GPMiner protocols

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GPMiner specifications

Information


Unique identifier OMICS_09581
Name GPMiner
Interface Web user interface
Restrictions to use None
Input data A query sequence in FASTA format
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Tzong-Yi Lee <>

Publication for GPMiner

GPMiner in pipeline

2015
PMCID: 4613502
PMID: 26268560
DOI: 10.1042/BJ20150730

[…] the regulatory elements of the gpat2 gene, the 5′ sequence flanking the transcription start site (tss) (−1320 to translation start site) was analysed by online programs and applications, such as gpminer, alibaba 2.0, methprimer and epigenomics (ncbi) to recognize promoter elements such as the tata box, ccaat box and gpc islands. the first intron was included because in other genes, […]


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GPMiner in publications

 (14)
PMCID: 5787476
PMID: 29416623
DOI: 10.18632/oncotarget.23057

[…] of pparδ through binding and activating the core promoter (−1079/−239 nt) of pparδ., we next explored the -1079/-239 nt promoter regions for a possible transcription factor binding sites by using gpminer (http://gpminer.mbc.nctu.edu.tw/). the promoter region −1079/−239 contains various different promoter elements, such as hsf1 and nf-κb/p65. it has been reported that nf-κb/p65 signaling […]

PMCID: 5626709
PMID: 28974731
DOI: 10.1038/s41598-017-12955-7

[…] did not identify any tata or caat boxes for exon 0 or exon 1. analysis with the gene promoter miner server (institute of bioinformatics, national chiao tung university, hsin-chu, taiwan) (http://gpminer.mbc.nctu.edu.tw/about.htm) revealed a specific feature of promoters for sp family transcription factors: a gc box 141 bp upstream of exon 1. the promoter 2.0 prediction server (center […]

PMCID: 5609056
PMID: 28934931
DOI: 10.1186/s12864-017-4140-5

[…] with mitos v806 [] and a circular alignment between the six available pangolin species were drawn in circos v0.69 []. the gc content of the four african pangolin mitogenomes were calculated using gpminer [] with a sliding window of 300 bp. arlequin v3.5.1 [] was used to validate the gc scores obtained for the four mitogenomes using anova analysis and the diagrams were plotted in r v3.3.1 []., […]

PMCID: 5476597
PMID: 28630472
DOI: 10.1038/s41598-017-03385-6

[…] and rnapii pser5, which is a required rnapii phosphorylation for the transcriptional initiation, to the mdc1, exo1, and rad54b promoter regions. the putative tata box (region ta) was retrieved from gpminer. chip experiments showed a direct binding of smyd3 to the mdc1 promoter (region s3) at ~500 bp upstream of the transcription start site (tss) (fig. ). smyd3 preferred to enrich at region s3 […]

PMCID: 5601656
PMID: 28938560
DOI: 10.18632/oncotarget.16873

[…] cancer cells., to gain insight into the mechanism by which tnf-α activates the promoter of hbxip, we predicted the transcription factor binding sites in hbxip promoter by gene promoter miner (http://gpminer.mbc.nctu.edu.tw/). interestingly, we observed that there were several binding elements of transcription factors involving inflammatory response in the region of hbxip promoter, including […]


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GPMiner institution(s)
Department of Computer Science and Engineering, Yuan Ze University, Taoyuan, Taiwan; Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan; Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu, Taiwan; Department of Multimedia and Game Science, Asia-Pacific Institute of Creativity, Miao-Li, Taiwan

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