BISON: Bio-interface for the semi-global analysis of network patterns

Source Code for Biology and Medicine

Volumn 1, Issue , 2006, Pages

  Besemann, Christopher ^a   Denton, Anne ^a   Carr, Nathan J ^b   Prüß, Birgit M ^b  

^a North Dakota State University   (United States)

^b NORTH DAKOTA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 34250825250     PISSN: None     EISSN: 17510473     Source Type: Journal    
DOI: 10.1186/1751-0473-1-8     Document Type: Article

References (54)

1. Tong AH Lesage G Bader GD Ding H Xu H Xin X Young J Berriz GF Brost RL Chang M Chen Y Cheng X Chua G Friesen H Goldberg DS Haynes J Humphries C He G Hussein S Ke L Krogan N Li Z Levinson JN Lu H Menard P Munyana C Parsons AB Ryan O Tonikian R Roberts T Sdicu AM Shapiro J Sheikh B Suter B Wong SL Zhang LV Zhu H Burd CG Munro S Sander C Rine J Greenblatt J Peter M Bretscher A Bell G Roth FP Brown GW Andrews B Bussey H Boone C Global mapping of the yeast genetic interaction network Science 2004 303 808-813 10.1126/science.1091317 14764870
2. Salgado H Gama-Castro S Peralta-Gil M az-Peredo E Sanchez-Solano F Santos-Zavaleta A Martinez-Flores I Jimenez-Jacinto V Bonavides-Martinez C Segura-Salazar J Martinez-Antonio A Collado-Vides J RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions Nucl Acids Res 2006 34 D394-D397 1347518 16381895 10.1093/nar/gkj156
3. Ito T Chiba T Ozawa R Yoshida M Hattori M Sakaki Y A comprehensive two-hybrid analysis to explore the yeast protein interactome Proc Natl Acad Sci U S A 2001 98 4569-4574 31875 11283351 10.1073/pnas.061034498
4. Uetz P Giot L Cagney G Mansfield TA Judson RS Knight JR Lockshon D Narayan V Srinivasan M Pochart P Qureshi-Emili A Li Y Godwin B Conover D Kalbfleisch T Vijayadamodar G Yang M Johnston M Fields S Rothberg JM A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae Nature 2000 403 623-627 10.1038/35001009 10688190
5. Truong K Ikura M Domain fusion analysis by applying relational algebra to protein sequence and domain databases BMC Bioinformatics 2003 4 16 156618 12734020 10.1186/1471-2105-4-16
6. Marcotte EM Pellegrini M Ng HL Rice DW Yeates TO Eisenberg D Detecting protein function and protein-protein interactions from genome sequences Science 1999 285 751-753 10.1126/science.285.5428.751 10427000
7. Wagner A Wu W Compactness and cycles in signal transduction and transcriptional regulation networks: A signature of natural selection? Adv Complex Syst 2005 7 419-432 10.1142/S0219525904000251
8. Przulj N Corneil DG Jurisica I Modeling interactome: Scale-free or geometric? Bioinformatics 2004 20 3508-3515 10.1093/bioinformatics/ bth436 15284103
9. Yu H Zhu X Greenbaum D Karro J Gerstein M TopNet: A tool for comparing biological sub-networks, correlating protein properties with topological statistics Nucleic Acids Res 2004 32 328-337 373274 14724320 10.1093/nar/ gkh164
10. Agrawal R Imielinski T Swami AN Mining association rules between sets of items in large databases: 1993/5/26. Washington, D.C. Proceedings of the ACM SIGMOD Conference 1993 207-216
11. Agrawal R Srikant R Fast algorithms for mining association rules in large databases: 1994/9/12. Santiago, Chile Proceedings of the Very Large Databases Conference 1994 487-499
12. Kuramochi M Karypis G Frequent subgraph discovery: 2001/11/29. San Jose, CA Proceedings of the IEEE International Conference on Data Mining 2001 313-320
13. Yan X Han J gSpan: Graph-based substructure pattern mining: 2002. Maebashi City, Japan Proceedings of the International Conference on Data Mining 2002
