• Molecules and Cells
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• v.42 no.8
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• pp.579-588
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• 2019

Gene set enrichment analysis (GSEA) is a popular tool to identify underlying biological processes in clinical samples using their gene expression phenotypes. GSEA measures the enrichment of annotated gene sets that represent biological processes for differentially expressed genes (DEGs) in clinical samples. GSEA may be suboptimal for functional gene sets; however, because DEGs from the expression dataset may not be functional genes per se but dysregulated genes perturbed by bona fide functional genes. To overcome this shortcoming, we developed network-based GSEA (NGSEA), which measures the enrichment score of functional gene sets using the expression difference of not only individual genes but also their neighbors in the functional network. We found that NGSEA outperformed GSEA in identifying pathway gene sets for matched gene expression phenotypes. We also observed that NGSEA substantially improved the ability to retrieve known anti-cancer drugs from patient-derived gene expression data using drug-target gene sets compared with another method, Connectivity Map. We also repurposed FDA-approved drugs using NGSEA and experimentally validated budesonide as a chemical with anti-cancer effects for colorectal cancer. We, therefore, expect that NGSEA will facilitate both pathway interpretation of gene expression phenotypes and anti-cancer drug repositioning. NGSEA is freely available at www.inetbio.org/ngsea.

• Journal of Plant Biotechnology
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• v.50
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• pp.163-168
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• 2023

Sweetpotato (Ipomoea batatas [L.]) is a globally important root crop cultivated for food and industrial processes. The crop is susceptible to the root-knot nematode (RKN) Meloidogyne incognita, a major plant-parasitic RKN that reduces the yield and quality of sweetpotato. Previous transcriptomic and proteomic analyses identified several genes that displayed differential expression patterns in susceptible and resistant cultivars in response to M. incognita infection. Among these, several sporamin genes were identified for RKN resilience. Sporamin is a storage protein primarily found in sweetpotato and morning glory (Ipomoea nil). In this study, transcriptional analysis was employed to investigate the role of sporamin genes in the defense response of sweetpotato against RKN infection in three susceptible and three resistant cultivars. Twenty-three sporamin genes were identified in sweetpotato and classified as group A or group B sporamin genes based on comparisons with characterized sweetpotato and Japanese morning glory sporamins. Two group A sporamin genes showed significantly elevated levels of expression in resistant but not in susceptible cultivars. These results suggest that the elevated expression of specific sporamin genes may play a crucial role in protecting sweetpotato roots from RKN infection.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.18
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• pp.7703-7705
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• 2014

Cancer-testis (CT) antigens are a group of tumor-associated antigens with restricted expression in normal tissues except for testis and expression in a wide variety of tumor tissues. This pattern of expression makes them suitable targets for immunotherapy as well as potential biomarkers for early detection of cancer. However, some genes attributed to this family are now known to be expressed in other normal tissues which put their potential applications in immunotherapy and cancer detection under question. Here we analyzed expression of two previously known CT antigens, RHOXF2 and PIWIL2, in AML patients versus normal donors and found no significant difference in the expression of these genes between the two groups. As these two genes showed expression in normal leukocytes, their expression pattern seems to be wider than to be attributed to the CT gene family. Future research should focus on the expression profiles of so called CT antigens to find those with more testis specific expression.

• International Journal of Industrial Entomology and Biomaterials
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• v.16 no.1
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• pp.21-27
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• 2008

The expression of heat shock protein genes (Hsp 70, Hsp 40, Hsp 20.8 and Hsp 20.4) against thermal stress in silkworm Bombyx mori was performed through semi-quantitative reverse transcriptase-polymerase chain reaction (RT-PCR). Upon exposure of silkworm to two temperature regimes ($38^{\circ}C$ and $42^{\circ}C$), significant change in the expression of Hsp gene was observed as compared to the control. Hsp 70 and Hsp 40 showed increased expression than the small heat shock protein genes Hsp 20.8 and Hsp 20.4. The Hsp 70 showed increased expression during the recovery period as compared to 1 hr thermal treatments ($38^{\circ}C$/1 hr and $42^{\circ}C$/1 hr). Whereas, Hsp 40, Hsp 20.8 and Hsp 20.4 genes showed higher expression level at initial stages that later gradually decrease during recovery period. Tissue specific expression of Hsp 70 showed variation in the level of expression amongst the tissues. The mid gut and fat body tissues showed higher expression than the cuticle and silk gland tissue. The Hsp 70, Hsp 40 gene expression was analyzed in thermotolerant (Nistari) and thermo susceptible silk worm strain (NB4D2) and results showed significant variation in their expression level. The Nistari showed higher expression of Hsp 70 and Hsp 40 genes than the NB4D2. These findings provide a better understanding of cellular protection mechanisms against environmental stress such as heat shock, as these Hsps are involved in an organism thermotolerance.

