ChickGCE: A novel germ cell EST database for studying the early developmental stage in chickens

Kim, Heebal,Lim, Dajeong,Han, Beom Ku,Sung, Samsun,Jeon, Mina,Moon, Sunjin,Kang, Yeonkyung,Nam, Jungrye,Han, Jae Yong Elsevier 2006 Genomics Vol.88 No.2

<P><B>Abstract</B></P><P>We established a database to study germ cells during the early developmental stage in the chicken. The ChickGCE database provides integrated expressed sequence tag (EST) data from chicken testis, ovary, embryonic gonads, and primordial germ cells. We gathered data on 10,294 ESTs from approximately 1000 embryonic gonads, and we experimentally determined 10,851 ESTs from primordial germ cells purified from 7955 embryonic gonads by magnetically activated cell sorting. The EST testis and ovary datasets were retrieved from the public database of The Institute for Genomic Research (TIGR). The EST data were clustered and assembled into unique sequences, contigs, and singletons. The ChickGCE database provides functional annotation, identification, and putative embryonic germ-cell-specific novel transcripts based on the Gene Ontology database, as well as statistical analyses of expression patterns and pair-wise comparisons of two types of tissue- and germ-cell-specific alternative splicing events in the chicken. The new database is accessible online and queries can be answered using several search options, including tissue database searches, keywords, clone IDs, expected values, and BLAST search scores.</P>

Comparative Analysis of Repetitive Elements of Imprinting Genes Reveals Eleven Candidate Imprinting Genes in Cattle

Kim, HyoYoung,Kim, Heebal Asian Australasian Association of Animal Productio 2009 Animal Bioscience Vol.22 No.6

Few studies have reported the existence of imprinted genes in cattle compared to the human and mouse. Genomic imprinting is expressed in monoallelic form and it depends on a single parent-specific form of the allele. Comparative analysis of mammals other than the human is a valuable tool for explaining the genomic basis of imprinted genes. In this study, we investigated 34 common imprinted genes in the human and mouse as well as 35 known non-imprinted genes in the human. We found short interspersed nuclear elements (SINEs), long interspersed nuclear elements (LINEs), and long terminal repeats (LTRs) in imprinted (human and mouse) and control (cattle) genes. Pair-wise comparisons for the three species were conducted using SINEs, LINEs, and LTRs. We also calculated 95% confidence intervals of frequencies of repetitive sequences for the three species. As a result, most genes had a similar interval between species. We found 11 genes with conserved SINEs, LINEs, and LTRs in the human, mouse, and cattle. In conclusion, eleven genes (CALCR, Grb10, HTR2A, KCNK9, Kcnq1, MEST, OSBPL5, PPP1R9A, Sgce, SLC22A18, and UBE3A) were identified as candidate imprinted genes in cattle.

Gene Expression Profiling in the Uterine Endometrium during the Estrous Cyc1e and Pregnancy

Mingoo Kim,Sunjin Moon,Heebal Kim,Changkyu Lee,Hakhyun Ka 한국동물번식학회 2007 Reproductive & Developmental Biology(Supplement) Vol.31 No.2s

Change in gene expression of mouse embryonic stem cells derived from parthenogenetic activation

Gong, Seung Pyo,Kim, Heebal,Lee, Eun Ju,Lee, Seung Tae,Moon, Sunjin,Lee, Ho-Joon,Lim, Jeong Mook Oxford University Press 2009 Human reproduction Vol.24 No.4

<P>BACKGROUND: We previously established parthenogenetic mouse embryonic stem cells (ESCs) and this study was subsequently conducted for elucidating the influence of oocyte parthenogenesis on gene expression profile of ESCs. METHODS: Gene expression of parthenogenetic ESC (pESC)-1 or pESC-2 was separately compared with that of two normally fertilized ESC (nfESC) lines (B6D2F1 and R1 strains), and quantification of mRNA expression was conducted for validating microarray data. RESULTS: In two sets of comparison, reaction of 11 347 and 15 454 gene probes were altered by parthenogenesis, while strain difference changed the expression of 15 750 and 14 944 probes. Level of correlation coefficient was higher in the comparisons between normal fertilization and parthenogenesis (0.974-0.985) than in the comparisons between strains of nfESCs (0.97-0.971). Overall, the expression of 3276-3329 genes was changed after parthenogenesis, and 88% (96/109) of major functional genes differentially (P < 0.01) expressed in one comparison set showed the same change in the other. When we monitored imprinted genes, expression of nine paternal and eight maternal genes were altered after parthenogenesis and 88% (14/16) of these was confirmed by mRNA quantification. CONCLUSIONS: The change in gene expression after parthenogenesis was similar to, or less than, the change induced by a strain difference under a certain genetic background. These results may suggest the clinical feasibility of parthenogenesis-derived, pluripotent cells.</P>

Gene Expression Profiling in the Uterine Endometrium during the Estrous Cyc1e and Pregnancy

Mingoo Kim,Sunjin Moon,Heebal Kim,Changkyu Lee,Hakhyun Ka 한국동물생명공학회(구 한국동물번식학회) 2007 Reproductive & developmental biology Vol.31 No.2

Comparative Analysis of Gene Expression in The Uterine Endometrium on Day 12 and 15 of the Estrous Cycle and Pregnancy in Pigs

Mingoo Kim,Heewon Seo,Yohan Choi,Heebal Kim,Chang-Kyu Lee,Hakhyun Ka 한국동물생명공학회(구 한국동물번식학회) 2009 Reproductive & developmental biology Vol.33 No.2

Repurposing existing drugs for monkeypox: applications of virtual screening methods

