• Asian Pacific Journal of Cancer Prevention
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• 제17권5호
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• pp.2519-2525
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• 2016

There are several existing reports of microarray chip use for assessment of altered gene expression in different diseases. In fact, there have been over 1.5 million assays of this kind performed over the last twenty years, which have influenced clinical and translational research studies. The most commonly used DNA microarray platforms are Affymetrix GeneChip and Quality Control Software along with their GeneChip Probe Arrays. These chips are created using several quality controls to confirm the success of each assay, but their actual impact on gene expression profiles had not been previously analyzed until the appearance of several bioinformatics tools for this purpose. We here performed a data mining analysis, in this case specifically focused on ovarian cancer, as well as healthy ovarian tissue and ovarian cell lines, in order to confirm quality control results and associated variation in gene expression profiles. The microarray data used in our research were downloaded from ArrayExpress and Gene Expression Omnibus (GEO) and analyzed with Expression Console Software using RMA, MAS5 and Plier algorithms. The gene expression profiles were obtained using Partek Genomics Suite v6.6 and data were visualized using principal component analysis, heat map, and Venn diagrams. Microarray quality control analysis showed that roughly 40% of the microarray files were false negative, demonstrating over- and under-estimation of expressed genes. Additionally, we confirmed the results performing second analysis using independent samples. About 70% of the significant expressed genes were correlated in both analyses. These results demonstrate the importance of appropriate microarray processing to obtain a reliable gene expression profile.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.63-68
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• 2005

Transcription factors regulate gene expression by binding to gene upstream region. Each transcription factor has the specific binding site in promoter region. So the analysis of gene upstream sequence is necessary for understanding regulatory mechanism of genes, under a plausible idea that assumption that DNA sequence motif profiles are closely related to gene expression behaviors of the corresponding genes. Here, we present an effective approach to the analysis of the relation between gene expression profiles and gene upstream sequences on the basis of kernel canonical correlation analysis (kernel CCA). Kernel CCA is a useful method for finding relationships underlying between two different data sets. In the application to a yeast cell cycle data set, it is shown that gene upstream sequence profile is closely related to gene expression patterns in terms of canonical correlation scores. By the further analysis of the contributing values or weights of sequence motifs in the construction of a pair of sequence motif profiles and expression profiles, we show that the proposed method can identify significant DNA sequence motifs involved with some specific gene expression patterns, including some well known motifs and those putative, in the process of the yeast cell cycle.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2002년도 제1차워크샵
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• pp.139-152
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• 2002

Gene-shaving(Hastie et al, 2000) is a very useful method to identify a meaningful group of genes when the variation of expression is large. By shaving off the low-correlated genes with the leading principal component, the primary genes with the coherent expression pattern can be identified. Gene-shaving method works well If expression levels are varied enough, but it may not catch the meaningful cluster in low expression level or different expression time even with coherent patterns. The sliding window gene-shaving method which is to apply gene-shaving in each sliding window after hierarchical clustering is to compensate losing a meaningful set of genes whose variation is not large but distinct. The performance to identify expression patterns is compared for the simulated profile data by the different variance and expression level.

• 방송공학회논문지
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• 제28권3호
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• pp.275-284
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• 2023

유전자 발현 데이터는 질병의 예후 예측, 약물 반응성 예측 등 질병에 대한 이해와 정밀 의료 실현을 위한 연구들에 활용될 수 있지만 충분한 양의 데이터를 수집하는 데 많은 비용적 문제가 있다. 본 논문에서는 Conditional VAE에 기반한 유전자 발현 데이터 생성 모델을 제안하였다. 이전 연구인 WGAN-GP기반의 유전자 발현 생성 모델과 정형 데이터 생성 모델인 CTGAN, TVAE와 비교하여 본 논문의 Conditional VAE기반 모델이 생물학적, 통계학적으로 더 유의미한 합성 데이터를 생성할 수 있음을 보였다.

