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References (54)
-
Robert Boyer, Strother Moore (1977)
A fast string searching algorithmCommun. ACM, 20
-
A. Brazma, P. Hingamp, John Quackenbush, G. Sherlock, P. Spellman, C. Stoeckert, J. Aach, W. Ansorge, C. Ball, H. Causton, T. Gaasterland, Patrick Glenisson, F. Holstege, Irene Kim, V. Markowitz, J. Matese, H. Parkinson, A. Robinson, Ugis Sarkans, S. Schulze-Kremer, Jason Stewart, Ronald Taylor, J. Vilo, M. Vingron (2001)
Minimum information about a microarray experiment (MIAME)—toward standards for microarray dataNature Genetics, 29
-
D. Boyes, A. Zayed, Robert Ascenzi, Amy McCaskill, N. Hoffman, K. Davis, J. Görlach (2001)
Growth Stage–Based Phenotypic Analysis of ArabidopsisThe Plant Cell Online, 13
-
Hunter Fraser, Aaron Hirsh, D. Wall, M. Eisen (2004)
Coevolution of gene expression among interacting proteinsProceedings of the National Academy of Sciences of the United States of America, 101
-
S. Harmer, J. Hogenesch, M. Straume, H. Chang, B. Han, Tong Zhu, X. Wang, J. Kreps, S. Kay (2000)
Orchestrated transcription of key pathways in Arabidopsis by the circadian clock.Science, 290 5499
-
Thijs (2002)
A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genesJ. Comput. Biol., 9
-
Ron Edgar, M. Domrachev, A. Lash (2002)
Gene Expression Omnibus: NCBI gene expression and hybridization array data repositoryNucleic acids research, 30 1
-
Linqu Han, M. Mason, E. Risseeuw, W. Crosby, D. Somers (2004)
Formation of an SCF(ZTL) complex is required for proper regulation of circadian timing.The Plant journal : for cell and molecular biology, 40 2
-
Uwe Ohler, Heinrich Niemann (2001)
Identification and analysis of eukaryotic promoters: recent computational approaches.Trends in genetics : TIG, 17 2
-
S. Rombauts, P. Déhais, M. Montagu, P. Rouzé (1999)
PlantCARE, a plant cis-acting regulatory element databaseNucleic acids research, 27 1
-
(2004)
Quantifying the relationship between co-expression, co-regulation and gene function -
M. Garcia-Hernandez, T. Berardini, Guanghong Chen, D. Crist, Aisling Doyle, E. Huala, E. Knee, M. Lambrecht, Neil Miller, L. Mueller, S. Mundodi, L. Reiser, S. Rhee, R. Scholl, Julie Tacklind, D. Weems, Yihe Wu, Iris Xu, Danny Yoo, Jungwon Yoon, Peifen Zhang (2002)
TAIR: a resource for integrated Arabidopsis dataFunctional & Integrative Genomics, 2
-
David Craigon, Nick James, J. Okyere, Janet Higgins, J. Jotham, S. May (2004)
NASCArrays: a repository for microarray data generated by NASC's transcriptomics serviceNucleic acids research, 32 Database issue
-
Hao Yu, Toshiro Ito, Yuanxiang Zhao, Jinrong Peng, Prakash Kumar, E. Meyerowitz (2004)
Floral homeotic genes are targets of gibberellin signaling in flower development.Proceedings of the National Academy of Sciences of the United States of America, 101 20
-
M. Hoon, S. Imoto, J. Nolan, S. Miyano (2004)
Open source clustering software.Bioinformatics, 20 9
-
T. Ulmasov, Zhan-Bin Liu, G. Hagen, T. Guilfoyle (1995)
Composite structure of auxin response elements.The Plant cell, 7
-
E. Risseeuw, T. Daskalchuk, Travis Banks, Enwu Liu, J. Cotelesage, H. Hellmann, M. Estelle, D. Somers, W. Crosby (2003)
