PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Usadel, Björn ^a   Nagel, Axel ^b   Steinhauser, Dirk ^a   Gibon, Yves ^a   Bläsing, Oliver E ^a   Redestig, Henning ^a   Sreenivasulu, Nese ^c   Krall, Leonard ^a   Hannah, Matthew A ^a   Poree, Fabien ^a   Fernie, Alisdair R ^a   Stitt, Mark ^d  

^a MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

^b German Genome Resource Center RZPD   (Germany)

^c LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

^d NONE

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL INFORMATION; FUNCTIONAL ONTOLOGIES; LARGE SCALE EXPERIMENTS; MICROARRAY DATA ANALYSIS; MICROARRAY EXPERIMENTS; MICROARRAY TECHNOLOGIES; PAIR-WISE COMPARISON; STAND-ALONE SOFTWARE;

CURRICULA; DATA VISUALIZATION; MICROARRAYS; TEACHING; TOOLS;

EXPERIMENTS;

ARTICLE; COLD STRESS; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; GENOME; INFORMATION PROCESSING; MICROARRAY ANALYSIS; MUTANT; RANK SUM TEST; SPECIES COMPARISON; STATISTICAL ANALYSIS; TRANSGENICS; DATA BASE; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETIC DATABASE; TRENDS;

DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 33846584605     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-535     Document Type: Article

References (28)

