Taking the Next Step: Building an Arabidopsis Information Portal

Baerenfaller K, Bastow R, Benyon J, Brady S, Brendel V, Donaldson S, Dooley R, Forster M, Friesner J, Gifford D, Grotewold E, et al. (2012)
The Plant Cell 24(6): 2248-2256.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
DOI
Autor*in
Baerenfaller, Katja; Bastow, Ruth; Benyon, James; Brady, Siobhan; Brendel, Voker; Donaldson, Sylvia; Dooley, Rion; Forster, Mark; Friesner, Joanna; Gifford, David; Grotewold, Erich; Gutierrez, Rodrigo
Alle
Einrichtung
Fakultät für Biologie
Centrum für Biotechnologie
Erscheinungsjahr
2012
Zeitschriftentitel
The Plant Cell
Band
24
Ausgabe
6
Seite(n)
2248-2256
ISSN
1040-4651
eISSN
1532-298X
Page URI
https://pub.uni-bielefeld.de/record/2523470

Zitieren

Baerenfaller K, Bastow R, Benyon J, et al. Taking the Next Step: Building an Arabidopsis Information Portal. The Plant Cell. 2012;24(6):2248-2256.
Baerenfaller, K., Bastow, R., Benyon, J., Brady, S., Brendel, V., Donaldson, S., Dooley, R., et al. (2012). Taking the Next Step: Building an Arabidopsis Information Portal. The Plant Cell, 24(6), 2248-2256. doi:10.1105/tpc.112.100669
Baerenfaller, Katja, Bastow, Ruth, Benyon, James, Brady, Siobhan, Brendel, Voker, Donaldson, Sylvia, Dooley, Rion, et al. 2012. “Taking the Next Step: Building an Arabidopsis Information Portal”. The Plant Cell 24 (6): 2248-2256.
Baerenfaller, K., Bastow, R., Benyon, J., Brady, S., Brendel, V., Donaldson, S., Dooley, R., Forster, M., Friesner, J., Gifford, D., et al. (2012). Taking the Next Step: Building an Arabidopsis Information Portal. The Plant Cell 24, 2248-2256.
Baerenfaller, K., et al., 2012. Taking the Next Step: Building an Arabidopsis Information Portal. The Plant Cell, 24(6), p 2248-2256.
K. Baerenfaller, et al., “Taking the Next Step: Building an Arabidopsis Information Portal”, The Plant Cell, vol. 24, 2012, pp. 2248-2256.
Baerenfaller, K., Bastow, R., Benyon, J., Brady, S., Brendel, V., Donaldson, S., Dooley, R., Forster, M., Friesner, J., Gifford, D., Grotewold, E., Gutierrez, R., Huala, E., Jaiswal, P., Joshi, H., Kersey, P., Liu, L., Loraine, A., Lyons, E., May, S., Mayer, K., McLean, D., Meyers, B., Mueller, L., Muller, R., Muller, H.-M., Ouellette, F., Pires, C., Provart, N., Staiger, D., Stazione, D., Taylor, C., Town, C., Toyoda, T., Vaughn, M., Walsh, S., Ware, D., Weckwerth, W.: Taking the Next Step: Building an Arabidopsis Information Portal. The Plant Cell. 24, 2248-2256 (2012).
Baerenfaller, Katja, Bastow, Ruth, Benyon, James, Brady, Siobhan, Brendel, Voker, Donaldson, Sylvia, Dooley, Rion, Forster, Mark, Friesner, Joanna, Gifford, David, Grotewold, Erich, Gutierrez, Rodrigo, Huala, Eva, Jaiswal, Pankaj, Joshi, Hiren, Kersey, Paul, Liu, Lei, Loraine, Ann, Lyons, Eric, May, Sean, Mayer, Klaus, McLean, Dan, Meyers, Blake, Mueller, Lukas, Muller, Robert, Muller, Hans-Michael, Ouellette, Francis, Pires, Chris, Provart, Nick, Staiger, Dorothee, Stazione, Dan, Taylor, Crispin, Town, Chris, Toyoda, Tetsuro, Vaughn, Matt, Walsh, Sean, Ware, Doreen, and Weckwerth, Wolfram. “Taking the Next Step: Building an Arabidopsis Information Portal”. The Plant Cell 24.6 (2012): 2248-2256.

