mbc.nctu.edu.tw

plantpan.mbc.nctu.edu.tw

PlantPAN

Plant Promoter Analysis Net. Best viewed with Netscape 7.0 and Internet Explorer 6.0. JavaScript must be enabled in your browser. WC Chang, T.Y. Lee, H.D. Huang*, H.Y. Huang and R.L. Pan*. (2008) "PlantPAN: Plant Promoter Analysis Navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene group", BMC Genomics, 9:561. [PubMed]. Plant Promoter Analysis Navigator. National Chio Tung University, Taiwan. Contact with Hsien-Da Huang. Contact with Rong-Long Pan.

mirstart.mbc.nctu.edu.tw

Welcome to miRStart

Published experimental evidences used in miRStart are described as follows:. 1) CAGE (Cap Analysis of Gene Expression) tags: Recognize 5’-end of a gene. 2) TSS Seq tags: More than 300 million 5’-end sequences of human and mouse cDNAs by combining oligo-capping method and Solexa sequencing technology. 3) H3K4me3 enrichment (histone H3 is trimethylated at its lysine 4 residue): Enriched surrounding TSSs. The following figure demonstrates the concept of miRStart. The human miRNA let-7a-1.

mirtarbase.mbc.nctu.edu.tw

miRTarBase: the experimentally validated microRNA-target interactions database

MiRTarBase: the experimentally validated microRNA-target interactions database. 1 The word cloud of miRNA-disease information. Shows the miRNA was major related to the liver related disease such as hepatocellular carcinoma. 2 miRNA-Target site viewer in CLIP-seq data. Example: The miRNA, hsa-miR-15a-5p : VEGFA, target gene was display in 17 CLIP-seq (HITS-CLIP and PAR-CLIP) data sets generated by 6 independent studies.[ 17 datasets. 3 Clinical microRNA and gene expression profiles from TCGA. A computatio...

mirnamap.mbc.nctu.edu.tw

miRNAMap - genomic maps of studying genes regulation by metazoan microRNAs

Previous version - miRNAMap 1.0. Hsu SD, Chu CH, Tsou AP, Chen SJ, Chen HC, Hsu PW, Wong YH, Chen YH, Chen GH, Huang HD (2008) 'miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.' Nucleic Acids Res. 2008 Jan;36(Database issue):D165-9. [ Pubmed. Department of Biological Science and Technology,. Institute of Bioinformatics National Chiao Tung University, Hsinchu, Taiwan. Contact with: bryan@mail.NCTU.edu.tw. Get Access to [ CBST, http:/ www.life.nctu.edu.tw/.

kinasephos.mbc.nctu.edu.tw

KinasePhos

Is to computationally predict phosphorylation sites within given protein sequences. The known phosphorylation sites are categorized by substrate sequences and their corresponding protein kinase classes. Profile Hidden Markov Model (HMM). HD Huang*, T.Y. Lee, S.W. Tseng, and J.T. Horng. (2005) "KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites" Nucleic Acids Research, Vol. 33, W226-229. [PubMed]. CP1BB HUMAN, Platelet glycoprotein Ib beta chain [Precursor]. Bid Lab, Inst...

kinasephos2.mbc.nctu.edu.tw

KinasePhos 2.0

Version of kinase-specific phosphorylation site prediction tool that is based the sequenece-based amino acid coupling-pattern analysis and solvent accessibility as new features of SVM (support vector machine). Paste a single sequence or several sequences in FASTA. Format into the field below:. Submit a file ( 2MB) in FASTA. Format directly from your local disk:. G protein-coupled receptor kinase(GRK). I kappa B kinase(IKK). Cell division cycle protein kinase(CDC2). G protein-coupled receptor kinase(GRK).

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.

fmm.mbc.nctu.edu.tw

FMM: From Metabolite to Metabolite - A Critical Tool for Synthetic Biology and Metabolic Engineering

FMM (From Metabolite to Metabolite). Etabolite) is a critical tool for synthetic biology. FMM can reconstruct metabolic pathways. Form one metabolite to the other one. The different KEGG maps can be connected by our system. Both local and global graphical views. Of the metabolic pathways were designed. Furthermore, metabolic pathways can be comparative between several species by FMM ( Comparative Analysis. Vol 37, W129-34 [ PubMed. L-Phenylalanine (C00079) Resveratrol (C03582) (Stilbene Synthase Pathway).

dbptm.mbc.nctu.edu.tw

dbPTM

DbPTM 10th Year Anniversary. An Integrated Resource for Protein Post-Translational Modifications. Drug binding-associated PTM sites. The Statistics of PTMs. Move to the Statistics Page. Modified residue Glycosylation Lipidation Crosslink. Structural characterization of PTM substrate sites. The Benchmark dataset of PTMs. ex: O-Glycosylation. Reconstruct the PTM Regulatory Network. ex: O-Glycosylation. Welcome to dbPTM 10th Year Anniversary. Integrative Platform for PTM Analysis. Large-scale identification...

methhc.mbc.nctu.edu.tw

MethHC: a database of DNA methylation and gene expression in human cancers

A database of DNA Meth. Ylation and gene expression in H. MethHC is a database for Human pan-cancer gene expression, methylation and microRNA expression. The human pan-cancer methylation database, MethHC. Is a web based resource focused on the DNA methylation of human diseases. MethHC integrated data such as DNA methylation, gene expression, microRNA methylation, microRNA expression, and the correlation of methylation and gene expression from TCGA (The Cancer Genome Atlas). 2 We offer the methylation lev...