1. Parkinson H Sarkans U Shojatalab M Abeygunawardena N Contrino S Coulson R Farne A Lara GG Holloway E Kapushesky M Lilja P Mukherjee G Oezcimen A Rayner T Rocca-Serra P Sharma A Sansone S Brazma A ArrayExpress - a public repository for microarray gene expression data at the EBI Nucleic Acids Res 33 Database D553-5 2005 Jan 1 540010 15608260
2. Barrett T Suzek TO Troup DB Wilhite SE Ngau WC Ledoux P Rudnev D Lash AE Fujibuchi W Edgar R NCBI GEO: Mining millions of expression profiles - database and tools Nucleic Acids Res 33 Database D562-6 2005 Jan 1 539976 15608262
3. Craigon DJ James N Okyere J Higgins J Jotham J May S NASCArrays: A repository for microarray data generated by NASC's transcriptomics service Nucleic Acids Res 2004 32 D575-7 308867 14681484 10.1093/nar/ gkh133
4. Blasing OE Gibon Y Gunther M Hohne M Morcuende R Osuna D Thimm O Usadel B Scheible WR Stitt M Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis Plant Cell 2005 17 3257-81 1315368 16299223 10.1105/ tpc.105.035261
5. http://web.uni-frankfurt.de/fb15/botanik/mcb/AFGN/atgenex.htm
6. Usadel B Nagel A Thimm O Redestig H Blaesing OE Palacios-Rojas N Selbig J Hannemann J Piques MC Steinhauser D Scheible WR Gibon Y Morcuende R Weicht D Meyer S Stitt M Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses Plant Physiol 2005 138 1195-204 1176394 16009995 10.1104/pp.105.060459
7. Tokimatsu T Sakurai N Suzuki H Ohta H Nishitani K Koyama T Umezawa T Misawa N Saito K Shibata KaPPA-view: A web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps Plant Physiol 2005 138 3 1289-300 1176402 16010003 10.1104/ pp.105.060525
8. Mueller LA Zhang P Rhee SY AraCyc: A biochemical pathway database for Arabidopsis Plant Physiol 2003 132 2 453-60 166988 12805578 10.1104/ pp.102.017236
9. Junker BH Klukas C Schreiber F VANTED: A system for advanced data analysis and visualization in the context of biological networks BMC Bioinformatics 2006 7 109 1413562 16519817 10.1186/1471-2105-7-109
10. The Gene Ontology Consortium Gene Ontology: Tool for the unification of biology Nature Genet 2000 25 25-29 10.1038/75556 10802651
11. Khatri P Draghici S Ontological analysis of gene expression data: current tools, limitations, and open problems Bioinformatics 2005 21 3587-3595 10.1093/bioinformatics/bti565 15994189
12. Lee HK Braynen W Keshav K Pavlidis P ErmineJ: Tool for functional analysis of gene expression data sets BMC Bioinformatics 2005 6 269 1310606 16280084 10.1186/1471-2105-6-269
13. R Development Core Team R A language and environment for statistical computing R Foundation for Statistical Computing, Vienna, Austria ISBN 3-900051-07-0
14. Thimm O Blasing O Gibon Y Nagel A Meyer S Kruger P Selbig J Muller LA Rhee SY Stitt M MAPMAN: A user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes Plant J 2004 37 6 914-39 10.1111/j.1365-313X.2004.02016.x 14996223
15. Gentleman RC Carey VJ Bates DM Bolstad B Dettling M Dudoit S Ellis B Gautier L Ge Y Gentry J Hornik K Hothorn T Huber W Iacus S Irizarry R Leisch F Li C Maechler M Rossini AJ Sawitzki G Smith C Smyth G Tierney L Yang JY Zhang J Bioconductor: Open software development for computational biology and bioinformatics Genome Biol 2004 5 R80 545600 15461798 10.1186/gb-2004-5-10-r80
16. Lanczos C A Precision Approximation of the Gamma Function SIAM Journal on Numerical Analysis series B 1964 1 86-96 10.1137/0701008
17. http://www.gnu.org/software/gsl/
18. Benjamini Y Hochberg Y Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing J Roy Stat Soc Ser B 1995 57 289-300
19. Benjamini Y Yekutieli D The control of the false discovery rate in multiple testing under dependency Annals of Statistics 2001 29 1165-1188 10.1214/aos/1013699998
20. Irizarry RA Hobbs B Collin F Beazer-Barclay YD Antonellis KJ Scherf U Speed TP Exploration, normalization, and summaries of high density oligonucleotide array probe level data Journal Biostatistics 2003 4 249-264 10.1093/biostatistics/4.2.249
21. Smyth GK Limma: Linear models for microarray data Bioinformatics and Computational Biology Solutions using R and Bioconductor Springer, New York Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W 397-420
22. Hannah MA Heyer AG Hincha DK A global survey of gene regulation during cold acclimation in Arabidopsis thaliana PLoS Genet 2005 1 2 e26 1189076 16121258 10.1371/journal.pgen.0010026
23. Scheer M Klawonn F Munch R Grote A Hiller K Choi C Koch I Schobert M Hartig E Klages U Jahn D JProGO: A novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information Nucleic Acids Res 2006 34 W510-5 1538798 16845060
24. Manoli T Gretz N Grone HJ Kenzelmann M Eils R Brors B Group testing for pathway analysis improves comparability of different microarray datasets Bioinformatics 2006 22 2500-6 10.1093/bioinformatics/btl424 16895928
25. Pelizzola M Pavelka N Foti M Ricciardi-Castagnoli P AMDA: An R package for the automated microarray data analysis BMC Bioinformatics 2006 7 335 1534071 16824223 10.1186/1471-2105-7-335
26. Zeeberg BR Qin H Narasimhan S Sunshine M Cao H Kane DW Reimers M Stephens RM Bryant D Burt SK Elnekave E Hari DM Wynn TA Cunningham-Rundles C Stewart DM Nelson D Weinstein JN High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID) BMC Bioinformatics 2005 6 168 1190154 15998470 10.1186/1471-2105-6-168
27. Urbanczyk-Wochniak E Usadel B Thimm O Nunes-Nesi A Carrari F Davy M Blasing O Kowalczyk M Weicht D Polinceusz A Meyer S Stitt M Fernie AR Conversion of MapMan to allow the analysis of transcript data from Solanaceous species: Effects of genetic and environmental alterations in energy metabolism in the leaf Plant Mol Biol 2006 60 773-92 10.1007/ s11103-005-5772-4 16649112
28. Tellström V Usadel B Thimm O Stitt M Küster H Niehaus K The lipopolysaccharide of Sinorhizobium meliloti suppresses defense-associated gene expression in cell cultures of the host plant Medicago truncatula Plant Physiol 2007