Protein interaction analysis of SCF ubiquitin E3 ligase subunits from Arabidopsis.The Plant journal : for cell and molecular biology, 34 6
-
J. Riechmann, Jacqueline Heard, George Martin, T. Reuber, C. Jiang, J. Keddie, L. Adam, O. Pineda, O. Ratcliffe, Raymond Samaha, R. Creelman, M. Pilgrim, P. Broun, James Zhang, D. Ghandehari, B. Sherman, Guo-Liang Yu (2000)
Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.Science, 290 5499
-
W. Chen, N. Provart, J. Glazebrook, F. Katagiri, Hur-Song Chang, T. Eulgem, F. Mauch, S. Luan, Guangzhou Zou, S. Whitham, P. Budworth, Yi Tao, Zhiyi Xie, Xi Chen, Steve Lam, J. Kreps, J. Harper, Azzedine Si-Ammour, B. Mauch-Mani, M. Heinlein, K. Kobayashi, T. Hohn, J. Dangl, Xun Wang, Tong Zhu (2002)
Expression Profile Matrix of Arabidopsis Transcription Factor Genes Suggests Their Putative Functions in Response to Environmental StressesThe Plant Cell Online, 14
-
K. Higo, Y. Ugawa, M. Iwamoto, Tomoko Korenaga (1999)
Plant cis-acting regulatory DNA elements (PLACE) database: 1999Nucleic acids research, 27 1
-
Catherine Curie, Sheila McCormick (1997)
A strong inhibitor of gene expression in the 5' untranslated region of the pollen-specific LAT59 gene to tomato.The Plant cell, 9 11
-
Lishuang Shen, Jian Gong, R. Caldo, D. Nettleton, D. Cook, R. Wise, J. Dickerson (2004)
BarleyBase—an expression profiling database for plant genomicsNucleic Acids Research, 33
-
Naoki Takahashi, H. Kuroda, T. Kuromori, T. Hirayama, M. Seki, K. Shinozaki, H. Shimada, M. Matsui (2004)
Expression and interaction analysis of Arabidopsis Skp1-related genes.Plant & cell physiology, 45 1
-
M. Hudson, P. Quail (2003)
Identification of Promoter Motifs Involved in the Network of Phytochrome A-Regulated Gene Expression by Combined Analysis of Genomic Sequence and Microarray Data1[w]Plant Physiology, 133
-
Cristel Carles, Natacha Bies-Ethève, L. Aspart, K. Léon-Kloosterziel, M. Koornneef, M. Echeverria, M. Delseny (2002)
Regulation of Arabidopsis thaliana Em genes: role of ABI5.The Plant journal : for cell and molecular biology, 30 3
-
O. Thimm, O. Bläsing, Y. Gibon, A. Nagel, S. Meyer, Peter Krüger, J. Selbig, Lukas Müller, S. Rhee, M. Stitt (2004)
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.The Plant journal : for cell and molecular biology, 37 6
-
R. Davuluri, Hao Sun, Saranyan Palaniswamy, Nicole Matthews, Carlos Molina, M. Kurtz, E. Grotewold (2003)
AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factorsBMC Bioinformatics, 4
-
C. Vicient, G. Hull, J. Guilleminot, M. Devic, M. Delseny (2000)
Differential expression of the Arabidopsis genes coding for Em-like proteins.Journal of experimental botany, 51 348
-
Linghui Xu, Fuquan Liu, E. Lechner, P. Genschik, W. Crosby, Hong Ma, W. Peng, Dafang Huang, D. Xie (2002)
The SCF(COI1) ubiquitin-ligase complexes are required for jasmonate response in Arabidopsis.The Plant cell, 14 8
-
