• Molecules and Cells
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• v.25 no.2
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• pp.279-288
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• 2008

The analysis of microarray data is essential for large amounts of gene expression data. In this review we focus on clustering techniques. The biological rationale for this approach is the fact that many co-expressed genes are co-regulated, and identifying co-expressed genes could aid in functional annotation of novel genes, de novo identification of transcription factor binding sites and elucidation of complex biological pathways. Co-expressed genes are usually identified in microarray experiments by clustering techniques. There are many such methods, and the results obtained even for the same datasets may vary considerably depending on the algorithms and metrics for dissimilarity measures used, as well as on user-selectable parameters such as desired number of clusters and initial values. Therefore, biologists who want to interpret microarray data should be aware of the weakness and strengths of the clustering methods used. In this review, we survey the basic principles of clustering of DNA microarray data from crisp clustering algorithms such as hierarchical clustering, K-means and self-organizing maps, to complex clustering algorithms like fuzzy clustering.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.7
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• pp.3145-3149
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• 2014

Gene expression profiling facilitates the understanding of biological characteristics of gliomas. Previous studies mainly used regression/variance analysis without considering various background biological and environmental factors. The aim of this study was to investigate gene expression differences between grade III and IV gliomas through partial least squares (PLS) based analysis. The expression data set was from the Gene Expression Omnibus database. PLS based analysis was performed with the R statistical software. A total of 1,378 differentially expressed genes were identified. Survival analysis identified four pathways, including Prion diseases, colorectal cancer, CAMs, and PI3K-Akt signaling, which may be related with the prognosis of the patients. Network analysis identified two hub genes, ELAVL1 and FN1, which have been reported to be related with glioma previously. Our results provide new understanding of glioma pathogenesis and prognosis with the hope to offer theoretical support for future therapeutic studies.

• BMB Reports
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• v.53 no.4
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• pp.181-190
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• 2020

Protein phosphatase 4 (PP4), one of serine/threonine phosphatases, is involved in many critical cellular pathways, including DNA damage response (DNA repair, cell cycle regulation, and apoptosis), tumorigenesis, cell migration, immune response, stem cell development, glucose metabolism, and diabetes. PP4 has been steadily studied over the past decade about wide spectrum of physiological activities in cells. Given the many vital functions in cells, PP4 has great potential to develop into the finding of key working mechanisms and effective treatments for related diseases such as cancer and diabetes. In this review, we provide an overview of the cellular and molecular mechanisms by which PP4 impacts and also discuss the functional significance of it in cell health.

• Journal of Plant Biotechnology
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• v.40 no.3
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• pp.111-124
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• 2013

Research on the basic interaction of radiation with biological systems has contributed to human society through various applications in pharmaceutical, medicine, agriculture and other technological developments. In the agricultural sciences and food technology sectors, the last few decades have witnessed a large number of pertinent works regarding the utilization of radiation for evolution of superior varieties of agricultural crops of economic importance. This review presents general information about the effect of radiation on plant specificity, dose response, and benefits. There has been summarized of the effects observed after exposure and influenced by several factors including plant characteristics and radiation features. We also report on the effect of ${\gamma}$-irradiations on plants, focusing on metabolic alterations, modifications of growth and development and changes in biochemical pathways.

• Animal cells and systems
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• v.16 no.1
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• pp.1-10
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• 2012

Most living organisms synchronize their physiological and behavioral activities with the daily changes in the environment using intrinsic time-keeping systems called circadian clocks. In mammals, the key molecular features of the internal clock are transcription- and translational-based negative feedback loops, in which clock-specific transcription factors activate the periodic expression of their own repressors, thereby generating the circadian rhythms. CLOCK and BMAL1, the basic helix-loop-helix (bHLH)/PAS transcription factors, constitute the positive limb of the molecular clock oscillator. Recent investigations have shown that various levels of posttranslational regulation work in concert with CLOCK/BMAL1 in mediating circadian and cellular stimuli to control and reset the circadian rhythmicity. Here we review how the CLOCK and BMAL1 activities are regulated by intracellular distribution, posttranslational modification, and the recruitment of various epigenetic regulators in response to circadian and cellular signaling pathways.

• Journal of Applied Biological Chemistry
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• v.43 no.4
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• pp.269-272
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• 2000

The ginseng growth-promoting bacterium Pseudomonas fluorescens KGPP 207 synthesized indole-3- acetic acid (IAA) from L-tryptophan, indole-3-pyruvic acid (IPyA), and indole-3-acetaldehyde (IAAld), but not from indole-3-acetamide (lAM) and other intermediates of various IAA biosynthetic pathways in the experiment with indole compound supplemented cell suspensions. TLC, HPLC, and GC-MS analyses revealed the presence of IPyA, indole-3-ethanol, indole-3-lactic acid and its methyl ester, IAA and its methyl, and ethyl esters in the culture supernatant of the bacterium. IAAld was detected in the supernatant using sodium bisulfite and TLC. The results indicate that unlike gall-forming bacteria which can synthesize IAA by lAM, the indole-3-pyruvic acid pathway is the route for IAA biosynthesis in this beneficial strain of P. fluorescens.

• Genomics & Informatics
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• v.12 no.4
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• pp.261-267
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• 2014

MicroRNAs (miRNAs) are known for their role in mRNA silencing via interference pathways. Repetitive elements (REs) share several characteristics with endogenous precursor miRNAs. In this study, 406 previously identified and 1,494 novel RE-derived miRNAs were sorted from the GENCODE v.19 database using the RepeatMasker program. They were divided into six major types, based on their genomic structure. More novel RE-derived miRNAs were confirmed than identified as RE-derived miRNAs. In conclusion, many miRNAs have not yet been identified, most of which are derived from REs.

• BMB Reports
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• v.46 no.4
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• pp.181-187
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• 2013

Caloric restriction is the most reliable intervention to prevent age-related disorders and extend lifespan. The reduction of calories by 10-30% compared to an ad libitum diet is known to extend the longevity of various species from yeast to rodents. The underlying mechanisms by which the benefits of caloric restriction occur have not yet been clearly defined. However, many studies are being conducted in an attempt to elucidate these mechanisms, and there are indications that the benefits of caloric restriction are related to alteration of the metabolic rate and the accumulation of reactive oxygen species. During molecular signaling, insulin/insulin-like growth factor signaling, target of rapamycin pathway, adenosine monophosphate activated protein kinase signaling, and Sirtuin are focused as underlying pathways that mediate the benefits of caloric restriction. Here, we will review the current status of caloric restriction.

• BMB Reports
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• v.52 no.12
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• pp.679-688
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• 2019

The decrease of metabolism in the brain has been observed as the important lesions of Alzheimer's disease (AD) from the early stages of diagnosis. The cumulative evidence has reported that the failure of mitochondria, an organelle involved in diverse biological processes as well as energy production, maybe the cause or effect of the pathogenesis of AD. Both amyloid and tau pathologies have an impact upon mitochondria through physical interaction or indirect signaling pathways, resulting in the disruption of mitochondrial function and dynamics which can trigger AD. In addition, mitochondria are involved in different biological processes depending on the specific functions of each cell type in the brain. Thus, it is necessary to understand mitochondrial dysfunction as part of the pathological phenotypes of AD according to each cell type. In this review, we summarize that 1) the effects of AD pathology inducing mitochondrial dysfunction and 2) the contribution of mitochondrial dysfunction in each cell type to AD pathogenesis.

• 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.