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Items: 1 to 20 of 24

1.

COXPRESdb: a database to compare gene coexpression in seven model animals.

Obayashi T, Kinoshita K.

Nucleic Acids Res. 2011 Jan;39(Database issue):D1016-22. doi: 10.1093/nar/gkq1147. Epub 2010 Nov 16.

2.

Cytoscape Web: an interactive web-based network browser.

Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD.

Bioinformatics. 2010 Sep 15;26(18):2347-8. doi: 10.1093/bioinformatics/btq430. Epub 2010 Jul 23.

3.

Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways.

Obayashi T, Kinoshita K.

J Plant Res. 2010 May;123(3):311-9. doi: 10.1007/s10265-010-0333-6. Epub 2010 Apr 10. Review.

PMID:
20383554
4.

Database resources of the National Center for Biotechnology Information.

Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, John Wilbur W, Yaschenko E, Ye J.

Nucleic Acids Res. 2010 Jan;38(Database issue):D5-16. doi: 10.1093/nar/gkp967. Epub 2009 Nov 12.

5.

Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression.

Obayashi T, Kinoshita K.

DNA Res. 2009 Oct;16(5):249-60. doi: 10.1093/dnares/dsp016. Epub 2009 Sep 18.

6.

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats.

Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, Provart NJ.

Plant Cell Environ. 2009 Dec;32(12):1633-51. doi: 10.1111/j.1365-3040.2009.02040.x. Epub 2009 Aug 27. Review.

7.

Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis.

Kinoshita K, Obayashi T.

Bioinformatics. 2009 Oct 15;25(20):2677-84. doi: 10.1093/bioinformatics/btp442. Epub 2009 Jul 20.

8.

A chloroplastic UDP-glucose pyrophosphorylase from Arabidopsis is the committed enzyme for the first step of sulfolipid biosynthesis.

Okazaki Y, Shimojima M, Sawada Y, Toyooka K, Narisawa T, Mochida K, Tanaka H, Matsuda F, Hirai A, Hirai MY, Ohta H, Saito K.

Plant Cell. 2009 Mar;21(3):892-909. doi: 10.1105/tpc.108.063925. Epub 2009 Mar 13.

9.

ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression.

Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone SA, Sklyar N, Zhao M, Sarkans U, Brazma A.

Nucleic Acids Res. 2009 Jan;37(Database issue):D868-72. doi: 10.1093/nar/gkn889. Epub 2008 Nov 10.

10.

ATTED-II provides coexpressed gene networks for Arabidopsis.

Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K.

Nucleic Acids Res. 2009 Jan;37(Database issue):D987-91. doi: 10.1093/nar/gkn807. Epub 2008 Oct 25.

11.

Conserved co-expression for candidate disease gene prioritization.

Oti M, van Reeuwijk J, Huynen MA, Brunner HG.

BMC Bioinformatics. 2008 Apr 23;9:208. doi: 10.1186/1471-2105-9-208.

12.

The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access.

Goda H, Sasaki E, Akiyama K, Maruyama-Nakashita A, Nakabayashi K, Li W, Ogawa M, Yamauchi Y, Preston J, Aoki K, Kiba T, Takatsuto S, Fujioka S, Asami T, Nakano T, Kato H, Mizuno T, Sakakibara H, Yamaguchi S, Nambara E, Kamiya Y, Takahashi H, Hirai MY, Sakurai T, Shinozaki K, Saito K, Yoshida S, Shimada Y.

Plant J. 2008 Aug;55(3):526-42. doi: 10.1111/j.0960-7412.2008.03510.x.

13.

The Arabidopsis Information Resource (TAIR): gene structure and function annotation.

Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, Radenbaugh A, Singh S, Swing V, Tissier C, Zhang P, Huala E.

Nucleic Acids Res. 2008 Jan;36(Database issue):D1009-14. Epub 2007 Nov 5.

14.

The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses.

Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D'Angelo C, Bornberg-Bauer E, Kudla J, Harter K.

Plant J. 2007 Apr;50(2):347-63. Epub 2007 Mar 21.

15.

Approaches for extracting practical information from gene co-expression networks in plant biology.

Aoki K, Ogata Y, Shibata D.

Plant Cell Physiol. 2007 Mar;48(3):381-90. Epub 2007 Jan 23. Review.

PMID:
17251202
16.

ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis.

Obayashi T, Kinoshita K, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D, Saito K, Ohta H.

Nucleic Acids Res. 2007 Jan;35(Database issue):D863-9. Epub 2006 Nov 27.

17.

NCBI GEO: mining tens of millions of expression profiles--database and tools update.

Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R.

Nucleic Acids Res. 2007 Jan;35(Database issue):D760-5. Epub 2006 Nov 11.

18.

The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses.

Toufighi K, Brady SM, Austin R, Ly E, Provart NJ.

Plant J. 2005 Jul;43(1):153-63.

19.

A gene expression map of Arabidopsis thaliana development.

Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Schölkopf B, Weigel D, Lohmann JU.

Nat Genet. 2005 May;37(5):501-6. Epub 2005 Apr 3.

PMID:
15806101
20.

CSB.DB: a comprehensive systems-biology database.

Steinhauser D, Usadel B, Luedemann A, Thimm O, Kopka J.

Bioinformatics. 2004 Dec 12;20(18):3647-51. Epub 2004 Jul 9.

PMID:
15247097

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