14. Goethals B Van den Bussche J Relational association rules: Getting WARMeR: 2002/9/16; London, UK. London, UK Pattern Detect and Disc 2002 125-139
15. Oyama T Kitano K Satou K Ito T Extraction of knowledge on protein-protein interaction by association rule discovery Bioinformatics 2002 18 705-714 10.1093/bioinformatics/18.5.705 12050067
16. Besemann C Denton A Yekkirala A Hutchison R Anderson M Differential association rules: Understanding annotations in protein interaction networks Advanced Data Mining Technologies in Bioinformatics Tamkang University, Taiwan, Idea Group Publishing Hsu HH 2006
17. Besemann C Denton A Yekkirala A Hutchison R Anderson M Differential association rule mining for the study of protein-protein interaction networks Seattle, Washington Zaki MJ, Morishita S and Rigoutsos I Proceedings of the 4th ACM SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD 2004) 2004 72-80
18. Osprey 2006 http://biodata.mshri.on.ca/osprey/servlet/Index
19. VisANT 2006 http://visant.bu.edu/
20. Cytoscape 2006 http://www.cytoscape.org/
21. Aragues R Jaeggi D Oliva B PIANA: Protein interactions and network analysis Bioinformatics 2006 22 1015-1017 10.1093/bioinformatics/btl072 16510498
22. Enright AJ Ouzounis CA BioLayout - an automatic graph layout algorithm for similarity visualization Bioinformatics 2001 17 853-854 10.1093/ bioinformatics/17.9.853 11590107
23. Hanisch D Sohler F Zimmer R ToPNet - an application for interactive analysis of expression data and biological networks Bioinformatics 2004 20 1470-1471 10.1093/bioinformatics/bth096 14962941
24. Iragne F Nikolski M Mathieu B Auber D Sherman D ProViz: Protein interaction visualization and exploration Bioinformatics 2005 21 272-274 10.1093/bioinformatics/bth494 15347570
25. Kolpakov FA Ananko EA Kolesov GB Kolchanov NA GeneNet: A gene network database and its automated visualization Bioinformatics 1998 14 529-537 10.1093/bioinformatics/14.6.529 9694992
26. Ju BH Han K Complexity management in visualizing protein interaction networks Bioinformatics 2003 19 Suppl 1 i177-i179 10.1093/bioinformatics/ btg1022 12855454
27. Bartlett DH Frantz BB Matsumura P Flagellar transcriptional activators FlbB and FlaI: Gene sequences and 5′ consensus sequences of operons under FlbB and FlaI control J Bacteriol 1988 170 1575-1581 211004 2832369
28. Prüß BM Campbell JW Van Dyk TK Zhu C Kogan Y Matsumura P FlhD/ FlhC is a regulator of anaerobic respiration and the Entner-Doudoroff pathway through induction of the methyl-accepting chemotaxis protein Aer J Bacteriol 2003 185 534-543 145316 12511500 10.1128/ JB.185.2.534-543.2003
29. Bertin P Terao E Lee EH Lejeune P Colson C Danchin A Collatz E The H-NS protein is involved in the biogenesis of flagella in Escherichia coli J Bacteriol 1994 176 5537-5540 196744 8071234
30. Francez-Charlot A Laugel B Van GA Dubarry N Wiorowski F Castanie-Cornet MP Gutierrez C Cam K RcsCDB His-Asp phosphorelay system negatively regulates the flhDC operon in Escherichia coli Mol Microbiol 2003 49 823-832 10.1046/j.1365-2958.2003.03601.x 12864862
31. Lehnen D Blumer C Polen T Wackwitz B Wendisch VF Unden G LrhA as a new transcriptional key regulator of flagella, motility and chemotaxis genes in Escherichia coli Mol Microbiol 2002 45 521-532 10.1046/ j.1365-2958.2002.03032.x 12123461
32. Shin S Park C Modulation of flagellar expression in Escherichia coli by acetyl phosphate and the osmoregulator OmpR J Bacteriol 1995 177 4696-4702 177235 7642497
