CGD Help: Candida Biochemical Pathways



The Candida Biochemical Pathways were created using the Pathway Tools software, which is developed and maintained by Peter Karp and his colleagues at the Bioinformatics Research Group at SRI International. While Pathway Tools supports curation of additional types of data, including general gene product information, small molecule transport reactions, enzyme kinetics, and some (prokaryotic-focused) gene regulatory information, CGD is using the software to create and curate biochemical pathways only. Therefore, some features of the Pathway Tools software will not be fully functional in CGD, and not all types of data will be curated.

Pathway prediction and curation

Initially, the CGD biochemical pathways were automatically generated using PathoLogic, a pathway prediction program built into the Pathway Tools. PathoLogic used information about the function of individual Candida gene products from CGD in conjunction with SRI's reference database of biochemical reaction and pathway information, MetaCyc, to create a set of predicted Candida albicans pathways. The starting set of Candida albicans enzymes that was input into the PathoLogic software was generated using the Gene Ontology curation from CGD. PathoLogic then compared the list of enzyme names against SRI's MetaCyc pathway database. For the purpose of generation of pathways for CGD, the software was also configured to consult the set of pathways curated at the Saccharomyces Genome database in addition to the pathways contained in MetaCyc pathway, such that curated S. cerevisiae pathways that are not included in MetaCyc were used as an additional basis for comparison. If Candida albicans contains one or more enzymes that participate in a pathway that exists in MetaCyc or SGD, the software predicted that a similar pathway exists in Candida albicans. Many of the pathways that were predicted have candidate Candida albicans enzyme assignments for a subset, but not all, of the reactions that comprise the pathway. The Pathway Hole Filler program that is built into Pathway Tools was used to identify genes encoding candidate enzymes for the other reactions (the "pathway holes"). To do so, the Pathway Hole Filler was configured to use sequence-based information only (not other possible data types, see Green et al. 2004); it made comparisons between GenBank sequences associated with each of the "pathway hole" enzymes and the ORF sequences from CGD, to assign candidate Candida albicans genes to these activities where possible.

The automatically generated pathway predictions are being manually reviewed and curated at CGD. Because the software intentionally overpredicts pathways (i.e., errs on the side of inclusion), the pathway set that was initially predicted contained a number of spurious and redundant pathways. Curators conducted an initial review of the pathway list to identify relevant literature for most of the pathways, and to remove most of the spurious predictions. When necessary, new Candida pathways have been added. Subsequently, each pathway is subject to more intensive review by CGD curators; any necessary updates are made to the pathway structure or reactions; links to any corresponding pathway(s) in SGD are formed; and literature relevant to the pathway in Candida albicans and other Candida is reviewed, summarized on the pathway page, and added to the pathway reference list. In many cases, a pathway may not be characterized directly in Candida, as indicated in the text of the summary on the pathway page.

Pathway curation at CGD is an ongoing process, and the pathway predictions contained in the database may be incomplete or incorrect. If you see any errors, please contact us.

Main query page

The main query page is organized into several sections that allow you to search the Candida Biochemical Pathways dataset in different ways. The only dataset that is available is for the Candida albicans strain SC5314, which is the reference strain at CGD.

Query box Browse Ontology Choose from a list of all... Cellular Overview Diagram/Omics viewer Links to summary information Comparative Analysis

Advanced Query Form

The Advanced Query form allows you to retrieve specific types of information from the Candida Biochemical Pathways. The data structure of the Candida Biochemical Pathways is shared with EcoCyc and other datasets created using the Pathway Tools. The Pathway Tools web site provides a detailed help document for the Advanced Query.

Viewing Candida Biochemical Pathways Pages

Many items on the pathway diagrams are hyperlinks to detail pages; these links are underlined or they appear as colored text.

Pathways Reactions Enzymes Compounds

Using the Expression Viewer

The Pathway Tools provides a help document that includes information about file formats, analysis options, and interpreting results.

Since the Candida Biochemical Pathways dataset only contains genes that are involved in metabolic pathways, only these genes in the dataset will be taken into consideration. In addition, if a metabolic enzyme has not been associated with a reaction, the results will not be shown on the Overview Diagram. As a consequence, the statistics produced by the Pathway Tools may be skewed.

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