11:10-12:00, Rm 103

Bioinformatics and systems biologyA-17-14Analysis of changes in ubiquitin-proteasome pathway gene expressioninduced by magnetic nanoparticlesSang Mi Hyun¹, Wooyoung Shim¹and Gwang Lee¹ , ²¹Department of Molecular Science and Technology, Ajou University, Suwon, Korea, ²Institute forMedical Science, Ajou University School of Medicine, Suwon, KoreaFor the application of magnetic nanoparticles (MNPs) in biomedicine, sufficient dataregarding the toxicity and biological fate of the MNPs should be accumulated. The aim ofthis study is to investigate impacts of MNPs according to the concentration of MNPs.MNPs MNPs@SiO₂(RITC), a silica coated MNPs containing Rhodamine Bisothiocyanate (RITC), were treated into the HEK 293 with 0.1 µg/µL or 1.0 µg/µL.Microarray was performed by Affymetrix Human Genome U133 plus 2.0 Array. Foridentification of pathways and functional networks, dataset of significantly changed geneswas overlayed to Ingenuity Pathway Analysis (IPA). At 0.1 µg/µL MNPs@SiO₂(RITC),HEK 293 had no significant change compared with control. But at 1.0 µg/µL MNPs@SiO₂(RITC), the level of genes related with ubiquitin-proteasome activity were disturbed. Fromamong these genes related to the ubiquitin-proteasome activity, 18 genes were upregulatedand 2 genes were down-regulated. In high dose MNPs@SiO₂(RITC) treatedcell group, ubiquitin-proteasome activity was decreased approximately 25%. Inconclusion, overdose of MNPs can be cause genomic and cellular disturbance of theactivity of ubiquitin-proteasome system. Therefore, MNPs should be used at the optimalconcentration for the application in bioscience and medicin.A-17-17Functional profiling of microRNAs through a novel approach calledGAPPS-miRTarGESeung Gu Park¹, Kyung-Hoon Kwon², Sun Shim Choi¹¹Department of Medical Biotechnology, College of Biomedical Science, and Institute of Bioscience &Biotechnology, Kangwon National University, Chuncheon 200-701, Korea, ²Korea Basic ScienceInstitute, Daejeon, KoreaMicroRNAs(miRNAs) expressed as small non-coding RNAs are one of the crucialregulators of gene expression in embryonic developmental processes. In the presentposter, we suggest a new method called GAPPS-miRTarGE, which is a novelmethodology for predicting function of miRNAs based on proportional information of theirtargets expressed in the embryonic development stage called Theilers stages (TS) inmice. A latent idea of this approach is that miRNA function can be dictated by their targetmRNAs. Since there is only limited knowledge available about miRNA targets, we firsttried to collect best sets through calculation of correlation coefficients from six differentDBs including Targetscan (http://www.targetscan.org), miRDB (http://mirdb.org/miRDB/),PITA (http://genie.weizmann.ac.il), miRanda (http://www.microrna.org), microcosm target(http://www.ebi.ac.uk), miRNAMAP (http:// mirnamap.mbc.nctu.edu.tw). From thisanalysis, we collected new miRNA-target set. We next constructed a Grouping Analysisof Proportional Pattern Similarity for MiRNA Target Gene Expression(GAPPS-miRTarGE)in embryonic development, and we found that the GAPPS-miRTarGE method not onlyconfirm for previsouly known function, but also it predict for unidentified function ofmiRNAs in embryonic developmentA-17-15Application of statistical KEGG subpathway identification into earlyonset nonhereditary colorectal cancerSeungyoon Nam and Taesung Park¹National Cancer Center, Goyang, ¹Department of Statistics, Seoul National University, Seoul,KoreaHigh throughput technology (e.g., microarray) has been widely applied in a various fieldsof biology. Traditional approach of gene expression data finds similarly expressed genegroups by utilizing unsupervised learning (e.g., clustering, principal component analysis)or identifies statistically differentially expressed genes. Currently, new approaches calledGSA (Gene Set Analysis) have been developed but molecular level regulation amongbiological entries in a given gene set has not been considered extensively. We present apermutation-based probabilistic model that integrates gene regulation information ofKEGG pathway prior knowledge database with gene expression data in order to explorephenotypically relevant subpathways (subsets) within a given pathway. We bring thesimple method overview and its results for an early onset nonhereditary colorectal cancerdata.A-17-18Structural and expressional comparative analysis between miRNAtargets and nontarget genes in human genomeYoung Joon Mok, Seung Gu Park, Sun Shim ChoiDepartment of