CINPER: An Interactive Web System for Pathway Prediction for Prokaryotes

PLoS ONE

Volumn 7, Issue 12, 2012, Pages

  Mao, Xizeng ^a,b   Chen, Xin ^c   Zhang, Yu ^c   Pangle, Spencer ^a   Xu, Ying ^a,b,c  

^a University of Georgia ^*  (United States)

^b UNIVERSITY OF GEORGIA   (United States)

^c JILIN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; GENE NETWORK; GENETIC DATABASE; INFORMATION PROCESSING; MOLECULAR GENETICS; PREDICTION; PROKARYOTE; SYNECHOCYSTIS; WEB BROWSER;

ARCHAEA; BACTERIA; DATABASES, GENETIC; GENE REGULATORY NETWORKS; INTERNET; MODELS, GENETIC; OPERON; PHYLOGENY; PROTEIN INTERACTION MAPS; SOFTWARE; TRANSCRIPTOME;

PROKARYOTA; SYNECHOCYSTIS SP.;

EID: 84870924247     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0051252     Document Type: Article

References (40)

1. Bader GD, Cary MP, Sander C, (2006) Pathguide: a pathway resource list. Nucleic Acids Res 34: D504-506.
2. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, et al. (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34: D354-357.
3. Kanehisa M, Goto S, (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30.
4. Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, et al. (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res 33: 6083-6089.
5. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, et al. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33: 5691-5702.
6. Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, et al. (2010) Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Briefings in Bioinformatics 11: 40-79.
7. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M, (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35: W182-185.
8. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, et al. (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: 75.
9. Kharchenko P, Chen L, Freund Y, Vitkup D, Church GM, (2006) Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics 7: 177.
10. Orth JD, Palsson BO, (2010) Systematizing the generation of missing metabolic knowledge. Biotechnology and Bioengineering 107: 403-412.
11. Osterman A, (2003) Missing genes in metabolic pathways: a comparative genomics approach. Current Opinion in Chemical Biology 7: 238-251.
12. Mao F, Su Z, Olman V, Dam P, Liu Z, et al. (2006) Mapping of orthologous genes in the context of biological pathways: An application of integer programming. Proc Natl Acad Sci U S A 103: 129-134.
13. Kharchenko P, Vitkup D, Church GM, (2004) Filling gaps in a metabolic network using expression information. Bioinformatics 20 (Suppl 1): i178-185.
14. Kharchenko P, Chen L, Freund Y, Vitkup D, Church GM, (2006) Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics 7: 177-177.
15. Chen L, Vitkup D, (2006) Predicting genes for orphan metabolic activities using phylogenetic profiles. Genome biology 7: R17-R17.
16. Su Z, Mao F, Dam P, Wu H, Olman V, et al. (2006) Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102. Nucleic Acids Res 34: 1050-1065.
17. Mao X, Olman V, Stuart R, Paulsen IT, Palenik B, et al. (2010) Computational prediction of the osmoregulation network in Synechococcus sp. WH8102. BMC Genomics 11: 291.
18. Su Z, Olman V, Mao F, Xu Y, (2005) Comparative genomics analysis of NtcA regulons in cyanobacteria: regulation of nitrogen assimilation and its coupling to photosynthesis. Nucleic Acids Res 33: 5156-5171.
19. Su Z, Olman V, Xu Y, (2007) Computational prediction of Pho regulons in cyanobacteria. BMC Genomics 8: 156.
20. Pruitt KD, Tatusova T, Klimke W, Maglott DR, (2009) NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res 37: D32-36.
21. Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, et al. (2010) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 38: D473-479.
22. Mao F, Dam P, Chou J, Olman V, Xu Y, (2009) DOOR: a database for prokaryotic operons. Nucleic Acids Res 37: D459-463.
23. Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39: D561-568.
24. Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, et al. (2010) Cytoscape Web: an interactive web-based network browser. Bioinformatics 26: 2347-2348.
25. Mushegian AR, Koonin EV, (1996) A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci U S A 93: 10268-10273.
26. Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, et al. (2012) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 40: D742-753.
27. Brouwer RW, Kuipers OP, van Hijum SA, (2008) The relative value of operon predictions. Briefings in Bioinformatics 9: 367-375.
28. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO, (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A 96: 4285-4288.
29. Gillis J, Pavlidis P, (2012) "Guilt by association" is the exception rather than the rule in gene networks. PLoS Comput Biol 8: e1002444.
30. Hansson M, Hederstedt L, (1994) Bacillus subtilis HemY is a peripheral membrane protein essential for protoheme IX synthesis which can oxidize coproporphyrinogen III and protoporphyrinogen IX. J Bacteriol 176: 5962-5970.
31. Du Q, Wang H, Xie J, (2011) Thiamin (vitamin B1) biosynthesis and regulation: a rich source of antimicrobial drug targets? Int J Biol Sci 7: 41-52.
32. Yu WB, Gao SH, Yin CY, Zhou Y, Ye BC, (2011) Comparative transcriptome analysis of Bacillus subtilis responding to dissolved oxygen in adenosine fermentation. PLoS One 6: e20092.
33. Andrews SC, Robinson AK, Rodriguez-Quinones F, (2003) Bacterial iron homeostasis. FEMS Microbiol Rev 27: 215-237.
34. Grass G, Otto M, Fricke B, Haney CJ, Rensing C, et al. (2005) FieF (YiiP) from Escherichia coli mediates decreased cellular accumulation of iron and relieves iron stress. Arch Microbiol 183: 9-18.
35. Kobayashi M, Ishizuka T, Katayama M, Kanehisa M, Bhattacharyya-Pakrasi M, et al. (2004) Response to oxidative stress involves a novel peroxiredoxin gene in the unicellular cyanobacterium Synechocystis sp. PCC 6803. Plant Cell Physiol 45: 290-299.
36. Shcolnick S, Summerfield TC, Reytman L, Sherman LA, Keren N, (2009) The mechanism of iron homeostasis in the unicellular cyanobacterium synechocystis sp. PCC 6803 and its relationship to oxidative stress. Plant Physiology 150: 2045-2056.
37. Morel FM, Price NM, (2003) The biogeochemical cycles of trace metals in the oceans. Science 300: 944-947.
38. Morrissey J, Bowler C, (2012) Iron utilization in marine cyanobacteria and eukaryotic algae. Front Microbiol 3: 43.
39. Katoh H, Hagino N, Grossman AR, Ogawa T, (2001) Genes essential to iron transport in the cyanobacterium Synechocystis sp. strain PCC 6803. J Bacteriol 183: 2779-2784.
40. van Iersel MP, Kelder T, Pico AR, Hanspers K, Coort S, et al. (2008) Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics 9: 399.