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Protocols

Amadeus specifications

Information


Unique identifier OMICS_06286
Name Amadeus
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Amadeus

Amadeus citations

 (31)
library_books

Arabidopsis SWI/SNF chromatin remodeling complex binds both promoters and terminators to regulate gene expression

2016
Nucleic Acids Res
PMCID: 5389626
PMID: 27994035
DOI: 10.1093/nar/gkw1273

[…] Differential motif analysis was performed for 500 bp located behind TTS of 3΄BRM-occupied and 5΄BRM-occupied genes as positive and negative sets respectively, using Amadeus tool () with default parameters. Sense promoters showed similar number of TATA elements per sequence with 10,7 for BRM5΄ and 10,5 for BRM3΄-occupied genes. BRM-enriched terminator regions show […]

library_books

Identification of miRNAs Potentially Involved in Bronchiolitis Obliterans Syndrome: A Computational Study

2016
PLoS One
PMCID: 5001701
PMID: 27564214
DOI: 10.1371/journal.pone.0161771

[…] to the RESTful APIs provided by TargetMine []. For a given gene, the “Upstream Transcription Factors Template Query” (Targetmine) enables the retrieval of all upstream regulatory genes (TFs) from the AMADEUS [][] and ORegAnno [] libraries of transcription factors-target gene relations. By applying this computational step, each pathway considered was extended to systematically include the TFs for a […]

library_books

Modeling protein–DNA binding via high throughput in vitro technologies

2016
Brief Funct Genomics
PMCID: 5439287
PMID: 27497616
DOI: 10.1093/bfgp/elw030

[…] discovery problem. De novo motif discovery has been tackled using a myriad of algorithmic techniques, such as Expectation Maximization (MEME []), Gibbs sampling (AlignACE []), efficient enumeration (Amadeus []) and neural networks (ANN-Spec []). Methods that use weights or a ranked list of genes include DRIM [] and MatrixREDUCE []. A survey of motif finding tools can be found in [, ].The problem […]

library_books

Transcriptome Alterations In X Irradiated Human Gingiva Fibroblasts

2016
Health Phys
PMCID: 4936435
PMID: 27356049
DOI: 10.1097/HP.0000000000000419

[…] relying on the default parameters and the EnsMart62Plus annotation for humans. The EnsMart62Plus comprises annotation from KEGG (), WikiPathways (), transcription factor-target relationships from the Amadeus Metazoan compendium () and the PAZAR transcription factor and regulatory sequence database (), and microRNA target sets as compiled in AltAnalyze (). The complete list of all detected genes se […]

library_books

Integrated analysis of global proteome, phosphoproteome, and glycoproteome enables complementary interpretation of disease related protein networks

2015
Sci Rep
PMCID: 4676070
PMID: 26657352
DOI: 10.1038/srep18189

[…] ng the DEPs, 304,217 protein-DNA interactions (PDIs) were first collected from the human transcriptional regulation interactions database (HTRIdb), transcriptional regulatory element database (TRED), Amadeus, the molecular signatures DB (MSigDB), EdgeExpress database (EEDB), a database of regulatory information for human bZIP transcription factors (bZIPDB), and MetaCore™ (GeneGo, St. Joseph, MI, U […]

library_books

RFX transcription factors are essential for hearing in mice

2015
Nat Commun
PMCID: 4634137
PMID: 26469318
DOI: 10.1038/ncomms9549

[…] were detected by DAVID using the set of all genes expressed in the data set as the background set.Analysis of cis-regulatory motifs. Over-represented sequence motifs in promoters were searched using AMADEUS. The set of promoters of all genes detected as expressed in each analysed data set was used as the background set. The promoter regions examined spanned from 1,000 nt upstream to 500 nt downst […]


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Amadeus institution(s)
School of Computer Science, Tel Aviv University, Tel Aviv, Israel

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