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Protocols

AthaMap specifications

Information


Unique identifier OMICS_00549
Name AthaMap
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana

Publications for AthaMap

AthaMap citations

 (10)
call_split

Evolutionary relationships and expression analysis of EUL domain proteins in rice (Oryza sativa)

2017
PMCID: 5449364
PMID: 28560587
DOI: 10.1186/s12284-017-0164-3
call_split See protocol

[…] Cis-regulatory elements were obtained from AGRIS (Palaniswamy et al. ), PLACE (Higo et al. ), Athamap (Steffens et al. ), CisBP (Weirauch et al. ), JASPAR (Mathelier et al. ) and TRANSFAC (Matys et al. ). These elements were mapped to 2 kb upstream promoter regions of all genes for Oryza sativ […]

library_books

Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection

2016
Sci Rep
PMCID: 5056366
PMID: 27721457
DOI: 10.1038/srep35064

[…] .After removing redundant interactions, we collected 50,824 TF-target binary interactions between 529 TFs and 22,793 target genes from the Arabidopsis Transcriptional Regulatory Map (ATRM), AGRIS and AthaMap (). In total, 13,879 interactions between 333 TFs and 5,371 targets were retained for further analysis by filtering out stably expressed genes under each condition (variance <0.2 in both condi […]

library_books

Genome wide discovery of G quadruplex forming sequences and their functional relevance in plants

2016
Sci Rep
PMCID: 4914980
PMID: 27324275
DOI: 10.1038/srep28211

[…] distachyon). De novo motifs of 12 bp length were identified in these GQSes using HOMER2 with their scrambled sequences as background. The motif matrices generated by HOMER were scanned against AGRIS, Athamap and PLACE in STAMP to identify similarity to known TF-binding sites. Similarly, TF binding sites were identified within G2L1-4 and G3L1-7 GQSes identified in promoter region of Arabidopsis gen […]

library_books

AtWRKY22 promotes susceptibility to aphids and modulates salicylic acid and jasmonic acid signalling

2016
J Exp Bot
PMCID: 4892728
PMID: 27107291
DOI: 10.1093/jxb/erw159

[…] with a frequency above 5%. For exons, only non-synonymous SNPs were included. A promoter region of 1000kb was used and gene domains were obtained from Interpro (). Promoter motifs were retrieved from Athamap (). […]

library_books

ChlamyNET: a Chlamydomonas gene co expression network reveals global properties of the transcriptome and the early setup of key co expression patterns in the green lineage

2016
BMC Genomics
PMCID: 4788957
PMID: 26968660
DOI: 10.1186/s12864-016-2564-y

[…] Transcription Factor Binding Sites (TFBS) enrichment analysis was performed using HOMER [] and the known TFBS sequences in plants from the databases AGRIS [], JASPAR [] and AthaMap []. The findMotifs.pl script, applying the default parameters, was used to perform a known and de-novo motif over-representation analysis.The background used for the over-representation analys […]

library_books

Cis regulatory motifs and antisense transcriptional control in the apicomplexan Theileria parva

2016
BMC Genomics
PMCID: 4761415
PMID: 26896950
DOI: 10.1186/s12864-016-2444-5

[…] iscovered and known motifs []. Motifs were searched against a collection of databases including two comprehensive eukaryotic motif databases JASPAR [] and TRANSFAC [], FLY [], FlyReg [] and Agris [], AthaMap [], PLACE [], Uniprobe [], other yeast motifs [, ], as well as the prokaryotic motif databases RegTransBase [] and DPInteract []. The Smith-Waterman local alignment method with a similarity sc […]


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AthaMap institution(s)
Technische Universität Braunschweig, Institut für Genetik, Braunschweig, Germany; Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Quedlinburg, Germany
AthaMap funding source(s)
AthaMap was supported by the German Ministry of Education and Research [BMBF grant Nos. 031U110C/031U210C, 0315037B and 0315459A].

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