• BMB Reports
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• v.49 no.11
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• pp.607-611
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• 2016

The Cancer Genome Atlas (TCGA) has compiled genomic, epigenomic, and proteomic data from more than 10,000 samples derived from 33 types of cancer, aiming to improve our understanding of the molecular basis of cancer development. Availability of these genome-wide information provides an unprecedented opportunity for uncovering new key regulators of signaling pathways or new roles of pre-existing members in pathways. To take advantage of the advancement, it will be necessary to learn systematic approaches that can help to uncover novel genes reflecting genetic alterations, prognosis, or response to treatments. This minireview describes the updated status of TCGA project and explains how to use TCGA data.

• Proceedings of the Korea Contents Association Conference
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• 2018.05a
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• pp.317-318
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• 2018

유전자는 alternative splicing으로 환경에 맞는 전사체를 발현함으로써 생명체의 복잡성을 야기한다. 하지만 대부분의 유전자는 dominant한 isoform 하나만이 주로 발현되며 그 외는 극히 미약하게 발현을 한다. 정상 대비 암조직에서 dominant하게 발현되는 isoform은 암의 생성과 발달에 영향을 끼칠 것으로 보인다. 이에 정상과 비교하여 암 특이적인 isoform, 즉 isoform switch가 일어나는 유전자를 찾기 위해 TCGA의 RNA-seq 데이터를 다운로드하여 isoform switch가 일어나는 유전자를 뽑았다. 12 조직에 대한 2,925 유전자는 기능분석을 통해 암과 밀접하게 연관되어 있음을 알 수 있었다.

• Biomolecules & Therapeutics
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• v.25 no.5
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• pp.482-489
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• 2017

Individual differences in drug responses are associated with genetic and epigenetic variability of pharmacogene expression. We aimed to identify the relevant miRNAs which regulate pharmacogenes associated with drug responses. The miRNA and mRNA expression profiles derived from data for normal and solid tumor tissues in The Cancer Genome Atlas (TCGA) Research Network. Predicted miRNAs targeted to pharmacogenes were identified using publicly available databases. A total of 95 pharmacogenes were selected from cholangiocarcinoma and colon adenocarcinoma, as well as kidney renal clear cell, liver hepatocellular, and lung squamous cell carcinomas. Through the integration analyses of miRNA and mRNA, 35 miRNAs were found to negatively correlate with mRNA expression levels of 16 pharmacogenes in normal bile duct, liver, colon, and lung tissues (p<0.05). Additionally, 36 miRNAs were related to differential expression of 32 pharmacogene mRNAs in those normal and tumorigenic tissues (p<0.05). These results indicate that changes in expression levels of miRNAs targeted to pharmacogenes in normal and tumor tissues may play a role in determining individual variations in drug response.

• Korean Journal of Microbiology
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• v.32 no.4
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• pp.301-305
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• 1994

In catalytic properties of the restriction enonuclease, SdiI, which was purified from Streptomyces diastatochromogenes, this enzyme was active at wide range between pH 7.0 and 12.5, and up to $60^{\circ}C$ and 500 mM of NaCl concentration. It was stable between 20^{\circ}C$ and $60^{\circ}C$, and essentially requires $MgCl_2$ for endonuclease activity. The restriction map of lambda DNA which was obtained by double digestion with various enzymes suggested SdiI to be an isoschizomer of XhoI. From the determination of restriction site based on DNA sequencing method, recognition and cleavage specificity of SdiI was concluded as: 5‘-C${\downarrow}$TCGA G-3' 3'-G AGCT${\uparrow}$C-5'

• The Transactions of The Korean Institute of Electrical Engineers
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• v.65 no.7
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• pp.1236-1241
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• 2016

Cancer has been the most frequent in Korea, and pathogenesis and progression of cancer have been known to be occurred through various causes and stages. Recently, the research of chromosomal and genetic disorder and the research about prognostic factor to predict occurrence, recurrence and progress of chromosomal and genetic disorder have been performed actively. In this paper, we analyzed DNA methylation data downloaded from TCGA (The Cancer Genome Atlas), open database, to research bladder cancer which is the most frequent among urinary system cancers. Using three level of methylation data which had the most preprocessing, 59 candidate CpG island were extracted from 480,000 CpG island, and then we analyzed extracted CpG island applying data mining technique. As a result, cg12840719 CpG island were analyzed significant, and in Cox's regression we can find the CpG island with high relative risk in comparison with other CpG island. Shown in the result of classification analysis, the CpG island which have high correlation with bladder cancer are cg03146993, cg07323648, cg12840719, cg14676825 and classification accuracy is about 76%. Also we found out that positive predictive value, the probability which predicts cancer in case of cancer was 72.4%. Through the verification of candidate CpG island from the result, we can utilize this method for diagnosing and treating cancer.

• KIPS Transactions on Software and Data Engineering
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• v.10 no.12
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• pp.547-554
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• 2021

Cancer patients can have different kinds of cancer driver genes, and identification of these patient-specific cancer driver genes is an important step in the development of personalized cancer treatment and drug development. Several bioinformatic methods have been proposed for this purpose, but there is room for improvement in terms of accuracy. In this paper, we propose NPD (Network based Patient-specific Driver gene identification) for identifying patient-specific cancer driver genes. NPD consists of three steps, constructing a patient-specific gene network, applying the modified PageRank algorithm to assign scores to genes, and identifying cancer driver genes through a score comparison method. We applied NPD on six cancer types of TCGA data, and found that NPD showed generally higher F1 score compared to existing patient-specific cancer driver gene identification methods.