19 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future.
International Arabidopsis Informatics Consortium., Plant Direct 3(1), 2019
PMID: 31245752
Eco-Metabolomics and Metabolic Modeling: Making the Leap From Model Systems in the Lab to Native Populations in the Field.
Nagler M, Nägele T, Gilli C, Fragner L, Korte A, Platzer A, Farlow A, Nordborg M, Weckwerth W., Front Plant Sci 9(), 2018
PMID: 30459786
Beyond Transcription: Fine-Tuning of Circadian Timekeeping by Post-Transcriptional Regulation.
Mateos JL, de Leone MJ, Torchio J, Reichel M, Staiger D., Genes (Basel) 9(12), 2018
PMID: 30544736
ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology.
Waese J, Fan J, Pasha A, Yu H, Fucile G, Shi R, Cumming M, Kelley LA, Sternberg MJ, Krishnakumar V, Ferlanti E, Miller J, Town C, Stuerzlinger W, Provart NJ., Plant Cell 29(8), 2017
PMID: 28808136
50 years of Arabidopsis research: highlights and future directions.
Provart NJ, Alonso J, Assmann SM, Bergmann D, Brady SM, Brkljacic J, Browse J, Chapple C, Colot V, Cutler S, Dangl J, Ehrhardt D, Friesner JD, Frommer WB, Grotewold E, Meyerowitz E, Nemhauser J, Nordborg M, Pikaard C, Shanklin J, Somerville C, Stitt M, Torii KU, Waese J, Wagner D, McCourt P., New Phytol 209(3), 2016
PMID: 26465351
Mobile small RNAs regulate genome-wide DNA methylation.
Lewsey MG, Hardcastle TJ, Melnyk CW, Molnar A, Valli A, Urich MA, Nery JR, Baulcombe DC, Ecker JR., Proc Natl Acad Sci U S A 113(6), 2016
PMID: 26787884
Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model.
Reiser L, Berardini TZ, Li D, Muller R, Strait EM, Li Q, Mezheritsky Y, Vetushko A, Huala E., Database (Oxford) 2016(), 2016
PMID: 26989150
The coffee genome hub: a resource for coffee genomes.
Dereeper A, Bocs S, Rouard M, Guignon V, Ravel S, Tranchant-Dubreuil C, Poncet V, Garsmeur O, Lashermes P, Droc G., Nucleic Acids Res 43(database issue), 2015
PMID: 25392413
Araport: the Arabidopsis information portal.
Krishnakumar V, Hanlon MR, Contrino S, Ferlanti ES, Karamycheva S, Kim M, Rosen BD, Cheng CY, Moreira W, Mock SA, Stubbs J, Sullivan JM, Krampis K, Miller JR, Micklem G, Vaughn M, Town CD., Nucleic Acids Res 43(database issue), 2015
PMID: 25414324
AtCAST3.0 update: a web-based tool for analysis of transcriptome data by searching similarities in gene expression profiles.
Kakei Y, Shimada Y., Plant Cell Physiol 56(1), 2015
PMID: 25505006
Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure.
Flis A, Fernández AP, Zielinski T, Mengin V, Sulpice R, Stratford K, Hume A, Pokhilko A, Southern MM, Seaton DD, McWatters HG, Stitt M, Halliday KJ, Millar AJ., Open Biol 5(10), 2015
PMID: 26468131
PhosPhAt goes kinases--searchable protein kinase target information in the plant phosphorylation site database PhosPhAt.
Zulawski M, Braginets R, Schulze WX., Nucleic Acids Res 41(database issue), 2013
PMID: 23172287
Integrating data to acquire new knowledge: Three modes of integration in plant science.
Leonelli S., Stud Hist Philos Biol Biomed Sci 44(4 pt a), 2013
PMID: 23571025
RNA-seq of Arabidopsis pollen uncovers novel transcription and alternative splicing.
Loraine AE, McCormick S, Estrada A, Patel K, Qin P., Plant Physiol 162(2), 2013
PMID: 23590974
Making open data work for plant scientists.
Leonelli S, Smirnoff N, Moore J, Cook C, Bastow R., J Exp Bot 64(14), 2013
PMID: 24043847
MASCP gator: an overview of the Arabidopsis proteomic aggregation portal.
Mann GW, Calley PC, Joshi HJ, Heazlewood JL., Front Plant Sci 4(), 2013
PMID: 24167507
From bench to bountiful harvests: a road map for the next decade of Arabidopsis research.
Lavagi I, Estelle M, Weckwerth W, Beynon J, Bastow RM., Plant Cell 24(6), 2012
PMID: 22751212
Correlation networks visualization.
Provart N., Front Plant Sci 3(), 2012
PMID: 23181065
UniProtKB amid the turmoil of plant proteomics research.
Schneider M, UniProt Consortium, Poux S., Front Plant Sci 3(), 2012
PMID: 23230445

