (Flattery-O'Brien and Dawes, 1998;Leroy et al., 2001). However, the arrest points are not similar for the two agents. MD was reported to arrest cells at the G1 phase of the cell cycle, whereas HP was suggested to cause a G2 arrest by an alternate mechanism from that affected by MD (Flattery-O'Brien and Dawes, 1998); others reported that HP exposure causes a delay in the S phase (Leroy et al., 2001).Hundreds of genes are regulated so that they are expressed at specific times in the cell cycle and not at others (Cho et al., 1998;Spellman et al., 1998). The major part of this coordination is achieved by the sequential activation of a small number of transcription regulators (reviewed in Mendenhall and Hodge, 1998): MBF (a complex of Mbp1p and Swi6p) and SBF (a complex of Swi4p and Swi6p) are responsible for activating G1 transcription (Koch et al., 1993); Fkh1p and a complex formed by the cooperative promoter binding of Mcm1p and Fkh2p and a later recruitment of Ndd1p are responsible for activating G2/M transcription (Koranda et al., 2000;Kumar et al., 2000;Pic et al., 2000;Hollenhorst et al., 2001); Swi5p and Ace2p...

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“…In the previous studies Arthur et al, 2015) we focused mainly on polyA tracks from human and yeast genomes, using the NCBI (Pruitt et al, 2014) database and SGD (Cherry et al, 1998) as data sources, respectively. Overall there is a good agreement between our previous analysis and this study for high eukaryotes, while we see some discrepancies for lower eukaryotes such as yeast.…”

Section: Polya Tracks Across Eukaryotic Organismsmentioning

confidence: 99%

PATACSDB—the database of polyA translational attenuators in coding sequences

Habich

Djuranović

Szczęsny

2016

PeerJ Computer Science

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Recent additions to the repertoire of gene expression regulatory mechanisms are polyadenylate (polyA) tracks encoding for poly-lysine runs in protein sequences. Such tracks stall the translation apparatus and induce frameshifting independently of the effects of charged nascent poly-lysine sequence on the ribosome exit channel. As such, they substantially influence the stability of mRNA and the amount of protein produced from a given transcript. Single base changes in these regions are enough to exert a measurable response on both protein and mRNA abundance; this makes each of these sequences a potentially interesting case study for the effects of synonymous mutation, gene dosage balance and natural frameshifting. Here we present PATACSDB, a resource that contain a comprehensive list of polyA tracks from over 250 eukaryotic genomes. Our data is based on the Ensembl genomic database of coding sequences and filtered with algorithm of 12A-1 which selects sequences of polyA tracks with a minimal length of 12 A's allowing for one mismatched base. The PATACSDB database is accessible at: http://sysbio.ibb.waw.pl/patacsdb. The source code is available at http://github.com/habich/PATACSDB, and it includes the scripts with which the database can be recreated.

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SGD: Saccharomyces Genome Database

Cited by 983 publications

References 24 publications

Diverse and Specific Gene Expression Responses to Stresses in Cultured Human Cells

Diverse and Specific Gene Expression Responses to Stresses in Cultured Human Cells

Disruption of Yeast Forkhead-associated Cell Cycle Transcription by Oxidative Stress

PATACSDB—the database of polyA translational attenuators in coding sequences

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