Curation and Integration of Pathway Tools at the Saccharomyces Genome - - PowerPoint PPT Presentation

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Dec 30, 2022 475 likes •714 views

Curation and Integration of Pathway Tools at the Saccharomyces Genome Database http://www.yeastgenome.org/ Scientific community Sequences Interactions Analysis & Search Phenotypes Tools Biochemical Pathways Functional Genomics Gene

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Curation and Integration of Pathway Tools at the Saccharomyces Genome Database http://www.yeastgenome.org/

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Scientific community

Sequences Interactions Phenotypes

Analysis & Search Tools

Biochemical Pathways Functional Genomics Gene Structures

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News and updates RSS feed Tools

http://www.yeastgenome.org/

Search Wiki

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Locus Summary Page

Curated data from published literature using controlled vocabularies Links to other databases Free text summaries

f published data

Links to SGD tools and other databases Data from high throughput experiments Sequence information Nomenclature References

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Creating YeastCyc

YeastCyc MetaCyc (PathoLogic) Gene Ontology

(use GO2EC mapping)

+

(circa 2002)

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Curation of YeastCyc

Experimental evidence Free text summaries References Curate enzymes, reactions, pathways for S. cerevisiae

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Curation Status

All pathways have been manually reviewed

* first pass completed in January 2008 * 140 manually curated pathways as of August 2009

Addition of fungal-specific pathways

* ergosterol biosynthesis * chitin (cell wall) biosynthesis

Continued improvement of pathways as data are published

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Future Curation Plans

Continued improvement of pathways as data are published
Reviewing orphan reactions
Metabolite levels
Kinetic data

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Search

Searching for Biochemical Pathways

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Accessing YeastCyc

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Accessing Locus Summaries

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Phenotypes Biochemical Pathways Sequences Gene Ontology Interactions

Data Consistency

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Consistency with MetaCyc

YeastCyc MetaCyc 2002 2009

= =

?

same IDs for the same pathway and compounds
syncing pathways
consistency with other fungal pathways (C. albicans)

Cindy Krieger (SGD); Ron Caspi and Liviu Popescu (MetaCyc); Martha Arnaud, Maria Costanzo, Marek Skrzypek (CGD)

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Same E.C. Number?

YeastCyc at SGD KEGG UniProt SGD EC links

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EC Number Agreement

YeastCyc KEGG UniProt SGD E.C. links

255 genes 303 genes Two sources with EC, both agree 847 genes Discrepancy with one source 269 genes

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Reasons for discrepancies

Changes to E.C. numbers

* obsoletions * merges * new E.C. numbers

Different philosophies of curation

* assign to only the catalytic subunit * assign to all subunits of a complex Updated data available at SGD

http://downloads.yeastgenome.org/chromosomal_feature/dbxref.tab

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Phenotypes Biochemical Pathways Sequences Gene Ontology Interactions

Analysis & Search Tools

Data Integration

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Analysis and Search Tools

What function or biological role does a list of genes share? What genes are involved in a particular function or biological role? Search Tools

http://www.yeastgenome.org/cgi-bin/search/featureSearch

GO Term Finder

http://www.yeastgenome.org/cgi-bin/GO/goTermFinder.pl

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Analyzing Gene Lists

Search Tools Analysis Tools Data Pages Pathway Omics Viewer

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Intermine: More flexible, powerful searches

Search or filter your list Find homologs in other organisms Input a list of genes Get a list of genes

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Accessing Data

publicly available

http://www.yeastgenome.org/

via FTP

http://downloads.yeastgenome.org/

Pathway Registry via Pathway tools

updated monthly

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yeast-curator@genome.stanford.edu http://www.yeastgenome.org/

Cindy Krieger, Rama Balakrishnan, Julie Park, Benjamin Vincent, Nastassia Patin

Supported by NIH Human Genome Research Institute