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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
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Genomics & Informatics
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Journal DOI :
Korea Genome Organization
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Volume & Issues
Volume 3, Issue 4 - Dec 2005
Volume 3, Issue 3 - Sep 2005
Volume 3, Issue 2 - Jun 2005
Volume 3, Issue 1 - Mar 2005
Selecting the target year
Prediction of Mammalian MicroRNA Targets - Comparative Genomics Approach with Longer 3' UTR Databases
Nam, Seungyoon ; Kim, Young-Kook ; Kim, Pora ; Kim, V. Narry ; Shin, Seokmin ; Lee, Sanghyuk ;
Genomics & Informatics, volume 3, issue 3, 2005, Pages 53~62
MicroRNAs play an important role in regulating gene expression, but their target identification is a difficult task due to their short length and imperfect complementarity. Burge and coworkers developed a program called TargetScan that allowed imperfect complementarity and established a procedure favoring targets with multiple binding sites conserved in multiple organisms. We improved their algorithm in two major aspects - (i) using well-defined UTR (untranslated region) database, (ii) examining the extent of conservation inside the 3' UTR specifically. Average length in our UTR database, based on the ECgene annotation, is more than twice longer than the Ensembl. Then, TargetScan was used to identify putative binding sites. The extent of conservation varies significantly inside the 3' UTR. We used the 'tight' tracks in the UCSC genome browser to select the conserved binding sites in multiple species. By combining the longer 3' UTR data, TargetScan, and tightly conserved blocks of genomic DNA, we identified 107 putative target genes with multiple binding sites conserved in multiple species, of which 85 putative targets are novel.
Detection of Mycoplasma Infection in Cultured Cells on the Basis of Molecular Profiling of Host Responses
Chung, Tae Su ; Kim, Ju Han ; Lee, Young-Ju ; Park, Woong-Yang ;
Genomics & Informatics, volume 3, issue 3, 2005, Pages 63~67
Adaptive responses to diverse microbial pathogens might be limited in relatively few types. Host cell responses to pathogens are believed to be patterned or stereotyped along with species or class. We tried to compose the host response to Mycoplasma in terms of cellular gene expression. Although gene expression profile of two host HeLa and 293 cells were quite different each other, 30 genes were differentially expressed by mycoplasma infection in both of HeLa and 293 cells. Six of them (PR48, MADH4, MKPX, CRK, RBM7, NEK3) were related to cell cycle or proliferation. Another category of genes like IL1 HY1, KLRF1, TNFSF14, GBP1 were host defense to elicit immune responses. With this set of genes, we establish the prediction model for mycoplasma contamination.
Development of a Knowledge Base for Korean Pharmacogenomics Research Network
Park, Chan Hee ; Lee, Su Yeon ; Jung, Yong ; Park, Yu Rang ; Lee, Hye Won ; Kim, Ju Han ;
Genomics & Informatics, volume 3, issue 3, 2005, Pages 68~73
Pharmacogenomics research requires an intelligent integration of large-scale genomic and clinical data with public and private knowledge resources. We developed a web-based knowledge base for KPRN (Korea Pharmacogenomics Research Network, http://kprn.snubi. org/). Four major types of information is integrated; genetic variation, drug information, disease information, and literature annotation. Eighteen Korean pharmacogenomics research groups in collaboration have submitted 859 genotype data sets for 91 disease-related genes. Integrative analysis and visualization of the large collection of data supported by integrated biomedical pathways and ontology resources are provided with a user-friendly interface and visualization engine empowered by Generic Genome Browser.