36 References

Daten bereitgestellt von Europe PubMed Central.

Gramene: a resource for comparative grass genomics.
Ware D, Jaiswal P, Ni J, Pan X, Chang K, Clark K, Teytelman L, Schmidt S, Zhao W, Cartinhour S, McCouch S, Stein L., Nucleic Acids Res. 30(1), 2002
PMID: 11752266
The 1001 genomes project for Arabidopsis thaliana.
Weigel D, Mott R., Genome Biol. 10(5), 2009
PMID: 19519932
ATTED-II provides coexpressed gene networks for Arabidopsis.
Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18953027
agriGO: a GO analysis toolkit for the agricultural community.
Du Z, Zhou X, Ling Y, Zhang Z, Su Z., Nucleic Acids Res. 38(Web Server issue), 2010
PMID: 20435677
An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets.
Winter D, Vinegar B, Nahal H, Ammar R, Wilson GV, Provart NJ., PLoS ONE 2(8), 2007
PMID: 17684564
GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists.
Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z., BMC Bioinformatics 10(), 2009
PMID: 19192299
Cytoscape 2.8: new features for data integration and network visualization.
Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T., Bioinformatics 27(3), 2010
PMID: 21149340
MASCP Gator: an aggregation portal for the visualization of Arabidopsis proteomics data.
Joshi HJ, Hirsch-Hoffmann M, Baerenfaller K, Gruissem W, Baginsky S, Schmidt R, Schulze WX, Sun Q, van Wijk KJ, Egelhofer V, Wienkoop S, Weckwerth W, Bruley C, Rolland N, Toyoda T, Nakagami H, Jones AM, Briggs SP, Castleden I, Tanz SK, Millar AH, Heazlewood JL., Plant Physiol. 155(1), 2010
PMID: 21075962
AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology.
Cui J, Li P, Li G, Xu F, Zhao C, Li Y, Yang Z, Wang G, Yu Q, Li Y, Shi T., Nucleic Acids Res. 36(Database issue), 2007
PMID: 17962307
MetaCyc and AraCyc. Metabolic pathway databases for plant research.
Zhang P, Foerster H, Tissier CP, Mueller L, Paley S, Karp PD, Rhee SY., Plant Physiol. 138(1), 2005
PMID: 15888675
Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes.
Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W, Zimmermann P., Adv Bioinformatics 2008(), 2008
PMID: 19956698
VirtualPlant: a software platform to support systems biology research.
Katari MS, Nowicki SD, Aceituno FF, Nero D, Kelfer J, Thompson LP, Cabello JM, Davidson RS, Goldberg AP, Shasha DE, Coruzzi GM, Gutierrez RA., Plant Physiol. 152(2), 2009
PMID: 20007449
The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses.
Toufighi K, Brady SM, Austin R, Ly E, Provart NJ., Plant J. 43(1), 2005
PMID: 15960624
The Sequence Alignment/Map format and SAMtools.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup., Bioinformatics 25(16), 2009
PMID: 19505943
GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox.
Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W., Plant Physiol. 136(1), 2004
PMID: 15375207
The KEGG database.
