Transcriptome analysis by GeneTrail revealed regulation of functional categories in response to alterations of iron homeostasis in Arabidopsis thaliana

BMC Plant Biology

Volumn 11, Issue , 2011, Pages

  Schuler, Mara ^a   Keller, Andreas ^a   Backes, Christina ^a   Philippar, Katrin ^b   Lenhof, Hans Peter ^a   Bauer, Petra ^a  

^a SAARLAND UNIVERSITY   (Germany)

^b UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA;

IRON; PLANT RNA;

ARABIDOPSIS; ARTICLE; CARBOHYDRATE METABOLISM; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA MINING; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HOMEOSTASIS; INTERNET; METABOLISM; METHODOLOGY; PHYSIOLOGY; PLANT GENE; PLANT LEAF; PLANT ROOT;

ARABIDOPSIS; CARBOHYDRATE METABOLISM; DATA MINING; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; HOMEOSTASIS; INTERNET; IRON; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT LEAVES; PLANT ROOTS; RNA, PLANT; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 79955979082     PISSN: None     EISSN: 14712229     Source Type: Journal    
DOI: 10.1186/1471-2229-11-87     Document Type: Article

References (24)

1. Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30:207-210. 10.1093/nar/30.1.207, 99122, 11752295.
2. Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese JC, Dwight SS, Kaloper M, Weng S, Jin H, Ball CA, Eisen MB, Spellman PT, Brown PO, Botstein D, Cherry MJ. The Stanford Microarray Database. Nucleic Acids Res 2001, 29:152-155. 10.1093/nar/29.1.152, 29818, 11125075.
3. Winter D, Vinegar B, Nahal H, Ammar R, Wilson, Greg V, Provart J. An "electronic fluorescent pictograph" browser for exploring and analyzing large-scale biological data sets. PLoS ONE 2007, 2:e718. 10.1371/journal.pone.0000718, 1934936, 17684564.
4. Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W. GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol 2004, 136:2621-2632. 10.1104/pp.104.046367, 523327, 15375207.
5. Toufighi K, Brady SM, Austin R, Ly E, Provart NJ. The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses. Plant J 2005, 43:153-163. 10.1111/j.1365-313X.2005.02437.x, 15960624.
6. 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, 37:914-939. 10.1111/j.1365-313X.2004.02016.x, 14996223.
7. Obayashi T, Kinoshita K, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D, Saito K, Ohta H. ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res 2007, 35:D863-9. 10.1093/nar/gkl783, 1716726, 17130150.
8. Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K. ATTED-II provides coexpressed gene networks for Arabidopsis. Nucleic Acids Res 2009, 37:D987-91. 10.1093/nar/gkn807, 2686564, 18953027.
9. Katari MS, Nowicki SD, Aceituno FF, Nero D, Kelfer J, Thompson LP, Cabello JM, Davidson RS, Goldberg AP, Shasha DE, Coruzzi GM, Gutierrez RA. VirtualPlant: a software platform to support systems biology research. Plant Physiol 2009, 152:500-515. 2815851, 20007449.
10. Backes C, Keller A, Kuentzer J, Kneissl B, Comtesse N, Elnakady YA, Muller R, Meese E, Lenhof HP. GeneTrail--advanced gene set enrichment analysis. Nucleic Acids Res 2007, 35:W186-92. 10.1093/nar/gkm323, 1933132, 17526521.
11. Keller A, Ludwig N, Backes C, Romeike BF, Comtesse N, Henn W, Steudel WI, Mawrin C, Lenhof HP, Meese E. Genome wide expression profiling identifies specific deregulated pathways in meningioma. Int J Cancer 2009, 124:346-351. 10.1002/ijc.23942, 19003955.
12. Elnakady YA, Rohde M, Sasse F, Backes C, Keller A, Lenhof HP, Weissman KJ, Muller R. Evidence for the mode of action of the highly cytotoxic Streptomyces polyketide kendomycin. Chembiochem 2007, 8:1261-1272. 10.1002/cbic.200700050, 17592829.
13. Fehrmann RS, de Jonge HJ, Ter Elst A, de Vries A, Crijns AG, Weidenaar AC, Gerbens F, de Jong S, van der Zee AG, de Vries EG, Kamps WA, Hofstra RM, Te Meerman GJ, de Bont ES. A new perspective on transcriptional system regulation (TSR): towards TSR profiling. PLoS ONE 2008, 3:e1656. 10.1371/journal.pone.0001656, 2250855, 18297136.
14. Klatte M, Schuler M, Wirtz M, Fink-Straube C, Hell R, Bauer P. The analysis of Arabidopsis nicotianamine synthase mutants reveals functions for nicotianamine in seed iron loading and iron deficiency responses. Plant Physiol 2009, 150:257-271. 10.1104/pp.109.136374, 2675739, 19304929.
15. Clausen C, Ilkavets I, Thomson R, Philippar K, Vojta A, Mohlmann T, Neuhaus E, Fulgosi H, Soll J. Intracellular localization of VDAC proteins in plants. Planta 2004, 220:30-37. 10.1007/s00425-004-1325-3, 15258762.
16. Duy D, Wanner G, Meda AR, von Wiren N, Soll J, Philippar K. PIC1, an Ancient Permease in Arabidopsis Chloroplasts, Mediates Iron Transport. Plant Cell 2007,
17. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:185-193. 10.1093/bioinformatics/19.2.185, 12538238.
18. Rafael IA. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Research 2003, 31:15e-15.
19. Keller A, Backes C, Al-Awadhi M, Gerasch A, Kuntzer J, Kohlbacher O, Kaufmann M, Lenhof HP. GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments. BMC Bioinformatics 2008, 9:552. 10.1186/1471-2105-9-552, 2627893, 19099609.
20. Keller A, Backes C, Lenhof HP. Computation of significance scores of unweighted Gene Set Enrichment Analyses. BMC Bioinformatics 2007, 8:290. 10.1186/1471-2105-8-290, 1994690, 17683603.
21. Sharov AA, Dudekula DB, Ko MS. A web-based tool for principal component and significance analysis of microarray data. Bioinformatics 2005, 21:2548-2549. 10.1093/bioinformatics/bti343, 15734774.
22. Dinneny JR, Long TA, Wang JY, Jung JW, Mace D, Pointer S, Barron C, Brady SM, Schiefelbein J, Benfey PN. Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science (New York, N.Y.) 2008, 320:942-5.
23. Brumbarova T, Matros A, Mock H-P, Bauer P. A proteomic study shows differential regulation of stress, redox regulation and peroxidase proteins by iron supply and the transcription factor FER. Plant J 2008,
24. Thomas YJW, Wolfgang Schmidt W-DL. Transcriptional Profiling of the Arabidopsis Iron Deficiency Response Reveals Conserved Transition Metal Homeostasis Networks. Plant Physiol 2010, 10:109.