Interactive analysis of systems biology molecular expression data

BMC Systems Biology

Volumn 2, Issue , 2008, Pages

  Zhang, Mingwu ^a,b   Ouyang, Qi ^a   Stephenson, Alan ^c   Kane, Michael D ^c   Salt, David E ^a   Prabhakar, Sunil ^b   Burgner, John ^a   Buck, Charles ^a   Zhang, Xiang ^d  

^a PURDUE UNIVERSITY   (United States)

^b Purdue University   (United States)

^c PURDUE UNIVERSITY   (United States)

^d UNIVERSITY OF LOUISVILLE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SIMULATION; DATA BASE; FACTUAL DATABASE; GENE EXPRESSION PROFILING; INFORMATION RETRIEVAL; METABOLISM; METHODOLOGY; PHYSIOLOGY; SIGNAL TRANSDUCTION; SYSTEM ANALYSIS; SYSTEMS BIOLOGY;

ALGORITHMS; COMPUTER GRAPHICS; COMPUTER SIMULATION; DATABASE MANAGEMENT SYSTEMS; DATABASES, FACTUAL; GENE EXPRESSION PROFILING; INFORMATION STORAGE AND RETRIEVAL; MODELS, BIOLOGICAL; PROTEOME; SIGNAL TRANSDUCTION; SOFTWARE; SYSTEMS BIOLOGY; SYSTEMS INTEGRATION; USER-COMPUTER INTERFACE;

EID: 42349097472     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-2-23     Document Type: Article

References (25)

1. Hood L Systems biology: Integrating technology, biology, and computation Mechanisms of Ageing and Development 2003, 124:9-16. 10.1016/ S0047-6374(02)00164-1
2. Asara JM Zhang X Zheng B Christofk HH Wu N Cantley LC In Gel stable isotope labeling: A strategy for mass spectrometry based relative quantification J Proteome Res 2006, 5:155-163. 10.1021/pr050334t 16396506
3. Wang S Zhang X Regnier FE Quantitative Proteomics strategy involving the selection of peptides containing both cysteine and histidine from tryptic digests of cell lysates J Chromatogr A 2002, 949:153-162. 10.1016/S0021-9673(01)01509-6 11999731
4. Weckwerth W Metabolomics in system biology Annu Rev Plant Biol 2003, 54:669-689. 10.1146/annurev.arplant.54.031902.135014 14503007
5. Goodacre R Vaidyanathan S Dunn WB Harrigan GG Kell DB Metabolomics by numbers: Acquiring and understanding global metabolite data TRENDS in Biotechnology 2004, 22:245-252. 10.1016/j.tibtech.2004.03.007 15109811
6. Lahner B Gong J Mohmoudian M Smith EL Abid KB Rogers EE Guerinot ML Harper JF Ward JM Mclntyre L Schroeder JI Salt DE Genomic scale profiling of nutrient and trace elements in Arabidopsis thaliana Nature Biotechnology 2003, 21:1215-1221. 10.1038/nbt865 12949535
7. Valet G Cytomics: An entry to biomedical cell systems biology Cytometry Part A 2005, 63:67-68. 10.1002/cyto.a.20110
8. Butcher EC Berg EL Kunkel EJ System biology in drug discovery Nature Biotechnology 2003, 22:1253-1259. 10.1038/nbt1017
9. Clish CB Davidov E Oresic M Plasterer T Lavine G Londo TR Meys M Snell P Stochaj W Adourian A Zhang X Morel N Neumann E Verheij E Vogels JTWE Havekes LM Afeyan N Regnier FE Greef J Naylor S Integrative biological analysis of the APOE*3Leiden transgenic mouse Omics: A Journal of Integrative Biology 2004, 8:3-13. 10.1089/153623104773547453 15107233
10. Zhang X Hines W Adamec J Asara J Naylor S Regnier FE An automated method for the analysis of stable isotope labeling data for proteomics J Am Soc Mass Spectrom 2005, 16:1181-1191. 10.1016/j.jasms.2005.03.016 15922621
11. Shannon P Markiel A Ozier O Baliga NS Wang JT Ramage D Amin N Schwikowski B Ideker T Cytoscape: A software environment for integrated models of biomolecular interaction networks Genome Res 2003, 13:2498-2504. 403769 14597658 10.1101/gr.1239303
12. Graphviz http://www.graphviz.org/
13. Adamcsek B Palla G Farkas IJ Derényi I Vicsek T CFinder: Locating cliques and overlapping modules in biological networks Bioinformatics 2006, 22:1021-1023. 10.1093/bioinformatics/btl039 16473872
14. TomSawyer http://www.tomsawyer.com
15. VisAnt http://visant.bu.edu/
16. BiologicalNetworks http://biologicalnetworks.net/
17. Chen M Zhu Q Chen Z An integrated interactive environment for knowledge discovery from heterogeneous data resource Information and Software Technology 2001, 43:487-496. 10.1016/S0950-5849(01)00159-8
18. Zhang X Asara JM Adamec J Oussani M Elmagarmid AK Data preprocessing in liquid chromatography mass spectrometry based proteomics Bioinformatics 2005, 21:4054-4059. 10.1093/bioinformatics/bti660 16150809
19. Fruchterman TMJ Reingold EM Graph drawing by force-directed placement Software-Pratice and Experience 1991, 21:1129-1164. 10.1002/ spe.4380211102
20. Tollis IG Battista GD Eades P Tamassia R Graph drawing - algorithms for the visualization of graphs Prentice Hall, Upper Saddle River, NJ; 1999.
21. Sheskin DJ Handbook of Parametric and Nonparametric Statistical Procedures Chapman & Hall/CRC, Washington, DC 2 2000 10846727
22. UniProt http://www.pir.uniprot.org/cgi-bin/textSearch
23. KEGG http://www.genome.jp/kegg/
24. GenBank http://www.ncbi.nlm.nih.gov/
25. Press WH Teukolsky SA Vetterling WT Flannery BP Numerical Recipes in C++, the art of scientific computing Cambridge University Press, Cambridge, UK 2 2002.