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Transcriptome visualization and data availability at the Saccharomyces Genome Database

2019 Nucleic Acids Research  
The Saccharomyces Genome Database (SGD; www.yeastgenome.org) maintains the official annotation of all genes in the Saccharomyces cerevisiae reference genome and aims to elucidate the function of these  ...  Accordingly, SGD has incorporated published transcript isoform data in our instance of JBrowse, a genome visualization platform.  ...  ACKNOWLEDGEMENTS We would like to thank Wei Wu and Lars Steinmetz for their feedback on transcript annotation and making these data available. Thank you to Sage T. Hellerstedt and Micheal J.  ... 
doi:10.1093/nar/gkz892 pmid:31612944 pmcid:PMC7061941 fatcat:hjfc5fetr5ggbbq2gnemjypnoa

YETI: Yeast Exploration Tool Integrator

R. J. Orton, W. I. Sellers, D. L. Gerloff
2004 Bioinformatics  
Yeast Exploration Tool Integrator (YETI) is a novel bioinformatics tool for the integrated visualization and analysis of functional genomic data sets from the budding yeast Saccharomyces cerevisiae.  ...  Availability: YETI is freely available for use over the WWW, or download under license, at  ...  Jean Beggs and her laboratory at the University of Edinburgh for their continued support and advice. R.J.O. is supported by a Special Bioinformatics Studentship from the Medical Research Council.  ... 
doi:10.1093/bioinformatics/btg408 pmid:14734325 fatcat:c6jqfbtsyfdyrcqp6gr6smblua

yMGV: a cross-species expression data mining tool

G. Lelandais
2004 Nucleic Acids Research  
This should enable the ®ssion yeast community to take advantage of the large amount of available information on budding yeast transcriptome. New tools and ongoing developments are also presented here.  ...  The yeast Microarray Global Viewer (yMGV @ http:// transcriptome.ens.fr/ymgv) was created 3 years ago as a database that houses a collection of Saccharomyces cerevisiae and Schizosaccharomyces pombe microarray  ...  This is the most common dif®culty confronting the mining and visualization of the vast amount of data produced by genomic technologies.  ... 
doi:10.1093/nar/gkh135 pmid:14681424 pmcid:PMC308869 fatcat:akyorkkwnfgpthhel3dprfda54

Ashbya Genome Database 3.0: a cross-species genome and transcriptome browser for yeast biologists

Alexandre Gattiker, Riccarda Rischatsch, Philippe Demougin, Sylvia Voegeli, Fred S Dietrich, Peter Philippsen, Michael Primig
2007 BMC Genomics  
The Ashbya Genome Database (AGD) 3.0 is an innovative cross-species genome and transcriptome browser based on release 40 of the Ensembl developer environment.  ...  The database is accessible at http://agd.vital-it.ch/.  ...  Jongeneel and R. Fabbretti for hosting and maintaining the database at Vital-IT and J. Moore for critical reading of the manuscript. A. Gattiker is supported by the Swiss Institute of Bioinformatics.  ... 
doi:10.1186/1471-2164-8-9 pmid:17212814 pmcid:PMC1779777 fatcat:wtui7iddzzbwtmwt4jwt56nu3a

MaGnET: a software tool for integrated visualisation of functional genomic data relating to the malaria parasite

Joanna L Sharman, Dietlind L Gerloff
2007 BMC Systems Biology  
Acknowledgements The project is funded by an MRC Bioinformatics Studentship.  ...  However, effective visual data exploration requires also that interfaces to different functional genomic data are integrated and that the user can carry forward a selected group of genes (not merely one  ...  However, the singleorganism focus of these tools required careful consideration of the specific needs of each user community and the differences in availability of functional genomic data for P. falciparum  ... 
doi:10.1186/1752-0509-1-s1-p32 fatcat:4gdpqjg2pjhf3ncxco6xz6mm3u

Octopus-toolkit: a workflow to automate mining of public epigenomic and transcriptomic next-generation sequencing data

