GeneACT protocols

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GeneACT specifications

Information


Unique identifier OMICS_27547
Name GeneACT
Interface Web user interface
Restrictions to use None
Input data A set of NCBI Entrez gene IDs or gene names and the selected region to visualize.
Computer skills Basic
Maintained No

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus

Maintainer


This tool is not available anymore.

Publication for GeneACT

GeneACT in pipeline

2009
PMCID: 2724271
PMID: 19491311
DOI: 10.1093/nar/gkp425

[…] de novo prediction of sequence motifs over-represented in proximal promoters compared to control sequences [for a review, see (,)]. examples for the former include storm in cread (), core_tf () and geneact () and for the latter dme () and the genomic identification of motifs described by xie et al. (). pwms of hif-1 have been previously used to identify genome-wide target genes. for instance, […]


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GeneACT in publications

 (5)
PMCID: 5605242
PMID: 28158820
DOI: 10.1093/nar/gkx079

[…] ()., primer extension assays were assembled that contained 1x thermopol buffer (new england biolabs, frankfurt, germany), 1 m betaine, 200 μm d-dntps (rovalab, teltow, germany) or l-dntps (geneact inc., shojima, kurume, fukuoka, japan), 4 μm each of ‘primer 19’ (19-mer d- or l-dna) and ‘template 83’ (83-mer d- or l-dna), and known amounts of polymerase. oligonucleotide sequences […]

PMCID: 3737233
PMID: 23951046
DOI: 10.1371/journal.pone.0070942

[…] dna synthesizer (nihon technoservice, ushiku, ibaraki, japan) using phosphoramidites from glen research (sterling, virginia, usa), and 1 µmol, pore size 500 å, controlled pore glass (cpg) beads from geneact (fukuoka, japan). for the synthesis of eprobes with paired thiazole orange or thiazole pink moieties (d570, or in eprobe name indicated as “tp”), the eprimer protocol was changed by replacing […]

PMCID: 3563611
PMID: 23046558
DOI: 10.1186/2044-5040-2-21

[…] seed matches with secondary elements that stabilize mrna. priority 1 calls had a destabilizing mrna element while priority 2 calls did not contain a destabilizing element in at least one species. geneact used the miranda algorithm to identify mirna target sites across three mammalian species. false-positives were eliminated with the differential binding site search against genes […]

PMCID: 3424578
PMID: 22638570
DOI: 10.1093/nar/gks466

[…] regulatory elements which are essential for d450-tata and p500/luc activities. to identify potential transcription factor binding motifs within these two sites, the sequences were queried using the geneact transcription factor binding site database. the analysis revealed that dr contains a putative e-box motif while pr contains a potential ikaros binding motif., to experimentally determine […]

PMCID: 1636466
PMID: 17012278
DOI: 10.1093/nar/gkl637

[…] ttp) were obtained from roche diagnostics. all modified nucleoside triphosphates used for pcr assays are listed in . tal, tpr, cal and cpr were purchased from trilink biotechnologies; tpa was from geneact; and cpa was from jena bioscience. the other modified nucleoside triphosphates were synthesized (see supplementary and ). primers 1f, 1r, 2f and 2r were purchased from jbios, and puc18 […]


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GeneACT institution(s)
Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA; Department of Computer Science, University of Colorado, Boulder, CO, USA
GeneACT funding source(s)
Supported by a predoctoral training grant from NHLBI (5T32HL07851), by grants from NIH (CA095527), US Army Breast Cancer Research Program (DAMD17-02-1-0350), and WM Keck Foundation Initiative in RNA science at the University of Colorado.

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