• Genomics & Informatics
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• v.9 no.4
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• pp.173-180
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• 2011

Recent trends in generating multiple, large-scale datasets provide new challenges to manipulating the relationship of different types of components, such as gene expression and drug response data. Integrative analysis of compound response and gene expression datasets generates an opportunity to capture the possible mechanism of compounds by using signature genes on diverse types of cancer cell lines. Here, we integrated datasets of compound response and gene expression profiles on NCI60 cell lines and constructed a network, revealing the relationship for 801 compounds and 341 gene probes. As examples, obtusol, which shows an exclusive sensitivity on a small number of colon cell lines, is related to a set of gene probes that have unique overexpression in colon cell lines. We also found that the SLC7A11 gene, a direct target of miR-26b, might be a key element in understanding the action of many diverse classes of anticancer compounds. We demonstrated that this network might be useful for studying the mechanisms of varied compound response on diverse cancer cell lines.

• Animal cells and systems
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• v.6 no.2
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• pp.181-181
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• 2002

Nek2 is a mammalian protein kinase that is structurally homologous to NIMA, a mitotic regulator in Aspergillus nidulans. We recently observed that the Nek2 protein was localized in multiple sites within a cell in a cell cycle state-specific manner. This suggests that Ndk2 is involved in diverse cellular functions during the cell cycle progression. To have a better understanding on cellular functions in which Nek2 participates, we carried out yeast two-hybrid screening and isolated six candidate clones whose products interact with Nek2. Most of Nek2-interacting proteins (NIPs) appear cytoplasmic, suggesting that Nek2 is involved in cellular functions in cytoplasm. Further experiments are under progress to confirm their interactions with Nek2 and to understand their biological significance.

• Korean Journal of Cleft Lip And Palate
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• v.11 no.2
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• pp.65-70
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• 2008

Cleft lip and/or palate are common birth defects in humans and the causes including multiple genetic and environmental factors are complex. Combinations of genetic, biochemical, and embryological approaches in the laboratory mice are used to investigate the molecular mechanisms underlying normal craniofacial development and the congenital craniofacial malformations including cleft lip and/or palate. Both forward and reverse genetic approaches are used. The forward genetic approach involves identification of causative genes and molecular pathways disrupted by uncharacterized mutations that cause craniofacial malformations including cleft lip and/or cleft palate. The reverse genetic approach involves generation and analyses of mice carrying null or conditional mutations using the Cre-loxP mediated gene targeting techniques.

• KOGO NEWS
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• v.6 no.1
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• pp.29-33
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• 2006

Gene set analysis is a new concept and method. to analyze and interpret microarray gene expression data and tries to extract biological meaning from gene expression data at gene set level rather than at gene level. Compared with methods which select a few tens or hundreds of genes before gene ontology and pathway analysis, gene set analysis identifies important gene ontology terms and pathways more consistently and performs well even in gene expression data sets with minimal or moderate gene expression changes. Moreover, gene set analysis is useful for comparing multiple gene expression data sets dealing with similar biological questions. This review briefly summarizes the rationale behind the gene set analysis and introduces several algorithms and tools now available for gene set analysis.

• Mycobiology
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• v.49 no.4
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• pp.297-307
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• 2021

A cordycipitoid fungus infecting Hepialidae sp. in Nepal was supposed to be identical to Cordyceps liangshanensis, originally described from southwestern China, and thus, transferred to the genus Metacordyceps or Papiliomyces in previous studies. However, our multi-gene (nrSSU-nrLSU-tef-1α-rpb1-rpb2) phylogenetic and morphological studies based on the type specimen and additional collections of C. liangshanensis revealed that the fungus belongs to the genus Ophiocordyceps (Ophiocordycipitaceae). Therefore, a new combination O. liangshanensis was made, and a detailed description of this species was provided.