Single Nucleotide Polymorph isms of a 16 kb Region on Human Chromosome 11 p15.5 that Includes the H19 Gene
Park, Mi-Hyun ; Ku, Hyeon-Jeong ; Lee, Hye-Ja ; Kim, Kwang-Joong ; Park, Chan ; Oh, Bermseok ; Kimm, Ku-Chan ; Lee, Jong-Young ;
Genomics & Informatics, volume 3, issue 3, 2005, Pages 74~79
The H19 gene, located at human chromosome 11p15.5, is imprinted in most normal human tissues. However, imprinting is often lost in tumors suggesting H19 is a putative tumor suppressor. We analyzed the single nucleotide polymorphisms (SNPs) of a 16 kb region that includes the H19 gene and its imprinting control region (ICR) in the Korean population. To identify SNPs, we directly sequenced this region in 18 Korean subjects. We identified 64 SNPs, of which 7 were in the exons of H19, 2 were in the introns, 14 were in the 3' intergenic region and 41 were in the 5' intergenic region. Of the 64 SNPs, 21 had not previously been reported and thus appear to be unique to the Korean population. The identified SNPs of H19 in the Korean population may eventually be useful as genetic markers associated with various diseases. In this study, 7 of the 64 identified SNPs were at CTCF binding sites in the ICR and may affect regulation of H19 gene imprinting. Thus, several genetic variations of the H19 gene may be important markers in human diseases that involve genomic imprinting, including cancer.
HExDB: Human EXon DataBase for Alternative Splicing Pattern Analysis
Park, Junghwan ; Lee, Minho ; Bhak, Jong ;
Genomics & Informatics, volume 3, issue 3, 2005, Pages 80~85
HExDB is a database for analyzing exon and splicing pattern information in Homo sapiens. HExDB is useful for specific purposes: 1) to design primers for exon amplification from cDNA and 2) to understand the change of ORFs by alternative splicing. HExDB was constructed by integrating data from AltExtron which is the computationally predicted exon database, Ensemble cDNA annotation, and Affymetrix genome tile published recently. Although it may contain false positive data, HExDB is good starting point due to its sensitivity. At present, there areas many as 2,046,519 exons stored in the HExDB. We found that
of the exons in the database was constitutive exons and
were novel gene exons.
KBUD: The Korea Brain UniGene Database
Jeon, Yeo-Jin ; Oh, Jung-Hwa ; Yang, Jin-Ok ; Kim, Nam-Soon ;
Genomics & Informatics, volume 3, issue 3, 2005, Pages 86~93
Human brain EST data provide important clues for our understanding of the molecular biology associated with the function of the normal brain and the molecular pathophysiology with brain disorders. To systematically and efficiently study the function and disorders of the human brain, 45,773 human brain ESTs were collected from 27 human brain cDNA libraries, which were constructed from normal brains and brain disorders such as brain tumors, Parkinson's disease (PO) and epilepsy. An analysis of 45,773 human brain ESTs using our EST analysis pipeline resulted in 38,396 high-quality ESTs and 35,906 ESTs, which were coalesced into 8,246 unique gene clusters, showing a significant similarity to known genes in the human RefSeq, human mRNAs and UniGene database. In addition, among 8,246 gene clusters, 4,287 genes (
) were found to contain full-length cONA clones. To facilitate the extraction of useful information in collected these human brain ESTs, we developed a user-friendly interface system, the Korea Brain Unigene Database (KBUD). The KBUD web interface allows access to our human brain data through three major search modes, the BioCarta pathway, keywords and BLAST searches. Each result when viewed in KBUD offers comprehensive information concerning the analyzed human brain ESTs provided by our data as well as data linked to various other publiC databases. The user-friendly developed KBUD, the first world-wide web interface for human brain EST data with ESTs of human brain disorders as well as normal brains, will be a helpful system for developing a better understanding of the underlying mechanisms of the normal brain well as brain disorders. The KBUD system is freely accessible at http://kugi.kribb.re.kr/KU/cgi -bin/brain. pI.
Patome: Database of Patented Bio-sequences
Kim, SeonKyu ; Lee, ByungWook ;
Genomics & Informatics, volume 3, issue 3, 2005, Pages 94~97
We have built a database server called Patome which contains the annotation information for patented bio-sequences from the Korean Intellectual Property Office (KIPO). The aims of the Patome are to annotate Korean patent bio-sequences and to provide information on patent relationship of public database entries. The patent sequences were annotated with Reference Sequence (RefSeq) or NCBI's nr database. The raw patent data and the annotated data were stored in the database. Annotation information can be used to determine whether a particular RefSeq ID or NCBI's nr ID is related to Korean patent. Patome infrastructure consists of three componentsthe database itself, a sequence data loader, and an online database query interface. The database can be queried using submission number, organism, title, applicant name, or accession number. Patome can be accessed at http://www.patome.net. The information will be updated every two months.