Cis Element/transcription Factor Analysis (cis/TF): a Method for Discovering Transcription Factor/cis Element Relationships

Overview

Journal Genome Res

Specialty Genetics

Date 2001 Sep 7

PMID 11544201

Citations 17

Authors

K Birnbaum

P N Benfey

D E Shasha

Affiliations

Soon will be listed here.

Abstract

We report a simple new algorithm, cis/TF, that uses genomewide expression data and the full genomic sequence to match transcription factors to their binding sites. Most previous computational methods discovered binding sites by clustering genes having similar expression patterns and then identifying over-represented subsequences in the promoter regions of those genes. By contrast, cis/TF asserts that B is a likely binding site of a transcription factor T if the expression pattern of T is correlated to the composite expression patterns of all genes containing B, even when those genes are not mutually correlated. Thus, our method focuses on binding sites rather than genes. The algorithm has successfully identified experimentally-supported transcription factor binding relationships in tests on several data sets from Saccharomyces cerevisiae.

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References

Wagner A . A computational genomics approach to the identification of gene networks. Nucleic Acids Res. 1997; 25(18):3594-604. PMC: 146952. DOI: 10.1093/nar/25.18.3594. View

Arnone M, Davidson E . The hardwiring of development: organization and function of genomic regulatory systems. Development. 1997; 124(10):1851-64. DOI: 10.1242/dev.124.10.1851. View

Chu S, Herskowitz I . Gametogenesis in yeast is regulated by a transcriptional cascade dependent on Ndt80. Mol Cell. 1998; 1(5):685-96. DOI: 10.1016/s1097-2765(00)80068-4. View

Wingender E, Chen X, Hehl R, Karas H, Liebich I, Matys V . TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res. 1999; 28(1):316-9. PMC: 102445. DOI: 10.1093/nar/28.1.316. View

Ball C, Jin H, Sherlock G, Weng S, Matese J, Andrada R . Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Res. 2000; 29(1):80-1. PMC: 29796. DOI: 10.1093/nar/29.1.80. View

Bussemaker H, Li H, Siggia E . Regulatory element detection using correlation with expression. Nat Genet. 2001; 27(2):167-71. DOI: 10.1038/84792. View

Derisi J, Penland L, Brown P, Bittner M, Meltzer P, Ray M . Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet. 1996; 14(4):457-60. DOI: 10.1038/ng1296-457. View

Albrecht G, Mosch H, Hoffmann B, Reusser U, Braus G . Monitoring the Gcn4 protein-mediated response in the yeast Saccharomyces cerevisiae. J Biol Chem. 1998; 273(21):12696-702. DOI: 10.1074/jbc.273.21.12696. View

Spellman P, Sherlock G, Zhang M, Iyer V, Anders K, Eisen M . Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell. 1998; 9(12):3273-97. PMC: 25624. DOI: 10.1091/mbc.9.12.3273. View

10.

Cho R, Campbell M, Winzeler E, Steinmetz L, Conway A, Wodicka L . A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell. 1998; 2(1):65-73. DOI: 10.1016/s1097-2765(00)80114-8. View

11.

Lockhart D, Dong H, Byrne M, Follettie M, Gallo M, Chee M . Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol. 1996; 14(13):1675-80. DOI: 10.1038/nbt1296-1675. View

12.

Driever W, Thoma G, Nusslein-Volhard C . Determination of spatial domains of zygotic gene expression in the Drosophila embryo by the affinity of binding sites for the bicoid morphogen. Nature. 1989; 340(6232):363-7. DOI: 10.1038/340363a0. View

13.

Xu C, Kauffmann R, Zhang J, Kladny S, Carthew R . Overlapping activators and repressors delimit transcriptional response to receptor tyrosine kinase signals in the Drosophila eye. Cell. 2000; 103(1):87-97. DOI: 10.1016/s0092-8674(00)00107-0. View

14.

Zhang M . Promoter analysis of co-regulated genes in the yeast genome. Comput Chem. 1999; 23(3-4):233-50. DOI: 10.1016/s0097-8485(99)00020-0. View

15.

Kuras L, Cherest H, Thomas D . A heteromeric complex containing the centromere binding factor 1 and two basic leucine zipper factors, Met4 and Met28, mediates the transcription activation of yeast sulfur metabolism. EMBO J. 1996; 15(10):2519-29. PMC: 450184. View

16.

Brazma A, Jonassen I, Vilo J, Ukkonen E . Predicting gene regulatory elements in silico on a genomic scale. Genome Res. 1998; 8(11):1202-15. PMC: 310790. DOI: 10.1101/gr.8.11.1202. View

17.

Flores G, Duan H, Yan H, Nagaraj R, Fu W, Zou Y . Combinatorial signaling in the specification of unique cell fates. Cell. 2000; 103(1):75-85. DOI: 10.1016/s0092-8674(00)00106-9. View

18.

Zhang M . Large-scale gene expression data analysis: a new challenge to computational biologists. Genome Res. 1999; 9(8):681-8. View

19.

van Helden J, Andre B, Collado-Vides J . Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J Mol Biol. 1998; 281(5):827-42. DOI: 10.1006/jmbi.1998.1947. View

20.

Schena M, Shalon D, Davis R, Brown P . Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995; 270(5235):467-70. DOI: 10.1126/science.270.5235.467. View