gpminer.mbc.nctu.edu.tw

GPMiner

To facilitate the investigation of gene promoters, this work presents an integrated system namely GPMiner. For identifying promoter regions and annotating regulatory features in user-input sequences. The proposed promoter identification method, whose predictive sensitivity and specificity are both 80%, incorporates the support vector machine (SVM) with nucleotide composition, over-represented hexamer nucleotides and DNA stability. Users can input the gene group. By Known Gene Ensembl ID.

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GPMiner | gpminer.mbc.nctu.edu.tw Reviews

<META> DESCRIPTION

To facilitate the investigation of gene promoters, this work presents an integrated system namely GPMiner. For identifying promoter regions and annotating regulatory features in user-input sequences. The proposed promoter identification method, whose predictive sensitivity and specificity are both 80%, incorporates the support vector machine (SVM) with nucleotide composition, over-represented hexamer nucleotides and DNA stability. Users can input the gene group. By Known Gene Ensembl ID.

<META> KEYWORDS

1 step 1

2 species

3 human

4 mouse

5 chimpanzee

6 step 2

7 query type

8 by chromosome location

9 step 3

10 format

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step 1,species,human,mouse,chimpanzee,step 2,query type,by chromosome location,step 3,format,step 4,cpg island,by cpgprod,g c content,by transfac match,core score =,matrix score =,over represented or oligonucleotide,z score,minimum occurence,report top

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GPMiner | gpminer.mbc.nctu.edu.tw Reviews

https://gpminer.mbc.nctu.edu.tw

To facilitate the investigation of gene promoters, this work presents an integrated system namely GPMiner. For identifying promoter regions and annotating regulatory features in user-input sequences. The proposed promoter identification method, whose predictive sensitivity and specificity are both 80%, incorporates the support vector machine (SVM) with nucleotide composition, over-represented hexamer nucleotides and DNA stability. Users can input the gene group. By Known Gene Ensembl ID.

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gpminer.mbc.nctu.edu.tw

1

GPMiner

http://gpminer.mbc.nctu.edu.tw/gene_group1.php

Gene Group Analysis - Step 1 : Input a group of gene names/symbols. Please paste a group of gene names/symbols seperated with ";". SMG5;GYG1;PAM;LAMB1;GNG4;NRP1;GCLC;CFTR;BAD;SNX11;AK2. Scanning the transcription factor binding sites (by TRANSFAC MATCH). Bid Lab, Institute of Bioinformatics, National Chiao Tung University , Taiwan. With questions or comments.

2

GPMiner - Comparison page

http://gpminer.mbc.nctu.edu.tw/comparison.htm

This work develops an integrated system, namely GPMiner,. Incorporates support vector machine. Stability for mammalian proximal promoter identification,. And mines the regulatory elements, including. Transcriptional start sites, transcription factor binding sites, CpG islands, tandem repeats, TATA box, CCAAT box, GC box, statistically over-represented sequence patterns, GC content. Additionally, 1,871 human promoter sequences. S ee Supplementary Materials). Furthermore, the distribution of promoter predi...

3

GPMiner

http://gpminer.mbc.nctu.edu.tw/index.php

To facilitate the investigation of gene promoters, this work presents an integrated system namely GPMiner. For identifying promoter regions and annotating regulatory features in user-input sequences. The proposed promoter identification method, whose predictive sensitivity and specificity are both 80%, incorporates the support vector machine (SVM) with nucleotide composition, over-represented hexamer nucleotides and DNA stability. Users can input the gene group. By Known Gene Ensembl ID.

4

GPMiner

http://gpminer.mbc.nctu.edu.tw/help.php

The system integrated numerous computational methods to comprehensively annotate the regulatory features of five mammalian genomes such as human, mouse, rat, chimp, and dog. The system integrated numerous computational methods to comprehensively annotate the regulatory features of five mammalian genomes such as human, mouse, rat, chimp, and dog. The related information of the. Users can also input a novel sequence to be annotated the putative TSS. The system integrates the TSS prediction tool, Eponine.

5

GPMiner - about page

http://gpminer.mbc.nctu.edu.tw/about.htm

GPMiner: a web server for mining transcriptional regulatory elements in mammalian gene promoter regions. Stability and GC-content. To facilitate the investigation of gene promoters, therefore, this work presents an integrated system for identifying promoter regions and annotating regulatory features in user-input sequences. The proposed promoter identification method, whose predictive sensitivity and specificity are both 80%, incorporates the support vector machine. The system flow of GPMiner. Illustrate...

