FunSpec: a web-based cluster interpreter for yeast

doi:10.1186/1471-2105-3-35

. 2002 Nov 13:3:35.

doi: 10.1186/1471-2105-3-35. Epub 2002 Nov 13.

FunSpec: a web-based cluster interpreter for yeast

Mark D Robinson¹, Jörg Grigull, Naveed Mohammad, Timothy R Hughes

Affiliations

PMID: 12431279
PMCID: PMC139976
DOI: 10.1186/1471-2105-3-35

FunSpec: a web-based cluster interpreter for yeast

Mark D Robinson et al. BMC Bioinformatics. 2002.

. 2002 Nov 13:3:35.

doi: 10.1186/1471-2105-3-35. Epub 2002 Nov 13.

Authors

Mark D Robinson¹, Jörg Grigull, Naveed Mohammad, Timothy R Hughes

Affiliation

¹ Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada. m.robinson@utoronto.ca

PMID: 12431279
PMCID: PMC139976
DOI: 10.1186/1471-2105-3-35

Abstract

Background: For effective exposition of biological information, especially with regard to analysis of large-scale data types, researchers need immediate access to multiple categorical knowledge bases and need summary information presented to them on collections of genes, as opposed to the typical one gene at a time.

Results: We present here a web-based tool (FunSpec) for statistical evaluation of groups of genes and proteins (e.g. co-regulated genes, protein complexes, genetic interactors) with respect to existing annotations (e.g. functional roles, biochemical properties, localization). FunSpec is available online at http://funspec.med.utoronto.ca

Conclusion: FunSpec is helpful for interpretation of any data type that generates groups of related genes and proteins, such as gene expression clustering and protein complexes, and is useful for predictive methods employing "guilt-by-association."

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Figures

**Figure 1**
A 2-D clustering analysis of yeast gene expression data from [8].

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References

1. Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M. SGD: Saccharomyces Genome Database. Nucleic Acids Res. 1998;26:73–79. doi: 10.1093/nar/26.1.73. - DOI - PMC - PubMed
1. Mewes HW, Frishman D, Gruber C, Geier B, Haase D, Kaps A, Lemcke K, Mannhaupt G, Pfeiffer F, Schuller C. MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 2000;28:37–40. doi: 10.1093/nar/28.1.37. - DOI - PMC - PubMed
1. Costanzo MC, Crawford ME, Hirschman JE, Kranz JE, Olsen P, Robertson LS, Skrzypek MS, Braun BR, Hopkins KL, Kondu P. YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucleic Acids Res. 2001;29:75–79. doi: 10.1093/nar/29.1.75. - DOI - PMC - PubMed
1. Greenbaum D, Luscombe NM, Jansen R, Qian J, Gerstein M. Interrelating different types of genomic data, from proteome to secretome: 'oming in on function. Genome Res. 2001;11:1463–1468. doi: 10.1101/gr.207401. - DOI - PubMed
1. Wu LF, Hughes TR, Davierwala AP, Robinson MD, Stoughton R, Altschuler SJ. Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat Genet. 2002;31:255–265. doi: 10.1038/ng906. - DOI - PubMed

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[1] Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M. SGD: Saccharomyces Genome Database. Nucleic Acids Res. 1998;26:73–79. doi: 10.1093/nar/26.1.73. - DOI - PMC - PubMed

[2] Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M. SGD: Saccharomyces Genome Database. Nucleic Acids Res. 1998;26:73–79. doi: 10.1093/nar/26.1.73. - DOI - PMC - PubMed

[3] Mewes HW, Frishman D, Gruber C, Geier B, Haase D, Kaps A, Lemcke K, Mannhaupt G, Pfeiffer F, Schuller C. MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 2000;28:37–40. doi: 10.1093/nar/28.1.37. - DOI - PMC - PubMed

[4] Mewes HW, Frishman D, Gruber C, Geier B, Haase D, Kaps A, Lemcke K, Mannhaupt G, Pfeiffer F, Schuller C. MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 2000;28:37–40. doi: 10.1093/nar/28.1.37. - DOI - PMC - PubMed

[5] Costanzo MC, Crawford ME, Hirschman JE, Kranz JE, Olsen P, Robertson LS, Skrzypek MS, Braun BR, Hopkins KL, Kondu P. YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucleic Acids Res. 2001;29:75–79. doi: 10.1093/nar/29.1.75. - DOI - PMC - PubMed

[6] Costanzo MC, Crawford ME, Hirschman JE, Kranz JE, Olsen P, Robertson LS, Skrzypek MS, Braun BR, Hopkins KL, Kondu P. YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucleic Acids Res. 2001;29:75–79. doi: 10.1093/nar/29.1.75. - DOI - PMC - PubMed

[7] Greenbaum D, Luscombe NM, Jansen R, Qian J, Gerstein M. Interrelating different types of genomic data, from proteome to secretome: 'oming in on function. Genome Res. 2001;11:1463–1468. doi: 10.1101/gr.207401. - DOI - PubMed

[8] Greenbaum D, Luscombe NM, Jansen R, Qian J, Gerstein M. Interrelating different types of genomic data, from proteome to secretome: 'oming in on function. Genome Res. 2001;11:1463–1468. doi: 10.1101/gr.207401. - DOI - PubMed

[9] Wu LF, Hughes TR, Davierwala AP, Robinson MD, Stoughton R, Altschuler SJ. Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat Genet. 2002;31:255–265. doi: 10.1038/ng906. - DOI - PubMed

[10] Wu LF, Hughes TR, Davierwala AP, Robinson MD, Stoughton R, Altschuler SJ. Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat Genet. 2002;31:255–265. doi: 10.1038/ng906. - DOI - PubMed

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FunSpec: a web-based cluster interpreter for yeast

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FunSpec: a web-based cluster interpreter for yeast

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