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STAMP specifications

Information


Unique identifier OMICS_08107
Name STAMP
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for STAMP

STAMP citations

 (73)
library_books

Identification, Validation and Utilization of Novel Nematode Responsive Root Specific Promoters in Arabidopsis for Inducing Host Delivered RNAi Mediated Root Knot Nematode Resistance

2017
Front Plant Sci
PMCID: 5733009
PMID: 29312363
DOI: 10.3389/fpls.2017.02049

[…] genes to identify nrrs motif (supplementary figure presentation ; supplementary figure ). to identify the transcription factors that might bind to these sites, we used poxo (kankainen et al., ) and stamp (mahony and benos, ) but no statistically significant similarity to known motifs was found. therefore, further characterization of these novel motifs is required to establish their functional […]

library_books

RNA Seq analysis reveals insight into enhanced rice Xa7 mediated bacterial blight resistance at high temperature

2017
PLoS One
PMCID: 5673197
PMID: 29107972
DOI: 10.1371/journal.pone.0187625

[…] with the density function from the r core package []. dreme [] was used for motif discovery with the 1000 bp sequences upstream of putative transcription start sites from the reference genome. stamp [] was used for dna motif matching., the authors would like to thank rene corral, emily delorean, jillian lang, paul langlois, bradley tonnessen, jesse ellgren, and troy aubol for technical […]

library_books

Identification of cis regulatory sequences reveals potential participation of lola and Deaf1 transcription factors in Anopheles gambiae innate immune response

2017
PLoS One
PMCID: 5640250
PMID: 29028826
DOI: 10.1371/journal.pone.0186435

[…] genes in a. gambiae, in vivo and in vitro. therefore, we investigated which other motifs co-occur with this type. focusing on siomics-detected crms containing a motif with the better matching stamp e value (9.2 x10-8) to the dorsal (dl)-type tfbs, the following rel potential partners were identified: rel, stat, lola and deaf1. these findings suggest that agdeaf1 and aglola are robust […]

library_books

The non canonical poly(A) polymerase FAM46C acts as an onco suppressor in multiple myeloma

2017
Nat Commun
PMCID: 5606997
PMID: 28931820
DOI: 10.1038/s41467-017-00578-5

[…] levels observed in fam46cmut-gfp cells. functional clustering of go terms analysis was performed using david. the search for common sequence motif was performed using homer and further analyzed by stamp., multiple alignments analyses were performed using profile alignement (praline) (http://ibivu.cs.vu.nl/programs/pralinewww/), ., ms analysis were performed essentially as described. briefly, […]

library_books

Conserved Transcription Factors Steer Growth Related Genomic Programs in Daphnia

2017
Genome Biol Evol
PMCID: 5569996
PMID: 28854641
DOI: 10.1093/gbe/evx127

[…] the mean auc. only motifs with a nes above a specified threshold (default 2.5) are considered enriched. to simplify the output, the enriched motifs are grouped into clusters of similar motifs using stamp (). motifs assigned to the same cluster are given the same color in the results table. to retrieve an optimal subset of the input gene set as putative target genes, a “leading edge” […]

library_books

Prognostic cancer gene signatures share common regulatory motifs

2017
Sci Rep
PMCID: 5500535
PMID: 28684851
DOI: 10.1038/s41598-017-05035-3

[…] the predicted motifs by siomics in each gs with those from all other gss from the same cancer type. we compared motifs with their motif position weight matrices (pwms), using the online version of stamp with the default parameters. for each predicted motif in one gs, all motifs from other gss with the stamp e-value smaller than 1e-08 were considered as its similar motifs. we used […]


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STAMP institution(s)
Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA

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