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csb.cse.yzu.edu.tw

CSB Lab 計算系統生物學實驗室

http://csb.cse.yzu.edu.tw/member.php

Lasted Update : 2015.08.01. Protein Functions and Structures. Graduate Program in Biomedical Informatics, Yuan Ze University. (2010-2015).

csb.cse.yzu.edu.tw

CSB Lab 計算系統生物學實驗室

http://csb.cse.yzu.edu.tw/publication.php

Lasted Update : 2015.08.01. Journal papers (*Corresponding author) :. Hsien-Da Huang, Tzong-Yi Lee. 2016, "dbPTM 2016: ten-year anniversary of a resource of post-translational modification of proteins" Nucleic Acids Research. 2016 Jan. 4, Vol. 44(D1):D435-D446. (SCI, 2014 IF: 9.112. 20/289 in BIOCHEMISTRY and MOLECULAR BIOLOGY). 2 Chi-Nga Chow, Han-Qin Zheng, Nai-Yun Wu, Chia-Hung Chien, Hsien-Da Huang, Tzong-Yi Lee. 2016 Jan. 4; Vol. 44(D1):D1154-D1160. (SCI, 2014 IF: 9.112. And Shun-Long Weng*, 2016, "...

csb.cse.yzu.edu.tw

CSB Lab 計算系統生物學實驗室

http://csb.cse.yzu.edu.tw/index.php

Lasted Update : 2015.08.01. 計算系統生物學實驗室 Computational Systems Biology Laboratory 成立於2010年，由李宗夷教授. 實驗室於2010年成立，至今已發表超過 50 篇 SCI國際期刊研究論文. 榮獲財團法人徐有庠紀念基金會頒發第十三屆有庠傑出教授獎. 發表論文海報 "Characterization and identification of protein O-linked glycosylation sites based on glycotransferase substrate specificities"，並獲得 Best Poster Presentation Award. 201505.20 - 由 CSB Lab 發佈. Protein Post-translational Modifications 蛋白質後轉譯修飾作用. Cheng-Tsung Lu , Kai-Yao Huang , Min-Gang Su ( joint first authorship), Tzong-Yi Lee.

csb.cse.yzu.edu.tw

CSB Lab 計算系統生物學實驗室

http://csb.cse.yzu.edu.tw/pi.php

Lasted Update : 2015.08.01. Dr Tzong-Yi Lee 李宗夷. Department of Computer Science and Engineering. Graduate Program in Biomedical Informatics. R3312C , Building #3. R1706C , Building #1. 886-3-4638800 ext. 3007. Francis@saturn.yzu.edu.tw. Http:/ csb.cse.yzu.edu.tw. Department of Computer Science and Engineering,. Graduate Program in Biomedical Informatics,. Department of Computer Science and Engineering,. Graduate Program in Biomedical Informatics,. Department of Computer Science and Engineering,. Yi-Fan C...

csb.cse.yzu.edu.tw

CSB Lab 計算系統生物學實驗室

http://csb.cse.yzu.edu.tw/collaborator.php

Lasted Update : 2015.08.01. Graduate Program in Biomedical Informatics, Yuan Ze University. (2010-2015).

csb.cse.yzu.edu.tw

CSB Lab 計算系統生物學實驗室

http://csb.cse.yzu.edu.tw/resource.php

Lasted Update : 2015.08.01. Resource : Tools and Databases 工具開發與資料庫建置. An informative resource for investigating substrate site specificity and functional association of protein post-translational modifications. (Nucl Acids Res, 2013). Http:/ dbptm.mbc.nctu.edu.tw/. An informative resource for exploring structural environment of SNO substrate sites and regulatory networks of S-nitrosylated proteins. (Bioinformatics, 2012). Http:/ dbsno.mbc.nctu.edu.tw/. Http:/ csb.cse.yzu.edu.tw/dbGSH/.

csb.cse.yzu.edu.tw

CSB Lab 計算系統生物學實驗室

http://csb.cse.yzu.edu.tw/link.php

Lasted Update : 2015.08.01. Nucleic Acids Research: Oxford Journals (NAR). Nucleic Acids Research (NAR) publishes the results of leading edge research into physical, chemical, biochemical and biological aspects of nucleic acids and proteins involved in nucleic acid metabolism and/or interactions. Http:/ nar.oxfordjournals.org/. Accelerating the Publication of Peer-reviewed Science. Http:/ www.plosone.org/. Http:/ bioinformatics.oxfordjournals.org/. Sixth International Course: Computational Genomics.

csb.cse.yzu.edu.tw

CSB Lab 計算系統生物學實驗室

http://csb.cse.yzu.edu.tw/meeting.php

Lasted Update : 2015.08.01. Regular Group Meeting 團體會議. Identification of tubular injury microRNA biomarkers in urine: comparison of next-generation sequencing and qPCR-based profiling platforms. Background: MicroRNAs (miRNAs) are small, non-coding RNAs that regulate protein levels post-transcriptionally. MiRNAs play important regulatory roles in many cellular processes and have been implicated in several diseases. That although miRNA-seq has superior specificity, it may not detect low abundant miRNAs in...

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gpminer.mbc.nctu.edu.tw

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To facilitate the investigation of gene promoters, this work presents an integrated system namely GPMiner. For identifying promoter regions and annotating regulatory features in user-input sequences. The proposed promoter identification method, whose predictive sensitivity and specificity are both 80%, incorporates the support vector machine (SVM) with nucleotide composition, over-represented hexamer nucleotides and DNA stability. Users can input the gene group. By Known Gene Ensembl ID.

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