33. Prüß BM Besemann C Denton A Wolfe AJ A complex transcription network controls the early stages of biofilm development by Escherichia coli J Bacteriol 2006 188 3731-3739 1482888 16707665 10.1128/JB.01780-05
34. Holland IB Schmitt L Young J Type 1 protein secretion in bacteria, the ABC-transporter dependent pathway (review) Mol Membr Biol 2005 22 29-39 16092522
35. Rodionov DA Hebbeln P Gelfand MS Eitinger T Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transporters J Bacteriol 2006 188 317-327 1317602 16352848 10.1128/JB.188.1.317-327.2006
36. Fruchterman TMJ Reingold EM Graph drawing by force-directed placement Software - Practice and Experience 1991 21 1129-1164 10.1002/ spe.4380211102
37. JUNG Java Universal Network/Graph Framework 2006 http://jung.sourceforge.net
38. Kanehisa M Goto S Hattori M oki-Kinoshita KF Itoh M Kawashima S Katayama T Araki M Hirakawa M From genomics to chemical genomics: New developments in KEGG Nucleic Acids Research 2006 34 D354-D357 1347464 16381885 10.1093/nar/gkj102
39. KEGG Kyoto Encyclopedia of Genes and Genomes 2006 http://www.genome.jp/ kegg 16442091
40. Lubitz SP Weiner JH The Escherichia coliynfEFGHI operon encodes polypeptides which are paralogues of dimethyl sulfoxide reductase (DmsABC) Arch Biochem Biophys 2003 418 205-216 10.1016/j.abb.2003.08.008 14522592
41. Galperin MY Bacterial signal transduction network in a genomic perspective Environ Microbiol 2004 6 552-567 1414778 15142243 10.1111/ j.1462-2920.2004.00633.x
42. Appleby JL Parkinson JS Bourret RB Signal transduction via the multi-step phosphorelay: Not necessarily a road less traveled Cell 1996 86 845-848 10.1016/S0092-8674(00)80158-0 8808618
43. Grunden AM Self WT Villain M Blalock JE Shanmugam KT An analysis of the binding of repressor protein ModE to modABCD (molybdate transport) operator/promoter DNA of Escherichia coli J Biol Chem 1999 274 24308-24315 10.1074/jbc.274.34.24308 10446207
44. Tanapongpipat S Reid E Cole JA Crooke H Transcriptional control and essential roles of the Escherichia coli ccm gene products in formate-dependent nitrite reduction and cytochrome c synthesis Biochem J 1998 334 (Pt 2) 355 365 1219697 9716493
45. Overton TW Griffiths L Patel MD Hobman JL Penn CW Cole JA Constantinidou C Microarray analysis of gene regulation by oxygen, nitrate, nitrite, FNR, NarL and NarP during anaerobic growth of Escherichia coli: New insights into microbial physiology Biochem Soc Trans 2006 34 104-107 10.1042/BST0340104 16417494
46. BISON 2006 http://denton.cs.ndsu.nodak.edu/bison/
47. RegulonDB 2006 http://regulondb.ccg.unam.mx/index.html
48. Oshima T Aiba H Masuda Y Kanaya S Sugiura M Wanner BL Mori H Mizuno T Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12 Mol Microbiol 2002 46 281-291 10.1046/ j.1365-2958.2002.03170.x 12366850
49. E. coli genome project 2006 http://www.genome.wisc.edu/
50. Blattner FR Plunkett G III Bloch CA Perna NT Burland V Riley M Collado-Vides J Glasner JD Rode CK Mayhew GF Gregor J Davis NW Kirkpatrick HA Goeden MA Rose DJ Mau B Shao Y The complete genome sequence of Escherichia coli K-12 Science 1997 277 1453-1474 10.1126/ science.277.5331.1453 9278503
51. Bateman A Coin L Durbin R Finn RD Hollich V Griffiths-Jones S Khanna A Marshall M Moxon S Sonnhammer EL Studholme DJ Yeats C Eddy SR The Pfam protein families database Nucleic Acids Res 2004 32 D138-D141 308855 14681378 10.1093/nar/gkh121
52. Pfam 2006 http://www.sanger.ac.uk/Software/Pfam/
53. Eddy SR Profile hidden Markov models Bioinformatics 1998 14 755-763 10.1093/bioinformatics/14.9.755 9918945
54. HMMER 2004 http://hmmer.janelia.org/