J. Alonso, A. Stepanova, Thomas Leisse, Christopher Kim, Huaming Chen, P. Shinn, Denise Stevenson, J. Zimmerman, Pascual Barajas, Rosa Cheuk, Carmelita Gadrinab, Collen Heller, Albert Jeske, Eric Koesema, Cristina Meyers, Holly Parker, Lance Prednis, Yasser Ansari, Nathan Choy, Hashim Deen, M. Geralt, N. Hazari, Emily Hom, Meagan Karnes, C. Mulholland, Ral Ndubaku, Ian Schmidt, P. Guzmán, Laura Aguilar-Henonin, M. Schmid, D. Weigel, D. Carter, T. Marchand, E. Risseeuw, Debra Brogden, Albana Zeko, W. Crosby, C. Berry, J. Ecker (2003)
Genome-Wide Insertional Mutagenesis of Arabidopsis thalianaScience, 301
-
A. Devoto, M. Nieto-Rostro, D. Xie, Christine Ellis, Rebecca Harmston, Elaine Patrick, Jackie Davis, L. Sherratt, M. Coleman, J. Turner (2002)
COI1 links jasmonate signalling and fertility to the SCF ubiquitin-ligase complex in Arabidopsis.The Plant journal : for cell and molecular biology, 32 4
-
L. Mueller, Peifen Zhang, S. Rhee (2003)
AraCyc: A Biochemical Pathway Database for Arabidopsis1Plant Physiology, 132
-
J. Helden, B. André, J. Collado-Vides (1998)
Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies.Journal of molecular biology, 281 5
-
Pascale Gaubier, M. Raynal, G. Hull, G. Huestis, F. Grellet, César Arenas, M. Pagés, M. Delseny (1993)
Two different Em-like genes are expressed in Arabidopsis thaliana seeds during maturationMolecular and General Genetics MGG, 238
-
Jun Yu, Songnian Hu, Jun Wang, G. Wong, Songgang Li, Bin Liu, Yajun Deng, L. Dai, Yan Zhou, Xiuqing Zhang, Mengliang Cao, Jing Liu, Jiandong Sun, Jiabin Tang, Yanjiong Chen, Xiaobing Huang, Wei Lin, C. Ye, W. Tong, Lijuan Cong, Jianing Geng, Yujun Han, Lin Li, Wei Li, G. Hu, Xiangang Huang, Wenjie Li, Jian Li, Zhanwei Liu, Long Li, Jianping Liu, Q. Qi, Jinsong Liu, Li Li, Tao Li, Xuegang Wang, Hong Lu, Tingting Wu, Miao Zhu, Peixiang Ni, Hua Han, Wei Dong, Xiaoyu Ren, Xiaoli Feng, P. Cui, Xianran Li, Hao Wang, Xin Xu, W. Zhai, Zhao Xu, Jinsong Zhang, Sijie He, Jianguo Zhang, Jichen Xu, Kunlin Zhang, Xianwu Zheng, Jianhai Dong, Wanyong Zeng, Lin Tao, Jia Ye, Jun Tan, Xide Ren, Xuewei Chen, Jun He, Daofeng Liu, W. Tian, Chaoguang Tian, Hong’ai Xia, Qiyu Bao, Gang Li, Hui Gao, Ting Cao, Juan Wang, Wenming Zhao, Ping Li, Wei Chen, Xudong Wang, Yong Zhang, Jian-Fei Hu, Jing Wang, Song Liu, Jian Yang, Guangyu Zhang, Yuqing Xiong, Zhijie Li, Long Mao, Chengshu Zhou, Zhen Zhu, Runsheng Chen, Bailin Hao, Wei-Mou Zheng, S. Chen, W. Guo, Guojie Li, Siqi Liu, M. Tao, Jian Wang, Lihuang Zhu, Longping Yuan, Huanming Yang (2002)
A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica)Science, 296
-
W. Butler, A. Cuming (2004)
Differential molecular responses to abscisic acid and osmotic stress in viviparous maize embryosPlanta, 189
-
The Initiative (2000)
Analysis of the genome sequence of the flowering plant Arabidopsis thalianaNature, 408
-
R. Hulzink, Han Weerdesteyn, A. Croes, T. Gerats, M. Herpen, J. Helden (2003)
In Silico Identification of Putative Regulatory Sequence Elements in the 5′-Untranslated Region of Genes That Are Expressed during Male GametogenesisPlant Physiology, 132
-
T. Zhu, Xun Wang (2000)
Large-scale profiling of the Arabidopsis transcriptome.Plant physiology, 124 4
-
G. Thijs, K. Marchal, M. Lescot, S. Rombauts, B. Moor, P. Rouzé, Y. Moreau (2001)