• 한국데이터정보과학회:학술대회논문집
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• 한국데이터정보과학회 2006년도 PROCEEDINGS OF JOINT CONFERENCEOF KDISS AND KDAS
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• pp.63-76
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• 2006

유전자 발현 자료(gene expression data)를 분석하기 위한 여러 가지 군집 알고리즘(clustering algorithm)과 군집 결과들을 검증하는 척도, 즉 군집 타당성분석 기법(cluster validation technique)이 제안되고 있지만, 이틀 군집 타당성을 분석하는 기법들에 대한 성능의 비교 평가는 매우 드물다. 본 논문에서는 모의 생성 자료로 몇 가지 특정 상황을 연출하여 군집 타당성 분석 기법들을 비교해 보고, 실제 유전자 발현 자료 두 가지에 대해서도 이들 기법의 성능을 비교 평가해 보았다.

• 응용통계연구
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• 제20권1호
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• pp.167-181
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• 2007

유전자 발현 자료(gene expression data)는 전형적인 고차원 자료이며, 이를 분석하기 위한 여러 가지 군집 알고리즘(clustering algorithm)과 군집 결과들을 검증하는 군집타당성분석 기법(cluster validation technique)이 제안되고 있지만, 이들 군집 타당성을 분석하는 기법의 성능에 대한 비교, 평가는 매우 드물다. 본 논문에서는 저차원의 모의실험 자료와 실제 유전자 발현 자료에 대하여 군집 타당성분석 기법들의 성능을 비교하였으며, 그 결과 내적 측도에서는 Dunn 지수, Silhouette 지수 순으로 뛰어났고 외적 측도에서는 Jaccard 지수가 성능이 가장 우수한 것으로 평가되었다.

• Molecules and Cells
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• 제42권8호
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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.

• Asian Pacific Journal of Cancer Prevention
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• 제14권1호
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• pp.457-461
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• 2013

Prostate cancer is a leading cause of death in male populations across the globe. With the advent of gene expression arrays, many microarray studies have been conducted in prostate cancer, but the results have varied across different studies. To better understand the genetic and biologic mechanisms of prostate cancer, we conducted a meta-analysis of two studies on prostate cancer. Eight key genes were identified to be differentially expressed with progression. After gene co-expression analysis based on data from the GEO database, we obtained a co-expressed gene list which included 725 genes. Gene Ontology analysis revealed that these genes are involved in actin filament-based processes, locomotion and cell morphogenesis. Further analysis of the gene list should provide important clues for developing new prognostic markers and therapeutic targets.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2001년도 제2회 생물정보 워크샵 (DNA Chip Bioinformatics)
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• pp.97-115
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• 2001

cDNA microarray technology allows the monitoring of expression levels for thousands of genes simultaneously. Many statistical analysis tools become widely applicable to the analysis of cDNA microarray data. In this talk, we consider a two-way ANOVA model to differentiate genes that have high variability and ones that do not. Using this model, we detect genes that have different gene expression profiles among experimental groups. The two-way ANOVA model is illustrated using cDNA microarrays of 3,800 genes obtained in an experiment to search for changes in gene expression profiles during neuronal differentiation of cortical stem cells.

• KSBB Journal
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• 제16권4호
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• pp.381-388
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• 2001

DNA칩의 유전자 발현 데이터의 통합적 분석을 위하여 매트랩을 기반으로 한 통합분석 프로그램을 구축하였다. 이 프로그램은 유전자 발현 분석을 위해 일반적으로 많이 쓰는 방법인 Hierarchical clustering(HC), K-means, Self-organizing map(SOM), Principal component analysis(PCA)를 지원하며, 이외에 Fuzzy c-means방법과 최근에 발표된 Singular value decomposition(SVD) 분석 방법도 지원하고 있다. 통합분석프로그램의 성능을 알아보기 위하여 효모의 포자형성(sporulation)과 정의 유전자발현 데이터를 사용하였으며, 각 분석 방법에 따른 분석 결과를 제시하였으며, 이 프로그램이 유전자 발현데이타의 통합적인 분석을 위해 효과적으로 사용될 수 있음을 제시하였다.