Li Vladimir,Lee Youngho,Lee Chul,Kim Heebal 한국유전학회 2023 Genes & Genomics Vol.45 No.11

Background Monkeypox is endemic to African region and has become of Global concern recently due to its outbreaks in non-endemic countries. Although, the disease was first recorded in 1970, no monkeypox specific drug or vaccine exists as of now. Methods We applied drug repositioning method, testing effectiveness of currently approved drugs against emerging disease, as one of the most affordable approaches for discovering novel treatment measures. Techniques such as virtual ligand-based and structure-based screening were applied to identify potential drug candidates against monkeypox. Results We narrowed down our results to 6 antiviral and 20 anti-tumor drugs that exhibit theoretically higher potency than tecovirimat, the currently approved drug for monkeypox disease. Conclusions Our results indicated that selected drug compounds displayed strong binding affinity for p37 receptor of monkeypox virus and therefore can potentially be used in future studies to confirm their effectiveness against the disease.

Semantic networks for genome-wide CNV associated with AST and ALT in Korean cohorts

Kim, Hyo-Young,Park, Jun-Hyung,Kim, Heebal,Kang, Byeong-Chul 대한독성유전단백체학회 2013 Molecular & cellular toxicology Vol.9 No.2

Copy number variation (CNV) is an emerging approach to study about human health and diseases. Liver-related biochemical tests (aspartate aminotransferase: AST, alanine aminotransferase: ALT) are useful for diagnosing a patient with liver injury. We analyzed a CNV-based GWAS of AST and ALT in 407 Korean. Affymetrix Human 6.0 Array was used to identify CNV, and CNV segmentation was performed using CNV analysis software. Univariate linear regression was used for the GWAS using R package. We identified 64 CNVs associated with AST or ALT, and screened 228 genes located within our CNVs. In this study, we focused on semantic networks about liver disease using knowledge integration software. This semantic networks about liver disease contained entities like gene, disease, pathway, chemical, drug, and contained relationships between two entities like gene-pathway, gene-disease, pathway-chemical, disease-pathway, chemical-drug. Application of semantic networks shown three clusters, including four diseases (hepatocellular carcinoma, liver neoplasm, liver cell adenoma, drug-induced liver injury), one pathway (hepatitis C pathway), and seven drugs (acetaminophen, chlormezanone, stavudine, enflurane, isoniazid, mebendazole, nitisinone).

PDStat : Statistical approach to protein domain frequency in various tissues and tumor

Mina Jeon,Jungrye Nam,Jae young Han,Heebal Kim 한국가금학회 2005 한국가금학회 정기총회 및 학술발표회 Vol.22 No.-

Protein domain은 단백질의 구조적, 기능적, 진화적 단위로 domain 빈도에 대한 분석을 통해 특정 유전자 그룹에 대한 특성 규명이 가능하다. 여기서는 Tigr TC sequence를 tumor 및 tissue 조직별로 분류하여 나타나는 domain의 빈도를 Zipf's law, Fisher exact test, bootstrapping과 같은 통계적 방법을 이용하여 분석함으로써 tumor 및 tissue 조직별 특이적인 domain을 찾고자 하였다. 그 결과 NIC, DUF890, TLE_N과 같은 tumor specific protein domain들을 규명할 수 있었다. Protein domains are the structural, functional and evolutionary units of proteins. A protein can be regarded as a sequence of its domains. Counting protein domain in a set of data, although it is a low level representation and classification, reveals a fundamental characteristic of the data.

Bayesian evolutionary hypernetworks for interpretable learning from high-dimensional data

Kim, Soo-Jin,Ha, Jung-Woo,Kim, Heebal,Zhang, Byoung-Tak Elsevier 2019 Applied soft computing Vol.81 No.-

<P><B>Abstract</B></P> <P>Higher-order representation is suitable for the complicated relationships among many factors. However, existing higher-order classification models have difficulties in learning from high-dimensional data due to their large combinatorial hypothesis spaces. The interpretability of models is also significant for causality analysis. Here we propose a Bayesian evolutionary method to learn a higher-order graphical model for high-dimensional data, called Bayesian evolutionary hypernetwork (BEHN). Our method represents the combinatorial feature space using a generalized graph, hypernetwork. A hypernetwork contains a large population of hyperedges encoding higher-order relationships among feature variables, and is optimized by an evolutionary algorithm formulated as sequential Bayesian sampling. This Bayesian evolutionary approach allows for probabilistic search through the higher-order feature space while satisfying soft constraints defined by the priors. We show that two information-theoretic and complexity-related priors are effective to balance model accuracy and parsimony. Also, BEHN provides interpretable representations to investigate feature interactions. Using two benchmarking and three real-world datasets we demonstrate that BEHN outperforms baseline classification models while tackling large-scale data of dimensionality up to <I>O</I>( 1 <SUP> 0 4 </SUP> ). We also analyze the stability and the scalability of the proposed method with respect to accuracy, computational cost, and the interpretability of the model structures.</P> <P><B>Highlights</B></P> <P> <UL> <LI> We propose a new hypergraph-based model for high-dimensional data (BEHN). </LI> <LI> We describe Bayesian evolutionary approach for learning our hypergraph model. </LI> <LI> BEHN employs two information-theoretic and complexity-regulating priors. </LI> <LI> The evolutionary learning of BEHN is formulated as a sequential Bayesian sampling. </LI> <LI> BEHN provides an interpretable result based on flexible hypergraph structures. </LI> <LI> BEHN is evaluated on real-world datasets including tens of thousands of variables. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>