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PMID: 17148485 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

AthaMap web tools for the analysis and identification of co-regulated genes.

Nucleic acids research ·Vol. 35 ·No. Database issue ·2007-01-00 ·Pages D857-62

Galuschka C, Schindler M, Bülow L, Hehl R

Abstract

The AthaMap database generates a map of cis-regulatory elements for the whole Arabidopsis thaliana genome. This database has been extended by new tools to identify common cis-regulatory elements in specific regions of user-provided gene sets. A resulting table displays all cis-regulatory elements annotated in AthaMap including positional information relative to the respective gene. Further tables show overviews with the number of individual transcription factor binding sites (TFBS) present and TFBS common to the whole set of genes. Over represented cis-elements are easily identified. These features were used to detect specific enrichment of drought-responsive elements in cold-induced genes. For identification of co-regulated genes, the output table of the colocalization function was extended to show the closest genes and their relative distances to the colocalizing TFBS. Gene sets determined by this function can be used for a co-regulation analysis in microarray gene expression databases such as Genevestigator or PathoPlant. Additional improvements of AthaMap include display of the gene structure in the sequence window and a significant data increase. AthaMap is freely available at http://www.athamap.de/.

MeSH Terms
Arabidopsis/genetics Binding Sites Cold Temperature Databases, Nucleic Acid Dehydration Gene Expression Regulation, Plant Internet Regulatory Elements, Transcriptional Software Transcription Factors/metabolism User-Computer Interface
Chemicals
Transcription Factors
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Galuschka Claudia
Institut für Genetik, Technische Universität Braunschweig, Spielmanstrasse 7, D-38106 Braunschweig, Germany.
Schindler Martin
Bülow Lorenz
Hehl Reinhard
References (47)
47 references, click to expand
  1. NCBI GEO: mining millions of expression profiles--database and tools.
    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D562-6 PMID: 15608262
  2. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science. 2000 Dec 15;290(5499):2105-10 PMID: 11118137
  3. A CELD-fusion method for rapid determination of the DNA-binding sequence specificity of novel plant DNA-binding proteins.
    Plant J. 2005 Feb;41(4):638-49 PMID: 15686526
  4. PathoPlant: a database on plant-pathogen interactions.
    In Silico Biol. 2004;4(4):529-36 PMID: 15752070
  5. Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release.
    BMC Biol. 2005;3:7 PMID: 15784138
  6. The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses.
    Plant J. 2005 Jul;43(1):153-63 PMID: 15960624
  7. PatMatch: a program for finding patterns in peptide and nucleotide sequences.
    Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W262-6 PMID: 15980466
  8. AthaMap web tools for database-assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana.
    Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W397-402 PMID: 15980498
  9. A basic helix-loop-helix transcription factor in Arabidopsis, MYC2, acts as a repressor of blue light-mediated photomorphogenic growth.
    Plant Cell. 2005 Jul;17(7):1953-66 PMID: 15923349
  10. Regulation of CAPRICE transcription by MYB proteins for root epidermis differentiation in Arabidopsis.
    Plant Cell Physiol. 2005 Jun;46(6):817-26 PMID: 15795220
  11. LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms.
    Proc Natl Acad Sci U S A. 2005 Jul 19;102(29):10387-92 PMID: 16006522
  12. Molecular cloning, phylogenetic analysis, expressional profiling and in vitro studies of TINY2 from Arabidopsis thaliana.
    J Biochem Mol Biol. 2005 Jul 31;38(4):440-6 PMID: 16053711
  13. Role of an Arabidopsis AP2/EREBP-type transcriptional repressor in abscisic acid and drought stress responses.
    Plant Cell. 2005 Aug;17(8):2384-96 PMID: 15994908
  14. Functional dissection of the plant-specific SBP-domain: overlap of the DNA-binding and nuclear localization domains.
    J Mol Biol. 2005 Sep 23;352(3):585-96 PMID: 16095614
  15. Isolation of a calmodulin-binding transcription factor from rice (Oryza sativa L.).
    J Biol Chem. 2005 Dec 9;280(49):40820-31 PMID: 16192280
  16. Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences.
    Bioinformatics. 2005 Dec 15;21(24):4411-3 PMID: 16223790