• Journal of Genetic Medicine
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• v.18 no.1
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• pp.24-30
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• 2021

Epigenetics deals with modifications in gene expression, without altering the underlying DNA sequence. Genomic imprinting is a complex epigenetic phenomenon that refers to parent-of-origin-specific gene expression. Beckwith-Wiedemann syndrome (BWS) and Silver-Russell syndrome (SRS) are congenital imprinting disorders with mirror opposite alterations at the genomic loci in 11p15.5 and opposite phenotypes. BWS and SRS are important imprinting disorders with the increase of knowledge of genetic and epigenetic mechanisms. Altered expression of the imprinted genes in 11p15.5, especially IGF2 and CDKN1C, affects fetal and postnatal growth. A wide range of imprinting defects at multiple loci, instead of a restricted locus, has been shown in some patients with either BWS or SRS. The development of new high-throughput assays will make it possible to allow accurate diagnosis, personalized therapy, and informative genetic counseling.

• Animal Bioscience
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• v.34 no.9
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• pp.1425-1438
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• 2021

Maintaining a high level of beef consumption requires paying attention not only to quantitative traits but also to the quality and dietary properties of meat. Growing consumer demands do not leave producers many options for how animals are selected for breeding and animal keeping. Meat and carcass fatness quality traits, which are influenced by multiple genes, are economically important in beef cattle breeding programs. The recent availability of genome sequencing methods and many previously identified molecular markers offer new opportunities for animal breeding, including the use of molecular information in selection programs. Many gene polymorphisms have thus far been analyzed and evaluated as potential candidates for molecular markers of meat quality traits. Knowledge of these markers can be further applied to breeding programs through marker-assisted selection. In this literature review, we discuss the most promising and well-described candidates and their associations with selected beef production traits.

• Clinical and Experimental Reproductive Medicine
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• v.47 no.4
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• pp.263-268
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• 2020

Autophagy, which has the literal meaning of self-eating, is a cellular catabolic process executed by arrays of conserved proteins in eukaryotes. Autophagy is dynamically ongoing at a basal level, presumably in all cells, and often carries out distinct functions depending on the cell type. Therefore, although a set of common genes and proteins is involved in this process, the outcome of autophagic activation or deficit requires scrutiny regarding how it affects cells in a specific pathophysiological context. The uterus is a complex organ that carries out multiple tasks under the influence of cyclic changes of ovarian steroid hormones. Several major populations of cells are present in the uterus, and the interactions among them drive complex physiological tasks. Mouse models with autophagic deficits in the uterus are very limited, but provide an initial glimpse at how autophagy plays a distinct role in different uterine tissues. Herein, we review recent research findings on the role of autophagy in the uterine mesenchyme in mouse models.

• Journal of Genetic Medicine
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• v.20 no.1
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• pp.15-24
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• 2023

Monogenic disorders are traditionally attributed to the presence of mutations in a single gene. However, recent advancements in genomics have revealed instances where the phenotypic expression of apparently monogenic disorders cannot be fully explained by mutations in a single gene alone. This review article aims to explore the emerging concept of digenic or oligogenic inheritance in seemingly monogenic disorders. We discuss the underlying mechanisms, clinical implications, and the challenges associated with deciphering the contribution of multiple genes in the development and manifestation of such disorders. We present relevant studies and highlight the importance of adopting a broader genetic approach in understanding the complex genetic architecture of these conditions.

• The Korean Journal of Physiology and Pharmacology
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• v.27 no.4
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• pp.289-298
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• 2023

Complex diseases including cardiovascular disease are caused by a combination of the alternation of many genes and the influence of environments. Recently, non-coding RNAs (ncRNAs) have been shown to be involved in diverse diseases, and the functions of various ncRNAs have been reported. Many researchers have elucidated the mechanisms of action of these ncRNAs at the cellular level prior to in vivo and clinical studies of the diseases. Due to the characteristics of complex diseases involving intercellular crosstalk, it is important to study communication between multiple cells. However, there is a lack of literature summarizing and discussing studies of ncRNAs involved in intercellular crosstalk in cardiovascular diseases. Therefore, this review summarizes recent discoveries in the functional mechanisms of intercellular crosstalk involving ncRNAs, including microRNAs, long non-coding RNAs, and circular RNAs. In addition, the pathophysiological role of ncRNAs in this communication is extensively discussed in various cardiovascular diseases.