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Items: 1 to 20 of 99

1.

COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals.

Obayashi T, Okamura Y, Ito S, Tadaka S, Motoike IN, Kinoshita K.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1014-20. doi: 10.1093/nar/gks1014. Epub 2012 Nov 29.

2.

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.

3.

COXPRESdb: a database of coexpressed gene networks in mammals.

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

Nucleic Acids Res. 2008 Jan;36(Database issue):D77-82. Epub 2007 Oct 11.

4.

COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems.

Okamura Y, Aoki Y, Obayashi T, Tadaka S, Ito S, Narise T, Kinoshita K.

Nucleic Acids Res. 2015 Jan;43(Database issue):D82-6. doi: 10.1093/nar/gku1163. Epub 2014 Nov 11.

5.

RiceFREND: a platform for retrieving coexpressed gene networks in rice.

Sato Y, Namiki N, Takehisa H, Kamatsuki K, Minami H, Ikawa H, Ohyanagi H, Sugimoto K, Itoh J, Antonio BA, Nagamura Y.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1214-21. doi: 10.1093/nar/gks1122. Epub 2012 Nov 24.

6.

ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants.

Obayashi T, Nishida K, Kasahara K, Kinoshita K.

Plant Cell Physiol. 2011 Feb;52(2):213-9. doi: 10.1093/pcp/pcq203. Epub 2011 Jan 7.

7.

Comparison of Gene Coexpression Profiles and Construction of Conserved Gene Networks to Find Functional Modules.

Okamura Y, Obayashi T, Kinoshita K.

PLoS One. 2015 Jul 6;10(7):e0132039. doi: 10.1371/journal.pone.0132039. eCollection 2015.

8.

STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data.

Jupiter D, Chen H, VanBuren V.

BMC Bioinformatics. 2009 Oct 14;10:332. doi: 10.1186/1471-2105-10-332.

9.

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.

10.

Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks.

Vandepoele K, Quimbaya M, Casneuf T, De Veylder L, Van de Peer Y.

Plant Physiol. 2009 Jun;150(2):535-46. doi: 10.1104/pp.109.136028. Epub 2009 Apr 8.

11.

ATTED-II in 2014: evaluation of gene coexpression in agriculturally important plants.

Obayashi T, Okamura Y, Ito S, Tadaka S, Aoki Y, Shirota M, Kinoshita K.

Plant Cell Physiol. 2014 Jan;55(1):e6. doi: 10.1093/pcp/pct178. Epub 2013 Dec 10.

12.

KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data.

Sakurai N, Ara T, Ogata Y, Sano R, Ohno T, Sugiyama K, Hiruta A, Yamazaki K, Yano K, Aoki K, Aharoni A, Hamada K, Yokoyama K, Kawamura S, Otsuka H, Tokimatsu T, Kanehisa M, Suzuki H, Saito K, Shibata D.

Nucleic Acids Res. 2011 Jan;39(Database issue):D677-84. doi: 10.1093/nar/gkq989. Epub 2010 Nov 19.

13.

Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches.

Fukushima A, Nishizawa T, Hayakumo M, Hikosaka S, Saito K, Goto E, Kusano M.

Plant Physiol. 2012 Apr;158(4):1487-502. doi: 10.1104/pp.111.188367. Epub 2012 Feb 3.

14.

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks.

Lepoivre C, Bergon A, Lopez F, Perumal NB, Nguyen C, Imbert J, Puthier D.

BMC Bioinformatics. 2012 Jan 31;13:19. doi: 10.1186/1471-2105-13-19.

15.

ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression.

Aoki Y, Okamura Y, Tadaka S, Kinoshita K, Obayashi T.

Plant Cell Physiol. 2016 Jan;57(1):e5. doi: 10.1093/pcp/pcv165. Epub 2015 Nov 6.

16.

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
17.

Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice.

Ficklin SP, Feltus FA.

Plant Physiol. 2011 Jul;156(3):1244-56. doi: 10.1104/pp.111.173047. Epub 2011 May 23.

18.

Identification by microarray technology of key genes involved in the progression of carotid atherosclerotic plaque.

Wang J, Wei B, Cao S, Xu F, Chen W, Lin H, Du C, Sun Z.

Genes Genet Syst. 2014;89(6):253-8. doi: 10.1266/ggs.89.253.

19.

NetVenn: an integrated network analysis web platform for gene lists.

Wang Y, Thilmony R, Gu YQ.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W161-6. doi: 10.1093/nar/gku331. Epub 2014 Apr 25.

20.

gsGator: an integrated web platform for cross-species gene set analysis.

Kang H, Choi I, Cho S, Ryu D, Lee S, Kim W.

BMC Bioinformatics. 2014 Jan 14;15:13. doi: 10.1186/1471-2105-15-13.

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