Taemook Kim, Hogyu David Seo, Lothar Hennighausen, Daeyoup Lee, Keunsoo Kang
2018 Nucleic Acids Research  
Overall, Octopus-toolkit facilitates the systematic and integrative analysis of available epigenomic and transcriptomic NGS big data.  ...  fly (Drosophila melanogaster), worm (Caenorhabditis elegans), and budding yeast (Saccharomyces cerevisiae) genomes.  ...  NGS data deposited in the GEO database can be visualized through the genome data viewer function provided by the national center for biotechnology information (NCBI) website.  ... 
doi:10.1093/nar/gky083 pmid:29420797 pmcid:PMC5961211 fatcat:qkcyzj2wa5g7ljxxvlzmke25ie

Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community

Farhana R. Pinu, David J. Beale, Amy M. Paten, Konstantinos Kouremenos, Sanjay Swarup, Horst J. Schirra, David Wishart
2019 Metabolites  
The use of multiple omics techniques (i.e., genomics, transcriptomics, proteomics, and metabolomics) is becoming increasingly popular in all facets of life science.  ...  the integration of these complex multi-omics data sets.  ...  Acknowledgments: The authors would like to thank the organizing committee of ANZMET 2018. Conflicts of Interest: The authors declare no conflict of interest. Metabolites 2019, 9, 76  ... 
doi:10.3390/metabo9040076 pmid:31003499 pmcid:PMC6523452 fatcat:deiwu7rgpnb3tfr7glbewoyar4

YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae

Miguel C Teixeira, Pedro T Monteiro, Margarida Palma, Catarina Costa, Cláudia P Godinho, Pedro Pais, Mafalda Cavalheiro, Miguel Antunes, Alexandre Lemos, Tiago Pedreira, Isabel Sá-Correia
2017 Nucleic Acids Research  
regulatory associations at the gene and genomic levels in Saccharomyces cerevisiae.  ...  This release of the YEASTRACT database provides new visualization tools to visualize each regulatory network in an interactive fashion, enabling the user to select and observe subsets of the network such  ...  ACKNOWLEDGEMENTS The information about yeast genes other than documented regulations, potential regulations and the transcription factor binding sites contained in YEASTRACT was gathered from SGD and the  ... 
doi:10.1093/nar/gkx842 pmid:29036684 pmcid:PMC5753369 fatcat:jtsufessujcrlnhytrcdtjxc3q

yMGV: a database for visualization and data mining of published genome-wide yeast expression data

P. Marc
2001 Nucleic Acids Research  
The yMGV interface is available at http://transcriptome.ens.fr/ymgv/.  ...  The yeast Microarray Global Viewer (yMGV) is an on-line database providing a synthetic view of the transcriptional expression profiles of Saccharomyces cerevisiae genes in most of the published expression  ...  ACKNOWLEDGEMENTS This work would not have been possible without the help of all the authors who made their data freely accessible. We thank GNU projects for providing such good free software.  ... 
doi:10.1093/nar/29.13.e63 pmid:11433039 pmcid:PMC55787 fatcat:gxcwbuzmlfdzxa2ipgdb7zzgru

An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum

Thomas Bock, Wei-Hua Chen, Alessandro Ori, Nayab Malik, Noella Silva-Martin, Jaime Huerta-Cepas, Sean T. Powell, Panagiotis L. Kastritis, Georgy Smyshlyaev, Ivana Vonkova, Joanna Kirkpatrick, Tobias Doerks (+11 others)
2014 Nucleic Acids Research  
Data were deposited in a publicly available repository and provide a rich source to the structural biology community.  ...  We considerably improved the genome annotation of Chaetomium thermophilum and characterized the transcripts and expression of thousands of genes.  ...  Proteome data are available for download at the new genome browser website (see visualization paragraph in the results section).  ... 
doi:10.1093/nar/gku1147 pmid:25398899 pmcid:PMC4267624 fatcat:odfumnarezhtddkcsmtuixkzbu

MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states

Gaëlle Lelandais, Philippe Marc, Pierre Vincens, Claude Jacq, Stéphane Vialette
2004 BMC Bioinformatics  
A relational database includes data linked to genome expression and graphical output makes it easy to visualize clusters of co-expressed genes in the context of available biological information.  ...  MiCoViTo (Microarray Comparison Visualization Tool) is a set of biologists' tools for exploring, comparing and visualizing changes in the yeast transcriptome by a gene-centric approach.  ...  foundation Center of Excellence in Integration of Genomics and Informatics (CEIGI), SV is supported by Hoechst Marion Roussel -Aventis grant number FRHMR2/9908.  ... 
doi:10.1186/1471-2105-5-20 pmid:15053844 pmcid:PMC375526 fatcat:tvwzxwggdfaylnrn73xbj5mw4y

Transcriptome structure variability in Saccharomyces cerevisiae strains determined with a newly developed assembly software

Alessandro Sardu, Laura Treu, Stefano Campanaro
2014 BMC Genomics  
By extending the transcriptome analysis to yeast species belonging to the Saccharomyces genus, it was possible to examine the conservation level of unknown non-coding RNAs and their putative functional  ...  Finally, we propose a regulatory role for some non-coding transcripts conserved within the Saccharomyces genus and localized in the antisense strand to genes involved in meiosis and cell wall biosynthesis  ...  Acknowledgments RNA-seq was performed at the CRIBI Biotechnology Centre (University of Padua) and we acknowledge the support of Michela D'Angelo in processing our samples.  ... 
doi:10.1186/1471-2164-15-1045 pmid:25441755 pmcid:PMC4302112 fatcat:e52gqrwjmfbwjjyhu5huqy4po4

The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources

M. B. Arnaud, G. C. Cerqueira, D. O. Inglis, M. S. Skrzypek, J. Binkley, M. C. Chibucos, J. Crabtree, C. Howarth, J. Orvis, P. Shah, F. Wymore, G. Binkley (+4 others)
2011 Nucleic Acids Research  
The Aspergillus Genome Database (AspGD; http:// www.aspgd.org) is a freely available, web-based resource for researchers studying fungi of the genus Aspergillus, which includes organisms of clinical, agricultural  ...  AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli.  ...  Improvement of gene structure As transcriptome data for the species and strains with genomic sequences stored in AspGD become available, we are mapping and incorporating these data into the structural  ... 
doi:10.1093/nar/gkr875 pmid:22080559 pmcid:PMC3245136 fatcat:hrjdhiblonfntjitnlnxqwl4ni

Predicting the fungal CUG codon translation with Bagheera

Stefanie Mühlhausen, Martin Kollmar
2014 BMC Genomics  
While most Saccharomycetes, including Saccharomyces cerevisiae, use the standard genetic code translating the CUG codon as leucine, some yeasts, including many but not all of the "Candida", translate the  ...  It has been proposed that the change in codon identity was accomplished by an almost complete loss of the original CUG codons, making the CUG positions within the extant species highly discriminative for  ...  All sequence related data (protein names, corresponding species, sequences, and gene structure reconstructions) and references to genome sequencing centres are available at CyMoBase (http://www.cymobase.org  ... 
doi:10.1186/1471-2164-15-411 pmid:24885275 pmcid:PMC4050208 fatcat:w7vj35v44vcuxpcafxk4huqb3y

Trips-Viz: a transcriptome browser for exploring Ribo-Seq data

Stephen J Kiniry, Patrick B F O'Connor, Audrey M Michel, Pavel V Baranov
2018 Nucleic Acids Research  
To provide access to publicly available ribosome profiling data in the context of transcriptomes we developed Trips-Viz (transcriptome-wide information on protein synthesis-visualized).  ...  Trips-Viz is available at https: //trips.ucc.ie.  ...  ACKNOWLEDGEMENTS We wish to thank Xiangwu Lu, Vimalkumar Velayudhan, Sara Dufour and James Mullan for their help during the development of Trips-Viz.  ... 
doi:10.1093/nar/gky842 pmid:30239879 fatcat:gpjrcj4abrcqtmcl77zpftyvwq
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