• Journal of Embryo Transfer
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• v.30 no.2
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• pp.99-107
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• 2015

The aim of the present study was to identify coat color associated genes that are differentially expressed in mature Korean brindle cattle (KBC) with different coat colors and in Hanwoo cows. KBC calves, before and after coat color appearance, were included. Total cellular RNA was isolated from the tail hair cells and used for microarray. The number of expressed coat color associated genes/probes was 5813 in mature KBC and Hanwoo cows. Among the expressed coat color associated genes/probes, 167 genes were the coat color associated genes listed in the Gene card database and 125 genes were the pigment and melanocyte genes listed in the Gene ontology_bovine database. There were 23 genes/probes commonly listed in both databases and their expressions were further studied. Out of the 23 genes/probes, MLPH, PMEL, TYR and TYRP1 genes were expressed at least two fold higher (p<0.01) levels in KBC with brindle color than either Hanwoo or KBC with brown color. TYRP1 expression was 22.96 or 19.89 fold higher (p<0.01) in KBC with brindle color than either Hanwoo or KBC with brown color, respectively, which was the biggest fold difference. The hierarchical clustering analysis indicated that MLPH, PMEL, TYR and TYRP1 were the highly expressed genes in mature cattle. There were only a few genes differentially expressed after coat color appearance in KBC calves. Studies on the regulation and mechanism of gene expression of highly expressed genes would be next steps to better understand coat color determination and to improve brindle coat color appearance in KBC.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.40 no.1
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• pp.69-76
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• 1995

Cold acclimation involves changes in gene expression. BN28 and BN115 are two genes which are regulated by cold temperature and assumed having roles in cold acclimation. The objectives of this experiment was to explore the expression of BN28 and BN115 under field conditions. Six winter cultivars were planted at three different dates during the fall. The expression of the genes was determined by northern blot analysis of total RNA taken from leaves 15 to 30 day-intervals after planting. The expression of the two genes was detected within 15 days after planting well before onset of freezing tolerance in plants. This suggestes either their expression was a prerequisite of the freezing tolerance or their expression was regulated by other environmental factors as well as temperature. Two genes showed a different expression pattern suggesting they had a different regulatory system. Although timecourse increase in expression of the cold-regulated genes was matched with increase in freezing tolerance, the difference of expression in cultivar level at specific times of measurement was not correlated with freezing tolerance at the moment.

• Biomedical Science Letters
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• v.18 no.2
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• pp.169-174
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• 2012

The placenta is an extraembryonic tissue that is formed between mother and fetus and mediates delivery of nutrients and oxygen from the mother to the fetus. Because of its essential role in sustaining the growth of the fetus during gestation, defects in its development and function frequently result in fetal growth retardation or intrauterine death, depending on its severity. Vertebrate Hox genes are well known transcription factors that are essential for the proper organization of the body plan during embryogenesis. However, certain Hox genes have been known to be expressed in placenta, implying that Hox genes not only play a crucial role during embryonic patterning but also play an important role in placental development. So far, there has been no report that shows the expression pattern of the whole Hox genes during placentation. In this study, therefore, we investigated the Hox gene expression pattern in mouse placenta, from day 10.5 to 18.5 of gestation using real-time RT-PCR method. In general, the 5' posterior Hox genes were expressed more in the developing placenta compared to the 3' Hox genes. Statistical analysis revealed that the expression of 15 Hox genes (Hoxa9, -a11, -a13/ -b8, -b9/ -c6, -c9, -c13/ -d1, -d3, -d8, -d9, -d10, -d11, -d12) were significantly changed in the course of gestation. The majority of these genes showed highest expression at gestational day 10.5, suggesting their possible role in the early stage during placental development.

