PASTAA protocols

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PASTAA specifications

Information


Unique identifier OMICS_08381
Name PASTAA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A list of Ensembl IDs, Gene Symbols or RefSeq IDs
Output data TFs will be ranked according to their association with your input set.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Versioning


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Information


Unique identifier OMICS_08381
Name PASTAA
Interface Web user interface
Restrictions to use None
Input data A list of Ensembl IDs, Gene Symbols or RefSeq Ids
Output data TFs will be ranked according to their association with your input set.
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Publication for PASTAA

PASTAA in pipeline

2016
PMCID: 4821839
PMID: 27110435
DOI: 10.1002/brb3.434

[…] all were found within genes with selection probability >0.4 in gggl‐1, indicating strong agreement between the two approaches table s8, table s9., analysis of transcriptional regulation using the pastaa algorithm (roider et al. ) indicated that expression of four of these five genes (acaa1, aqp7, me1, and slc27a1) is controlled by a common transcription factor, early growth response (egr‐4), […]


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PASTAA in publications

 (25)
PMCID: 5940679
PMID: 29740078
DOI: 10.1038/s41598-018-25517-2

[…] to evaluate the different capacity of recognition and binding of rna pol ii under hyposmotic modulation. to identify the tfs that might promote that specific rna pol ii binding profile we used pastaa, a tool from max planck institute (http://trap.molgen.mpg.de/cgi-bin/pastaa.cgi). this method detects tfs that are associated with particular functional categories of genes. pastaa stands for: […]

PMCID: 5709375
PMID: 29192143
DOI: 10.1038/s41598-017-16687-6

[…] we used a discovery-motivated approach to identify potential regulatory transcriptional factors associated with the genes upregulated by atra treatment in either mda-mb-231 or mda-mb-468. we used pastaa (predicting associated transcription factors from annotated affinities) to identify transcription factors with high binding affinities within our upregulated gene lists. the top matrices […]

PMCID: 5678682
PMID: 29117258
DOI: 10.1371/journal.pone.0187773

[…] relatively stringent cut-off improves the detection of changes of biological relevance to cell functions when using detection with database resources such as genemania [], string [], panther [] and pastaa []. also, as previously reported [], the expression of key inflammatory genes were examined using taqman real-time quantitative pcr. similar to these reports these qpcr checks confirmed […]

PMCID: 5759031
PMID: 29110491
DOI: 10.1021/acs.jproteome.7b00595

[…] (r = −0.62, a). to understand better the connection between beta-alanine and fox genes family, we performed motif enrichment analysis for the enzymes interacted with beta-alanine in b using pastaa tool. interestingly, foxo1 was one of most significant transcription factors (p = 5.89e–04) that targeted the promoter regions of beta-alanine interacting enzymes., metabolomics has become […]

PMCID: 5679164
PMID: 28935693
DOI: 10.1084/jem.20170412

[…] modules”) were annotated using a combination of knowledge-based and data-driven approaches, including ingenuity pathway analysis (ipa), gene ontology, interferome (; fig. s1, c and d), and pastaa () upstream transcription factor binding site enrichment analyses (table s2). modular fingerprints were derived for each stimulus and hierarchically clustered (). five modules were associated […]


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PASTAA institution(s)
Max Planck Institute for Molecular Genetics, Berlin, germany

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