A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genesJournal of computational biology : a journal of computational molecular cell biology, 9 2
-
S. Rhee, W. Beavis, T. Berardini, Guanghong Chen, D. Dixon, Aisling Doyle, M. Garcia-Hernandez, E. Huala, Gabriel Lander, Mary Montoya, Neil Miller, L. Mueller, S. Mundodi, L. Reiser, Julie Tacklind, D. Weems, Yihe Wu, Iris Xu, Danny Yoo, Jungwon Yoon, Peifen Zhang (2003)
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and communityNucleic acids research, 31 1
-
P. Rocca-Serra, A. Brazma, H. Parkinson, Ugis Sarkans, Mohammadreza Shojatalab, S. Contrino, J. Vilo, Niran Abeygunawardena, Gaurab Mukherjee, Ele Holloway, M. Kapushesky, P. Kemmeren, G. Lara, A. Oezcimen, Susanna-Assunta Sansone (2003)
ArrayExpress: a public database of gene expression data at EBI.Comptes rendus biologies, 326 10-11
-
C. Kao, S. Cocciolone, I. Vasil, D. McCarty (1996)
Localization and interaction of the cis-acting elements for abscisic acid, VIVIPAROUS1, and light activation of the C1 gene of maize.The Plant cell, 8
-
M. Schmid, T. Davison, Stefan Henz, U. Pape, Monika Demar, M. Vingron, B. Scholkopf, D. Weigel, J. Lohmann (2005)
A gene expression map of Arabidopsis thaliana developmentNature Genetics, 37
-
G. Sherlock, T. Hernandez-Boussard, A. Kasarskis, G. Binkley, J. Matese, S. Dwight, Miroslava Kaloper, S. Weng, Heng Jin, C. Ball, M. Eisen, P. Spellman, P. Brown, D. Botstein, J. Cherry (2001)
The Stanford Microarray DatabaseNucleic acids research, 29 1
-
Alina Nakhamchik, Zhiying Zhao, N. Provart, Shin-Han Shiu, S. Keatley, R. Cameron, D. Goring (2004)
A comprehensive expression analysis of the Arabidopsis proline-rich extensin-like receptor kinase gene family using bioinformatic and experimental approaches.Plant & cell physiology, 45 12
-
Tokunori Hobo, M. Asada, Y. Kowyama, T. Hattori (1999)
ACGT-containing abscisic acid response element (ABRE) and coupling element 3 (CE3) are functionally equivalent.The Plant journal : for cell and molecular biology, 19 6
-
Kayoko Yamada, Jun-Man Lim, Joseph Dale, Huaming Chen, P. Shinn, C. Palm, Audrey Southwick, Hank Wu, Christopher Kim, M. Nguyen, Paul Pham, Rosa Cheuk, George Karlin-Newmann, Shirley Liu, Bao Lam, H. Sakano, Troy Wu, Guixia Yu, Molly Miranda, H. Quach, M. Tripp, Charlie Chang, J. Lee, Mitsue Toriumi, Marie Chan, C. Tang, C. Onodera, Justine Deng, Kenji Akiyama, Yasser Ansari, T. Arakawa, Jenny Banh, Fumika Banno, Leah Bowser, Shelise Brooks, Piero Carninci, Qimin Chao, Nathan Choy, A. Enju, A. Goldsmith, M. Gurjal, Nancy Hansen, Y. Hayashizaki, Chanda Johnson-Hopson, Vickie Hsuan, K. Iida, Meagan Karnes, Shehnaz Khan, Eric Koesema, Junko Ishida, P. Jiang, Ted Jones, J. Kawai, Asako Kamiya, Cristina Meyers, Maiko Nakajima, M. Narusaka, M. Seki, Tetsuya Sakurai, Masakazu Satou, R. Tamse, M. Vaysberg, Erika Wallender, Cecilia Wong, Y. Yamamura, Shiaulou Yuan, K. Shinozaki, Ronald Davis, A. Theologis, J. Ecker (2003)
Empirical Analysis of Transcriptional Activity in the Arabidopsis GenomeScience, 302
-
Julia Redman, B. Haas, G. Tanimoto, C. Town (2004)
Development and evaluation of an Arabidopsis whole genome Affymetrix probe array.The Plant journal : for cell and molecular biology, 38 3