• The Korean Journal of Physiology and Pharmacology
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• v.28 no.3
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• pp.265-273
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• 2024

This study aims to explore possible effect of RNA polymerase I subunit D (POLR1D) on proliferation and angiogenesis ability of colorectal cancer (CRC) cells and mechanism herein. The correlation of POLR1D and Yin Yang 1 (YY1) expressions with prognosis of CRC patients in TCGA database was analyzed. Quantitative realtime polymerase chain reaction (qRT-PCR) and Western blot were applied to detect expression levels of POLR1D and YY1 in CRC cell lines and CRC tissues. SW480 and HT-29 cells were transfected with si-POLR1D or pcDNA3.1-POLR1D to achieve POLR1D suppression or overexpression before cell migration, angiogenesis of human umbilical vein endothelial cells were assessed. Western blot was used to detect expressions of p38 MAPK signal pathway related proteins and interaction of YY1 with POLR1D was confirmed by dual luciferase reporter gene assay and chromatin immunoprecipitation (ChIP). TCGA data showed that both POLR1D and YY1 expressions were up-regulated in CRC patients. High expression of POLR1D was associated with poor prognosis of CRC patients. The results showed that POLR1D and YY1 were highly expressed in CRC cell lines. Inhibition or overexpression of POLR1D can respectively suppress or enhance proliferation and angiogenesis of CRC cells. YY1 inhibition can suppress CRC progression and deactivate p38 MAPK signal pathway, which can be counteracted by POLR1D overexpression. JASPAR predicted YY1 can bind with POLR1D promoter, which was confirmed by dual luciferase reporter gene assay and ChIP. YY1 transcription can up-regulate POLR1D expression to activate p38 MAPK signal pathway, thus promoting proliferation and angiogenesis ability of CRC cells.

• Communications for Statistical Applications and Methods
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• v.29 no.6
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• pp.655-664
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• 2022

On the motivation by an integrative study of multi-omics data, we are interested in estimating the structure of the sparse cross correlation matrix of two high-dimensional random vectors. We rewrite the problem as a multiple testing problem and propose a new method to estimate the sparse structure of the cross correlation matrix. To do so, we test the correlation coefficients simultaneously and threshold the correlation coefficients by controlling FRD at a predetermined level α. Further, we apply the proposed method and an alternative adaptive thresholding procedure by Cai and Liu (2016) to the integrative analysis of the protein expression data (X) and the mRNA expression data (Y) in TCGA breast cancer cohort. By varying the FDR level α, we show that the new procedure is consistently more efficient in estimating the sparse structure of cross correlation matrix than the alternative one.

• Proceedings of the Korea Information Processing Society Conference
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• 2023.05a
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• pp.490-492
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• 2023

시퀀싱(sequencing) 기술의 발달로 다양한 오믹스(omics) 데이터의 축적과 인공 지능 기술의 발달로 인하여 다양한 드라이버 유전자 분류기법이 제안되어왔다. 최근에는 암 데이터가 대용량으로 축적되며 기계 학습 기반의 다양한 기법들이 활발히 제안되었다. 특히 다양한 오믹스 데이터를 결합한 고차원 데이터에서 높은 정확도를 확보하기 위한 시도가 활발히 이루어지고 있다. 본 논문에서는 멀티 오믹스와 네트워크 관련 특징을 기반으로 암의 증식 및 발생에 중요한 역할을 하는 드라이버 유전자를 분류하는 딥러닝 모델을 제시한다. 또한 The Cancer Genome Atlas(TCGA) 데이터를 통해서 모델 학습 후 기존 통계 및 머신러닝 기반 기법과 비교하여 성능이 개선되었음을 확인하였다.

• Molecules and Cells
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• v.41 no.5
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• pp.390-400
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• 2018

Studies have revealed that miR-103a-3p contributes to tumor growth in several human cancers, and high miR-103a-3p expression is associated with poor prognosis in advanced gastric cancer (GC) patients. Moreover, bioinformatics analysis has shown that miR-103a-3p is upregulated in The Cancer Genome Atlas (TCGA) stomach cancer cohort. These results suggest that miR-103a-3p may function as an oncogene in GC. The present study aimed to investigate the role of miR-103a-3p in human GC. miR-103a-3p expression levels were increased in 33 clinical GC specimens compared with adjacent nontumor stomach tissues. Gain- and loss-of-function studies were performed to identify the correlation between miR-103a-3p and tumorigenesis in human GC. Inhibiting miR-103a-3p suppressed GC cell proliferation and blocked the S-G2/M transition in MKN-45/SGC-7901 cells, whereas miR-103a-3p overexpression improved GC cell proliferation and promoted the S-G2/M transition in vitro. Bioinformatics and dual-luciferase reporter assays confirmed that ATF7 is a direct target of miR-103a-3p. Analysis of the TCGA stomach cancer cohort further revealed that miR-103a-3p expression was inversely correlated with ATF7 expression. Notably, silencing ATF7 showed similar cellular and molecular effects as miR-103a-3p overexpression, namely, increased GC cell proliferation, improved CDK2 expression and decreased P27 expression. ATF7 overexpression eliminated the effects of miR-103a-3p expression. These findings indicate that miR-103a-3p promotes the proliferation of GC cell by targeting and suppressing ATF7 in vitro.