pDAWG: An integrated database for plant cell wall genes

Bioenergy Research

Volumn 2, Issue 4, 2009, Pages 209-216

  Mao, Fenglou ^a,b   Yin, Yanbin ^a,b   Zhou, Fengfeng ^a,b   Chou, Wen Chi ^a,b   Zhou, Chan ^a,b   Chen, Huiling ^a,b   Xu, Ying ^a,b  

^a University of Georgia ^*  (United States)

^b DOE BioEnergy Science Center BESC   (United States)

Author keywords

Biofuel; Bioinformatics; Biological database; Cell wall genes

Indexed keywords

BIOLOGICAL DATABASE; CELL WALL GENES; CELL WALLS; COMPARATIVE ANALYSIS; GRAPHICAL INTERFACE; INDIVIDUAL PROTEINS; INTEGRATED DATABASE; KNOWLEDGE DISCOVERY; PHYLOGENETIC TREES; PLANT CELL WALL; PLANT GENOMES; PROTEIN STRUCTURES; QUERYING SYSTEMS; SUBCELLULAR LOCALIZATIONS;

BIOFUELS; CARBOHYDRATES; DATABASE SYSTEMS; GENES; MODELS; PLANT CELL CULTURE; PROTEINS;

BIOINFORMATICS;

ALGAE;

EID: 70449556676     PISSN: 19391234     EISSN: 19391242     Source Type: Journal    
DOI: 10.1007/s12155-009-9052-z     Document Type: Article

References (44)

1. Duvick J et al (2008) PlantGDB: A resource for comparative plant genomics. Nucl Acids Res 36(suppl_1): D959-D965.
2. JGI (2009) Phytozome: A tool for green plant comparative genomics. Available from http://www.phytozome.net/.
3. Wall PK et al (2008) PlantTribes: A gene and gene family resource for comparative genomics in plants. Nucleic Acids Res 36(Database issue): D970-D976.
4. Conte MG et al (2008) GreenPhylDB: A database for plant comparative genomics. Nucleic Acids Res 36(Database issue): D991-D998.
5. Hartmann S et al (2006) Phytome: A platform for plant comparative genomics. Nucleic Acids Res 34(Database issue): D724-D730.
6. Girke T et al (2004) The Cell Wall Navigator database. A systems-based approach to organism-unrestricted mining of protein families involved in cell wall metabolism. Plant Physiol 136(2): 3003-3008 discussion 3001.
7. Yong W et al (2005) Genomics of plant cell wall biogenesis. Planta 221(6): 747-51.
8. Cao P-J et al (2008) Construction of a rice glycosyltransferase phylogenomic database and identification of rice-diverged glycosyltransferases. Molecular Plant 1(5): 858-877.
9. Punta M, Ofran Y (2008) The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function. PLoS Comput Biol 4(10): e1000160.
10. Minshull J et al (2005) Predicting enzyme function from protein sequence. Curr Opin Chem Biol 9(2): 202-209.
11. Watson JD, Laskowski RA, Thornton JM (2005) Predicting protein function from sequence and structural data. Curr Opin Struct Biol 15(3): 275-284.
12. Lee D, Redfern O, Orengo C (2007) Predicting protein function from sequence and structure. Nat Rev Mol Cell Biol 8(12): 995-1005.
13. Mazumder R, Vasudevan S (2008) Structure-guided comparative analysis of proteins: Principles, tools, and applications for predicting function. PLoS Comput Biol 4(9): e1000151.
14. Sjolander K (2004) Phylogenomic inference of protein molecular function: Advances and challenges. Bioinformatics 20(2): 170-179.
15. Brown DM et al (2005) Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell 17(8): 2281-2295.
16. Nariai N, Kolaczyk ESD, Kasif S (2007) Probabilistic protein function prediction from heterogeneous genome-wide data. PLoS One 2(3): e337.
17. Yin Y, Huang J, Xu Y (2009) The cellulose synthase superfamily in fully sequenced plants and algae. BMC Plant Biol 9(1): 99.
18. Ming R et al (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452(7190): 991-996.
19. Cantarel BL et al (2009) The Carbohydrate-Active EnZymes database (CAZy): An expert resource for glycogenomics. Nucleic Acids Res 37(Database issue): D233-D238.
20. Altschul SF et al (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25(17): 3389-3402.
21. Marchler-Bauer A et al (2009) CDD: Specific functional annotation with the Conserved Domain Database. Nucleic Acids Res 37(Database issue): D205-D210.
22. Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14(9): 755-763.
23. Katoh K et al (2005) MAFFT version 5: Improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33(2): 511-518.
24. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52(5): 696-704.
25. Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56(4): 564-577.
26. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17(4): 540-552.
27. Wu S, Zhang Y (2008) MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins 72(2): 547-556.
28. Berman HM et al (2000) The protein data bank. Nucleic Acids Res 28(1): 235-242.
29. Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234(3): 779-815.
30. Zhang Y, Skolnick J (2005) TM-align: A protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33(7): 2302-2309.
31. Kerrien S et al (2007) IntAct-open source resource for molecular interaction data. Nucleic Acids Res 35(Database issue): D561-D565.
32. Geisler-Lee J et al (2007) A predicted interactome for Arabidopsis. Plant Physiol 145(2): 317-329.
33. Cui J et al (2007) AtPID: Arabidopsis thaliana protein interactome database-an integrative platform for plant systems biology. Nucleic Acids Res 36(Database issue): D999-D1008.
34. Raghavachari B et al (2008) DOMINE: A database of protein domain interactions. Nucleic Acids Res 36(Database issue): D656-D661.
35. Nakai K, Horton P (1999) PSORT: A program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem Sci 24(1): 34-35.
36. Small I et al (2004) Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences. PROTEOMICS 4(6): 1581-1590.
37. Chen H, Huang N, Sun Z (2006) SubLoc: A server/client suite for protein subcellular location based on SOAP. Bioinformatics 22(3): 376-377.
38. Kaundal R, Zhao PX (2009) AtSubP: The Arabidopsis subcellular localization prediction server. Available from http://bioinfo3. noble. org/AtSubP/index. html.
39. Kaundal R, Raghava GPS (2009) RSLpred: An integrative system for predicting subcellular localization of rice proteins combining compositional and evolutionary information. PROTEOMICS 9(9): 2324-2342.
40. York WS, O'Neill MA (2008) Biochemical control of xylan biosynthesis-which end is up? Curr Opin Plant Biol 11(3): 258-265.
41. Mohnen D (2008) Pectin structure and biosynthesis. Curr Opin Plant Biol 11(3): 266-277.
42. Singh SK et al (2005) Cell adhesion in Arabidopsis thaliana is mediated by ECTOPICALLY PARTING CELLS 1-a glycosyltransferase (GT64) related to the animal exostosins. Plant J 43(3): 384-397.
43. Zhong R, Demura T, Ye ZH (2006) SND1, a NAC domain transcription factor, is a key regulator of secondary wall synthesis in fibers of Arabidopsis. Plant Cell 18(11): 3158-3170.
44. Dereeper A et al (2008) Phylogeny.fr: Robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 36(Web Server issue): W465-W469.