  17. AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks.
    Plant Physiol. 2006 Mar;140(3):818-29 PMID: 16524982
  18. Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis.
    Proc Natl Acad Sci U S A. 2006 Feb 28;103(9):3468-73 PMID: 16492731
  19. The Arabidopsis co-expression tool (ACT): a WWW-based tool and database for microarray-based gene expression analysis.
    Plant J. 2006 Apr;46(2):336-48 PMID: 16623895
  20. Physical and functional interactions between pathogen-induced Arabidopsis WRKY18, WRKY40, and WRKY60 transcription factors.
    Plant Cell. 2006 May;18(5):1310-26 PMID: 16603654
  21. Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis.
    Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W504-9 PMID: 16845059
  22. The Stanford Microarray Database: a user's guide.
    Methods Mol Biol. 2006;338:191-208 PMID: 16888360
  23. AthaMap: from in silico data to real transcription factor binding sites.
    In Silico Biol. 2006;6(3):243-52 PMID: 16922688
  24. Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses.
    Plant J. 2003 Apr;34(2):137-48 PMID: 12694590
  25. MATCH: A tool for searching transcription factor binding sites in DNA sequences.
    Nucleic Acids Res. 2003 Jul 1;31(13):3576-9 PMID: 12824369
  26. Regulatory sequence analysis tools.
    Nucleic Acids Res. 2003 Jul 1;31(13):3593-6 PMID: 12824373
  27. AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors.
    BMC Bioinformatics. 2003 Jun 23;4:25 PMID: 12820902
  28. AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D368-72 PMID: 14681436
  29. MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D373-6 PMID: 14681437
  30. NASCArrays: a repository for microarray data generated by NASC's transcriptomics service.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D575-7 PMID: 14681484
  31. Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems.
    Plant J. 2004 Jun;38(6):982-93 PMID: 15165189
  32. Combinatorial control of gene expression.
    Nat Struct Mol Biol. 2004 Sep;11(9):812-5 PMID: 15332082
  33. GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox.
    Plant Physiol. 2004 Sep;136(1):2621-32 PMID: 15375207
  34. MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data.
    Nucleic Acids Res. 1995 Dec 11;23(23):4878-84 PMID: 8532532
  35. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences.
    Nucleic Acids Res. 2002 Jan 1;30(1):325-7 PMID: 11752327
  36. A calmodulin-binding/CGCG box DNA-binding protein family involved in multiple signaling pathways in plants.
    J Biol Chem. 2002 Nov 22;277(47):45049-58 PMID: 12218065
  37. PlantProm: a database of plant promoter sequences.
    Nucleic Acids Res. 2003 Jan 1;31(1):114-7 PMID: 12519961
  38. The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community.
    Nucleic Acids Res. 2003 Jan 1;31(1):224-8 PMID: 12519987
  39. The Stanford Microarray Database accommodates additional microarray platforms and data formats.
    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D580-2 PMID: 15608265
  40. DNA binding properties of two Arabidopsis MADS domain proteins: binding consensus and dimer formation.
    Plant Cell. 1996 Jan;8(1):81-94 PMID: 8597661
  41. Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit.
    Proc Natl Acad Sci U S A. 1997 Feb 4;94(3):1035-40 PMID: 9023378
  42. The two homeodomains of the ZmHox2a gene from maize originated as an internal gene duplication and have evolved different target site specificities.
    Nucleic Acids Res. 1998 Oct 15;26(20):4714-20 PMID: 9753741
  43. Plant cis-acting regulatory DNA elements (PLACE) database: 1999.
    Nucleic Acids Res. 1999 Jan 1;27(1):297-300 PMID: 9847208
  44. Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression.
    Plant J. 1998 Nov;16(4):433-42 PMID: 9881163
  45. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences.
    Bioinformatics. 1999 Jul-Aug;15(7-8):563-77 PMID: 10487864
  46. CSB.DB: a comprehensive systems-biology database.
    Bioinformatics. 2004 Dec 12;20(18):3647-51 PMID: 15247097
  47. TRANSFAC: transcriptional regulation, from patterns to profiles.
    Nucleic Acids Res. 2003 Jan 1;31(1):374-8 PMID: 12520026
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkl1006
Published
2007-01-00
Epub
2006-00-05
Pages
D857-62
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1761422
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkl1006 PMC Full Text View journal details
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