Medical Biotechnology, College of Biomedical Science, Kangwon NationalUniversity, Chuncheon 200-701, KoreaPrevious miRNA reports showed that miRNA target genes are longer and evolve moreslowly than non-target genes. In the present study, we also confirmed that TGs aresignificantly longer than those of NTGs. To do this, we downloaded mRNAs of eachchromosome in human from GenBank flat file format and sorted out 5’UTR, CDS, 3’UTR and intron length information from the file format. We also downloaded predictedmiRNA target gene datasets estimated by TargetScan or PITA program, and obtainedreal target genes from miRTarBase. We then tried to investigate, using direct lengthcomparison and a novel approach called FGA, what is the most discriminant parameterbetween real target genes(rTG), predicted target genes(pTGs), and predicted non-targetgenes(pNTGs). In result, structural patterns of rTG and pTG showed a similar pattern inoverall, while 3’UTR and intron lengths of rTG and pTG are dramatically different fromthose of pNTG. We also proved that pTG are degraded faster than pNTGs. Expressionlevels of pTGs were lower than those of pNTG in human adult tissues. Further, we foundthat expression breadth is significantly different between pTG and pNTG. We believe thatall these efforts can contribute to understand the characteristics of miRNA and itsregulation in the future.A-17-16CaGe: a cancer gene annotation system for NGS data-based cancergenomicsYoung-Kyu Park¹ , ², Tae-Wook Kang¹, Su-jin Baek¹, Seong-Min Park¹, Yong SungKim¹, Doheon Lee²and Seon-Young Kim¹¹Medical Genomics Research Center, KRIBB, Daejeon 305-806, ²Bio and Brain EngineeringDepartment, KAIST, Daejeon 305-701, KoreaOne of the hurdles in the next-generation sequencing (NGS)-based cancer genomics isto identify causative mutations out of many candidates. One useful approach is to refer toknown cancer gene list and associated information. The list of known cancer genes canbe used for determining candidates of cancer driver mutations and cancer gene relatedinformation including gene expression, interaction and pathways can be also useful forscoring novel candidates. We developed a web-accessible, cancer genome annotationsystem called CaGe to provide users information on cancer genes, mutations andassociated annotations. CaGe is based on several cancer gene databases composed ofreported cancer causative genes and associated cancer pathways. For a given gene list,CaGe searches cancer gene databases with converted standard gene symbols andprovides cancer gene related annotation through intuitive web user interfaces. We hopeCaGe will be useful in the identification of cancer causative mutations in the NGS-basedcancer genomics. [Supported by a KRIBB research initiative grant]A-17-19Selenium stimulates cell proliferation through PI3K/Akt pathway andinduces migration in 3T3-L1 preadipocytesShin-Hyung Park¹, Jeong-Hwan Kim3, Gyoo Yong Chi¹, Hyun Sup Eom¹and YungHyun Choi² , ³ , ⁴ , *Departments of ¹Pathology and ²Biochemistry, and Research Institute of Oriental Medicine,Dongeui University College of Oriental Medicine, Busan 614-052, ³Department of BiomaterialControl (BK21 program), Graduate School and Blue-Bio Industry RIC, Dongeui University, Busan614-714, KoreaIn the present study, we investigated the stem cell behaviors of selenium in 3T3-L1preadipocytes and the molecular mechanisms. In the process, we showed the potential ofselenium to promote cell proliferation and migration in 3T3-L1 cells. Selenium applied for24 h stimulated cell proliferation up to 20% compared to the untreated control. Seleniumup-regulated the expressions of CDK1, CDK-2 and Cyclin B, which are known to regulateG2/M progression, and significantly down-regulated CDK inhibitor p21. Selenium alsoincreased the expressions of PI3K and pAkt which have been reported to play a crucialrole in cell growth. However, LY 294002 suppressed the expressions of PI3K and pAkt,and also significantly inhibited selenium-induced cell proliferation, indicating that seleniumstimulated cell proliferation through PI3K/Akt activation. Furthermore, selenium inducedthe overexpression of stemness acting signals and significantly increased cell migrationthrough the activation of MMP-2 and MMP-9 coupled with the inhibition of TIMP-1 andTIMP-2. Taken together, our findings suggest that selenium can stimulate stem cellpotency via the increased proliferation and migration of 3T3-L1 cells. [Supported by NRFfunded by the MEST (2010-0001730).]162 Korean Society for Biochemistry and Molecular Biology