Kanehisa M., Novartis Found. Symp. 247(), 2002
PMID: 12539951
Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome.
Zhang G, Guo G, Hu X, Zhang Y, Li Q, Li R, Zhuang R, Lu Z, He Z, Fang X, Chen L, Tian W, Tao Y, Kristiansen K, Zhang X, Li S, Yang H, Wang J, Wang J., Genome Res. 20(5), 2010
PMID: 20305017
Reading the second code: mapping epigenomes to understand plant growth, development, and adaptation to the environment.
EPIC Planning Committee, Berger F, Cao XF, Chandler V, Dennis L, Martienssen R, Meyers B, Pikaard C, Peacock J, Richards E, Wagner D, Weigel D, Colot V, Deal R, Dean C, Ecker J, Gehring M, Gregory B, Rodrigo G, Gutierrez-Marcos J, Hasebe M, Hwang ID, Jacobsen S, Kakutani T, Li J, Michaels S, Noh YS, Provart N, Vaughn M., Plant Cell 24(6), 2012
PMID: 22751210
Mining Arabidopsis thaliana RNA-seq data with Integrated Genome Browser reveals stress-induced alternative splicing of the putative splicing regulator SR45a.
Gulledge AA, Roberts AD, Vora H, Patel K, Loraine AE., Am. J. Bot. 99(2), 2012
PMID: 22291167
Gramene database in 2010: updates and extensions.
Youens-Clark K, Buckler E, Casstevens T, Chen C, Declerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, Thomason J, Wei S, Ware D., Nucleic Acids Res. 39(Database issue), 2010
PMID: 21076153
Phytozome: a comparative platform for green plant genomics.
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22110026
The IntAct molecular interaction database in 2012.
Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, Jandrasits C, Jimenez RC, Khadake J, Mahadevan U, Masson P, Pedruzzi I, Pfeiffenberger E, Porras P, Raghunath A, Roechert B, Orchard S, Hermjakob H., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22121220
The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.
Nicol JW, Helt GA, Blanchard SG Jr, Raja A, Loraine AE., Bioinformatics 25(20), 2009
PMID: 19654113
Arabidopsis reactome: a foundation knowledgebase for plant systems biology.
Tsesmetzis N, Couchman M, Higgins J, Smith A, Doonan JH, Seifert GJ, Schmidt EE, Vastrik I, Birney E, Wu G, D'Eustachio P, Stein LD, Morris RJ, Bevan MW, Walsh SV., Plant Cell 20(6), 2008
PMID: 18591350
PosMed-plus: an intelligent search engine that inferentially integrates cross-species information resources for molecular breeding of plants.
Makita Y, Kobayashi N, Mochizuki Y, Yoshida Y, Asano S, Heida N, Deshpande M, Bhatia R, Matsushima A, Ishii M, Kawaguchi S, Iida K, Hanada K, Kuromori T, Seki M, Shinozaki K, Toyoda T., Plant Cell Physiol. 50(7), 2009
PMID: 19528193
Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid.
Dugas DV, Monaco MK, Olsen A, Klein RR, Kumari S, Ware D, Klein PE., BMC Genomics 12(), 2011
PMID: 22008187
TableView: portable genomic data visualization.
Johnson JE, Stromvik MV, Silverstein KA, Crow JA, Shoop E, Retzel EF., Bioinformatics 19(10), 2003
PMID: 12835275
