• Proceedings of the Korean Society for Bioinformatics Conference
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• 2006.02a
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• pp.20-28
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• 2006

최근의 microarray 기술의 발달로 인해 점점 더 많은 양의 mRNA 발현 데이터가 쌓여 가고 있다. 이제는 데이터를 만드는 단계보다는 데이터로부터 중요한 생물학적 의미를 끌어내는 것이 더욱 중요한 일이 되었다. micorarray 기술이 처음 도입된 이후로, 많은 앨고리즘과 소프트웨어가 개발되어, 실험자들이 microarray 데이터로부터 생물학적 의미를 끌어내는 작업을 도와주어 왔다. 그런데, 이전의 데이터 마이닝 방법들은 거의 예외 없이 전체 데이터로부터 선택된 몇 십, 몇 백 개의 유전자 리스트로부터 출발한다. 그런데, 이러한 방법 (over-representation analysis, ORA로 줄임)은 몇 가지 한계를 가지고 있어서, 최근에는 전체 데이터로부터 의미 있는 유전자 세트 (gene set)를 찾아내는 방법들이 도입되었다. 본 세미나는 이런 방법들, 줄여서 gene set analysis라 함, 에 사용되는 앨고리즘들과 소프트웨어들을 비교, 검토하고자 한다.

• The Korean Journal of Applied Statistics
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• v.22 no.5
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• pp.1059-1072
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• 2009

In the analysis of microarray data with a small number of arrays, the most important task is the detection of differentially expressed genes by a significance test. For this purpose, one needs to construct a null distribution based on a large number of genes and one of the best way for constructing the null distribution for a small number of arrays is by means of permutation methods. In this paper we propose simple test statistics and permutation methods that are appropriate in constructing the null distribution. In a simulation study, we compare the null distributions generated by the proposed test statistics and permutation methods with the previous ones. With an example microarray data, differentially expressed genes are determined by applying these methods.

• Journal of Life Science
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• v.20 no.2
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• pp.213-218
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• 2010

In the present study, we investigated anti-proliferative activities of capsaicin and gene expression changes in response to capsaicin treatment in human colorectal HCT116 cells. The results showed that capsaicin decreased cell viabilities in a dose dependent manner and induced global gene expression changes. We found that 103 genes were up-regulated more than twofold, whereas 153 genes were down-regulated more than twofold by $100\;{\mu}M$ capsaicin treatment. Among the up-regulated genes, we selected 4 genes (NAG-1, DDIT3, GADD45A and PCK2) and performed RT-PCR to confirm the microarray data. We found that $100\;{\mu}M$ of capsaicin increased tumor suppressor p53 gene expression. In addition, the results showed that NAG-1, DDIT3 and GADD45A expressions were not dependent on p53 presence, whereas PCK2 expression. The results of this study may help to increase our understandings of the molecular mechanism of anti-proliferative activity mediated by capsaicin in human colorectal cancer cells.