DASS: Efficient discovery and p-value calculation of substructures in unordered data

Bioinformatics

Volumn 23, Issue 1, 2007, Pages 77-83

  Hollunder, Jens ^a   Friedel, Maik ^a   Beyer, Andreas ^a,b   Workman, Christopher T ^b   Wilhelm, Thomas ^a  

^a FRITZ LIPMANN INSTITUTE   (Germany)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN; TRANSCRIPTION FACTOR;

ALGORITHM; ARTICLE; AUTOMATED PATTERN RECOGNITION; BIOINFORMATICS; COMPUTER PROGRAM; DISCOVERY OF ALL SIGNIFICANT SUBSTRUCTURES; INFORMATION RETRIEVAL; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN INTERACTION; STATISTICAL SIGNIFICANCE; STRUCTURAL BIOINFORMATICS; SYSTEMS BIOLOGY;

EID: 33845875680     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl511     Document Type: Article

References (41)

1. Altschul,S.F. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
3. Agrawal,R. and Srikant,R. (1994) Fast algorithms for mining association rules. In Proceedings of 20th International Conference on Very Large Data Bases, 487-499.
4. Aloy,P. et al. (2004) Structure-based assembly of protein complexes in yeast. Science, 303, 2026-2029.
5. Andreeva,A. et al. (2004) SCOP database in 2004: Refinements integrate structure and sequence family data. Nucleic Acids Res., 32, D226-D229.
6. Apic,G. et al. (2001) Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J. Mol. Biol., 310, 311-325.
7. Beyer,A. et al. (2006) Integrated assessment and prediction of transcription factor binding. PLOS Comput. Biol., 2, e70.
8. Blaiseau,P.L. and Thomas,D. (1998) Multiple transcriptional activation complexes tether the yeast activator Met4 to DNA. EMBO J., 17, 6327-6336.
9. Burdick,D. et al. (2001) MAFIA: A maximal frequent itemset algorithm for transactional databases. In Proceedings of the 17th International Conference on Data Engineering (ICDE 2001), pp. 443-452.
10. Christie,K.R. et al. (2004) Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Res., 32, D311-D314.
11. DeRisi,J. et al. (2000) Genome microarray analysis of transcriptional activation in multidrug resistance yeast mutants. FEBS Lett., 470, 156-160.
12. Eddy,S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
13. Fan,J.S. and Zhang,M. (2002) Signaling complex organization by PDZ domain proteins. Neurosignals, 11, 315-321.
14. Gavin,A.-C. and Superti-Furga,G. (2003) Protein complexes and proteome organization from yeast to man. Curr. Opin. Chem. Biol., 7, 21-27.
15. Harbison,C.T. et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104.
16. Hoffmann,R. and Valencia,A. (2004) A gene network for navigating the literature. Nat. Genet., 36, 664.
17. Hollunder,J. et al. (2005a) Identification and characterization of protein subcomplexes in yeast. Proteomics, 5, 2082-2089.
18. Hollunder, J. et al. (2005b) Exploiting combinatorial complexity - searching for new functional entities in the cell. In Proceedings of Foundation of System Biology in Engineering (FOSBE 2005), pp. 363-366.
19. Ihmels,J. et al. (2004) Defining transcription modules using large-scale gene expression data. Bioinformatics, 20, 1993-2003.
20. Kang,S. et al. (2000) PCD1, a novel gene containing PDZ and LIM domains, is overexpressed in several human cancers. Cancer Res., 60, 5296-5302.
21. Krogan,N.J. et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature, 440, 637-643.
22. Kuras,L. et al. (1996) 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., 15, 2519-2529.
23. Li,S. et al. (2004) A map of the interactome network of the metazoan C. elegans. Science, 303, 540-543.
24. Madera,M. et al. (2004) The SUPERFAMILY database in 2004: Additions and improvements. Nucleic Acids Res., 32, D235-D239.
25. Mamnun,Y.M. et al. (2002) The yeast zinc finger regulators Pdr1p and Pdr3p control pleiotropic drug resistance (PDR) as homo- and heterodimers in vivo. Mol. Microbiol., 46, 1429-1440.
26. Mewes,H.W. et al. (2004) MIPS: Analysis and annotation of proteins from whole genomes. Nucleic Acids Res., 32, D41-D44.
27. Ouzounis,C.A. and Valencia,A. (2003) Early bioinformatics: The birth of a discipline - a personal view. Bioinformatics, 19, 2176-2190.
28. Pasquier,N. et al. (1999) Discovering frequent closed itemsets for association rules. In Proceedings of the 7th International Conference on Database Theory (ICDT 1999), Lecture Notes in Computer Science, Vol. 1540, Springer, pp. 398-416.
29. Pei,J. et al. (2000) CLOSET: An efficient algorithm for mining frequent closed itemsets. In Proceedings of ACM SIGMOD International Workshop on Data Mining and Knowledge Discovery, (DMKD 2000), pp. 21-30.
30. Pearson,W.R. and Lipman,D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
31. Ponting,C.P. (1997) Evidence for PDZ domains in bacteria, yeast, and plants. Protein Sci., 6, 464-468.
32. Robinson,M.D. et al. (2002) FunSpec: A web-based cluster interpreter for yeast. BMC Bioinformatics, 3, 35.
33. Sharan,R. et al. (2005) Conserved patterns of protein interaction in multiple species. Proc. Natl Acad. Sci. USA, 102, 1974-1979.
34. Stormo,G.D. (2000) DNA binding sites: Representation and discovery. Bioinformatics, 16, 16-23.
35. Tompa,M. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol., 23, 137-144.
36. Vogel,C. et al. (2004) Supra-domains. Evolutionary units larger than protein domains. J. Mol. Biol., 336, 809-823.
37. Wilhelm,T. et al. (2003) Physical and functional modularity of the protein network in yeast. Mol. Cell. Prot., 2.5, 292-298.
38. Workman,C.T. and Stormo,G.D. (2000) ANN-Spec: A method for discovering transcription factor binding sites with improved specificity. Pac. Symp. Biocomput., 5, 467-478.
39. Yaffe,M.B. (2002) Phosphotyrosine-binding domains in signal transduction. Nat. Rev. Mol. Cell Biol., 3, 177-186.
40. Zaki,M.J. and Hsiao,C.-J. (2002) CHARM: An efficient algorithm for closed itemset mining. In Proceedings of the 2nd SIAM International Conference on Data Mining (SDM 2002), pp. 457-473.
41. Zhu,Y. and Xiao,W. (2004) Pdr3 is required for DNA damage induction of MAG1 and DDI1 via a bi-directional promoter element. Nucleic Acids Res., 32, 5066-5075.