-
Boyes (2001)
Growth stage-based phenotypic analysis of Arabidopsis: a model for high throughput functional genomics in plantsPlant Cell, 13
-
H. Schoof, P. Zaccaria, H. Gundlach, K. Lemcke, S. Rudd, G. Kolesov, Roland Arnold, H. Mewes, K. Mayer (2002)
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genomeNucleic acids research, 30 1
-
S. Goff, D. Ricke, T. Lan, G. Presting, Ronglin Wang, Molly Dunn, J. Glazebrook, A. Sessions, P. Oeller, H. Varma, D. Hadley, Don Hutchison, Christopher Martin, F. Katagiri, B. Lange, Todd Moughamer, Yumei Xia, P. Budworth, Jingping Zhong, Trini Miguel, U. Paszkowski, Shiping Zhang, M. Colbert, Wei-lin Sun, Lili Chen, B. Cooper, Sylvia Park, T. Wood, Long Mao, P. Quail, R. Wing, R. Dean, Yeisoo Yu, A. Zharkikh, Richard Shen, S. Sahasrabudhe, Alun Thomas, R. Cannings, A. Gutin, D. Pruss, J. Reid, S. Tavtigian, Jeff Mitchell, G. Eldredge, T. Scholl, R. Miller, Satish Bhatnagar, N. Adey, T. Rubano, N. Tusneem, Rosann Robinson, Jane Feldhaus, T. Macalma, A. Oliphant, S. Briggs (2002)
A draft sequence of the rice genome (Oryza sativa L. ssp. japonica).Science, 296 5565
-
N. Leonhardt, J. Kwak, Nadia Robert, D. Waner, Guillaume Leonhardt, J. Schroeder (2004)
Microarray Expression Analyses of Arabidopsis Guard Cells and Isolation of a Recessive Abscisic Acid Hypersensitive Protein Phosphatase 2C Mutant Online version contains Web-only data.The Plant Cell Online, 16
-
Philip Zimmermann, Matthias Hirsch-Hoffmann, L. Hennig, W. Gruissem (2004)
GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox1[w]Plant Physiology, 136
- Publisher
- Wiley
- Copyright
- Copyright © 2005 Wiley Subscription Services, Inc., A Wiley Company
- ISSN
- 0960-7412
- eISSN
- 1365-313X
- DOI
- 10.1111/j.1365-313X.2005.02437.x
- pmid
- 15960624
- Publisher site
- See Article on Publisher Site
Abstract
The Botany Array Resource provides the means for obtaining and archiving microarray data for Arabidopsis thaliana as well as biologist‐friendly tools for viewing and mining both our own and other's data, for example, from the AtGenExpress Consortium. All the data produced are publicly available through the web interface of the database at http://bbc.botany.utoronto.ca. The database has been designed in accordance with the Minimum Information About a Microarray Experiment [Brazma, A., Hingamp, P., Quackenbush, J. et al. (2001) Minimum information about a microarray experiment (MIAME) – toward standards for microarray data. Nat. Genet.29, 365] convention – all expression data are associated with the corresponding experimental details. The database is searchable and it also provides a set of useful and easy‐to‐use web‐based data‐mining tools for researchers with sophisticated yet understandable output graphics. These include Expression Browser for performing ‘electronic Northerns’, Expression Angler for identifying genes that are co‐regulated with a gene of interest, and Promomer for identifying potential cis‐elements in the promoters of individual or co‐regulated genes.
Journal
The Plant Journal – Wiley
Published: Jul 1, 2005
Keywords: ; ; ; ; ;