An international bioinformatics infrastructure to underpin the Arabidopsis community.
International Arabidopsis Informatics Consortium, Bastow R, Beynon J, Estelle M, Friesner J, Grotewold E, Lavagi I, Lindsey K, Meyers B, Provart N, Benfey P, Birney E, Braun P, Brendel V, Buell R, Caccamo M, Carrington J, Cherry M, Ecker J, Eppig J, Forster M, Gutierrez R, Hilson P, Huala E, Katari M, Kersey P, Kudla J, Ma H, Matsui M, Matthews K, May S, Mayer K, Millar A, Millar H, Mjolsness E, Mockler T, Nikolau B, Nordborg M, Rawlings C, Schofield P, Schoof H, Schroeder JI, Sen TZ, Stanzione D, Town C, Toyoda T, Vision T, Walsh S, Wang X, Ware D, Weckwerth W, Yang W., Plant Cell 22(8), 2010
PMID: 20807877
A predicted interactome for Arabidopsis.
Geisler-Lee J, O'Toole N, Ammar R, Provart NJ, Millar AH, Geisler M., Plant Physiol. 145(2), 2007
PMID: 17675552
Integrating biological data--the Distributed Annotation System.
Jenkinson AM, Albrecht M, Birney E, Blankenburg H, Down T, Finn RD, Hermjakob H, Hubbard TJ, Jimenez RC, Jones P, Kahari A, Kulesha E, Macias JR, Reeves GA, Prlic A., BMC Bioinformatics 9 Suppl 8(), 2008
PMID: 18673527
The iPlant Collaborative: Cyberinfrastructure for Plant Biology.
Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, Muir A, Merchant N, Lowry S, Mock S, Helmke M, Kubach A, Narro M, Hopkins N, Micklos D, Hilgert U, Gonzales M, Jordan C, Skidmore E, Dooley R, Cazes J, McLay R, Lu Z, Pasternak S, Koesterke L, Piel WH, Grene R, Noutsos C, Gendler K, Feng X, Tang C, Lent M, Kim SJ, Kvilekval K, Manjunath BS, Tannen V, Stamatakis A, Sanderson M, Welch SM, Cranston KA, Soltis P, Soltis D, O'Meara B, Ane C, Brutnell T, Kleibenstein DJ, White JW, Leebens-Mack J, Donoghue MJ, Spalding EP, Vision TJ, Myers CR, Lowenthal D, Enquist BJ, Boyle B, Akoglu A, Andrews G, Ram S, Ware D, Stein L, Stanzione D., Front Plant Sci 2(), 2011
PMID: 22645531
Tabix: fast retrieval of sequence features from generic TAB-delimited files.
Li H., Bioinformatics 27(5), 2011
PMID: 21208982
Dissecting plant genomes with the PLAZA comparative genomics platform.
Van Bel M, Proost S, Wischnitzki E, Movahedi S, Scheerlinck C, Van de Peer Y, Vandepoele K., Plant Physiol. 158(2), 2011
PMID: 22198273
AGRIS: the Arabidopsis Gene Regulatory Information Server, an update.
Yilmaz A, Mejia-Guerra MK, Kurz K, Liang X, Welch L, Grotewold E., Nucleic Acids Res. 39(Database issue), 2010
PMID: 21059685
The developmental dynamics of the maize leaf transcriptome.
Li P, Ponnala L, Gandotra N, Wang L, Si Y, Tausta SL, Kebrom TH, Provart N, Patel R, Myers CR, Reidel EJ, Turgeon R, Liu P, Sun Q, Nelson T, Brutnell TP., Nat. Genet. 42(12), 2010
PMID: 21037569
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G., Nat. Genet. 25(1), 2000
PMID: 10802651
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 22751211
PubMed | Europe PMC

Suchen in

Google Scholar