Bu D, Zhao Y, Cai L, Xue H, Zhu X, Lu H, Zhang J, Sun S, Ling L, Zhang N, Li G, Chen R: Topological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Res 2003, 31: 2443–2450. 10.1093/nar/gkg340
Article
PubMed Central
CAS
PubMed
Google Scholar
Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL: The large-scale organization of metabolic networks. Nature 2000, 407: 651–654. 10.1038/35036627
Article
CAS
PubMed
Google Scholar
Guelzim N, Bottani S, Bourgine P, Kepes F: Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet 2002, 31: 60–63. 10.1038/ng873
Article
CAS
PubMed
Google Scholar
Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA: Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002, 298: 799–804. 10.1126/science.1075090
Article
CAS
PubMed
Google Scholar
Kanehisa M, Goto S, Kawashima S, Nakaya A: The KEGG databases at GenomeNet. Nucleic Acids Res 2002, 30: 42–46. 10.1093/nar/30.1.42
Article
PubMed Central
CAS
PubMed
Google Scholar
Karp PD, Riley M, Paley SM, Pellegrini-Toole A: The MetaCyc Database. Nucleic Acids Res 2002, 30: 59–61. 10.1093/nar/30.1.59
Article
PubMed Central
CAS
PubMed
Google Scholar
Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC, Conklin BR: GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet 2002, 31: 19–20. 10.1038/ng0502-19
Article
CAS
PubMed
Google Scholar
Ideker T, Ozier O, Schwikowski B, Siegel AF: Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 2002, 18 Suppl 1: S233–40.
Article
PubMed
Google Scholar
Breitkreutz BJ, Stark C, Tyers M: Osprey: a network visualization system. Genome Biol 2003, 4: R22. 10.1186/gb-2003-4-3-r22
Article
PubMed Central
PubMed
Google Scholar
Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 1998, 95: 14863–14868. 10.1073/pnas.95.25.14863
Article
PubMed Central
CAS
PubMed
Google Scholar
Quackenbush J: Computational analysis of microarray data. Nat Rev Genet 2001, 2: 418–427. 10.1038/35076576
Article
CAS
PubMed
Google Scholar
Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM: Systematic determination of genetic network architecture. Nat Genet 1999, 22: 281–285. 10.1038/10343
Article
CAS
PubMed
Google Scholar
Gasch AP, Eisen MB: Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol 2002, 3: RESEARCH0059. 10.1186/gb-2002-3-11-research0059
Article
PubMed Central
PubMed
Google Scholar
Cheng Y, Church GM: Biclustering of expression data. Proc Int Conf Intell Syst Mol Biol 2000, 8: 93–103.
CAS
PubMed
Google Scholar
Mewes HW, Frishman D, Guldener U, Mannhaupt G, Mayer K, Mokrejs M, Morgenstern B, Munsterkotter M, Rudd S, Weil B: MIPS: a database for genomes and protein sequences. Nucleic Acids Res 2002, 30: 31–34. 10.1093/nar/30.1.31
Article
PubMed Central
CAS
PubMed
Google Scholar
Dwight SS, Harris MA, Dolinski K, Ball CA, Binkley G, Christie KR, Fisk DG, Issel-Tarver L, Schroeder M, Sherlock G, Sethuraman A, Weng S, Botstein D, Cherry JM: Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res 2002, 30: 69–72. 10.1093/nar/30.1.69
Article
PubMed Central
CAS
PubMed
Google Scholar
van Helden J: Regulatory sequence analysis tools. Nucleic Acids Res 2003, 31: 3593–3596. 10.1093/nar/gkg567
Article
PubMed Central
CAS
PubMed
Google Scholar
Le Crom S, Devaux F, Jacq C, Marc P: yMGV: helping biologists with yeast microarray data mining. Nucleic Acids Res 2002, 30: 76–79. 10.1093/nar/30.1.76
Article
PubMed Central
CAS
PubMed
Google Scholar
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 2001, 29: 365–371. 10.1038/ng1201-365
Article
CAS
PubMed
Google Scholar
Edgar R, Domrachev M, Lash AE: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30: 207–210. 10.1093/nar/30.1.207
Article
PubMed Central
CAS
PubMed
Google Scholar
Brazma A, Parkinson H, Sarkans U, Shojatalab M, Vilo J, Abeygunawardena N, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Rocca-Serra P, Sansone SA: ArrayExpress--a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 2003, 31: 68–71. 10.1093/nar/gkg091
Article
PubMed Central
CAS
PubMed
Google Scholar
JpGraph - An 00 Graph library for PHP4[http://www.aditus.nu/jpgraph]
Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ, Davis RW: A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell 1998, 2: 65–73.
Article
CAS
PubMed
Google Scholar
Ogas J, Andrews BJ, Herskowitz I: Transcriptional activation of CLN1, CLN2, and a putative new G1 cyclin (HCS26) by SWI4, a positive regulator of G1-specific transcription. Cell 1991, 66: 1015–1026.
Article
CAS
PubMed
Google Scholar
Guacci V, Koshland D, Strunnikov A: A direct link between sister chromatid cohesion and chromosome condensation revealed through the analysis of MCD1 in S. cerevisiae. Cell 1997, 91: 47–57. 10.1016/S0092-8674(01)80008-8
Article
PubMed Central
CAS
PubMed
Google Scholar
Elledge SJ, Davis RW: Two genes differentially regulated in the cell cycle and by DNA-damaging agents encode alternative regulatory subunits of ribonucleotide reductase. Genes Dev 1990, 4: 740–751.
Article
CAS
PubMed
Google Scholar
Stuart JM, Segal E, Koller D, Kim SK: A gene-coexpression network for global discovery of conserved genetic modules. Science 2003, 302: 249–255. 10.1126/science.1087447
Article
CAS
PubMed
Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25: 25–29. 10.1038/75556
Article
PubMed Central
CAS
PubMed
Google Scholar
Gasch AP, Werner-Washburne M: The genomics of yeast responses to environmental stress and starvation. Funct Integr Genomics 2002, 2: 181–192. 10.1007/s10142-002-0058-2
Article
CAS
PubMed
Google Scholar