• Fisheries and Aquatic Sciences
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• v.19 no.4
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• pp.21.1-21.11
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• 2016

Background: The evaluation of suitable reference genes as normalization controls is a prerequisite requirement for launching quantitative reverse transcription-PCR (RT-qPCR)-based expression study. In order to select the stable reference genes in abalone Haliotis discus hannai tissues (gill and hepatopancreas) under heavy metal exposure conditions (Cu, Zn, and Cd), 12 potential candidate housekeeping genes were subjected to expression stability based on the comprehensive ranking while integrating four different statistical algorithms (geNorm, NormFinder, BestKeeper, and ${\Delta}CT$ method). Results: Expression stability in the gill subset was determined as RPL7 > RPL8 > ACTB > RPL3 > PPIB > RPL7A > EF1A > RPL4 > GAPDH > RPL5 > UBE2 > B-TU. On the other hand, the ranking in the subset for hepatopancreas was RPL7 > RPL3 > RPL8 > ACTB > RPL4 > EF1A > RPL5 > RPL7A > B-TU > UBE2 > PPIB > GAPDH. The pairwise variation assessed by the geNorm program indicates that two reference genes could be sufficient for accurate normalization in both gill and hepatopancreas subsets. Overall, both gill and hepatopancreas subsets recommended ribosomal protein genes (particularly RPL7) as stable references, whereas traditional housekeepers such as ${\beta}-tubulin$ (B-TU) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes were ranked as unstable genes. The validation of reference gene selection was confirmed with the quantitative assay of MT transcripts. Conclusions: The present analysis showed the importance of validating reference genes with multiple algorithmic approaches to select genes that are truly stable. Our results indicate that expression stability of a given reference gene could not always have consensus across tissue types. The data from this study could be a good guide for the future design of RT-qPCR studies with respect to metal regulation/detoxification and other related physiologies in this abalone species.

• Genomics & Informatics
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• v.3 no.1
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• pp.8-14
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• 2005

Although much is known about the molecular biology of platelets, the megakaryocytes' (MKs) molecular biology was not understood so well because of their rareness. By the cloning and characterization of thrombopoietin (TPO), which is the principal regulator of the growth and development of the MKs, researches on the MKs have been growing rapidly. To understand megakaryocytopoiesis, we investigated the gene expression profile of the MKs using oligonucleotide microarray where 10,108 unique genes were spotted. Comparing the fluorescence intensities of which ratio is $\ge$ ${\mid}2{\mid}$, 372 genes were up-regulated and 541 genes were down-regulated in MKs. For confirmatory expression, RNase protection assay (RPA) establishing abundant apoptotic gene expression was carried out. In MKs, many of the known genes, including several platelet related genes, GATA binding protein were highly expressed. Particularly, TGF beta, clusterin (complement lysis inhibitor), and thymosin beta 4 (actin-sequestering molecules) were expressed highly in MKs. As MKs specific expressed genes may regulate normal and pathologic platelet (and/or MK) functions, the transcript profiling using microarray was useful on molecular understanding of MKs,

• Journal of fish pathology
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• v.16 no.3
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• pp.139-146
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• 2003

We have investigated the biological effects of recombinant IL-1$\beta$ (rIL-1$\beta$) on the expression of antiviral genes such as Myxovirus-3 (MX-3) and Interferon regulating factor-1 (IRF-1), which are related to type I interferon. When ten micrograms of rIL-1$\beta$ were treated, we observed the stimulatory effect on the expression of these antiviral genes. Interestingly, at the early stage of stimulation, these genes were down-regulated and then up-regulated by the results obtained that the expressions of these genes were decreased at day 1 post-injection and gradually increased at day 3 post-injection. Thus, the stimulatory effect of rIL-1$\beta$ on the expression of MX-3 and IRF-3 gene might be an indirect stimulatory effect because significant up-regulation was delayed until day 3 post-injection.