• Tuberculosis and Respiratory Diseases
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• v.79 no.2
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• pp.85-90
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• 2016

Background: Lung cancer is the most common cause of cancer related death. Alterations in gene sequence, structure, and expression have an important role in the pathogenesis of lung cancer. Fusion genes and alternative splicing of cancer-related genes have the potential to be oncogenic. In the current study, we performed RNA-sequencing (RNA-seq) to investigate potential fusion genes and alternative splicing in non-small cell lung cancer. Methods: RNA was isolated from lung tissues obtained from 86 subjects with lung cancer. The RNA samples from lung cancer and normal tissues were processed with RNA-seq using the HiSeq 2000 system. Fusion genes were evaluated using Defuse and ChimeraScan. Candidate fusion transcripts were validated by Sanger sequencing. Alternative splicing was analyzed using multivariate analysis of transcript sequencing and validated using quantitative real time polymerase chain reaction. Results: RNA-seq data identified oncogenic fusion genes EML4-ALK and SLC34A2-ROS1 in three of 86 normal-cancer paired samples. Nine distinct fusion transcripts were selected using DeFuse and ChimeraScan; of which, four fusion transcripts were validated by Sanger sequencing. In 33 squamous cell carcinoma, 29 tumor specific skipped exon events and six mutually exclusive exon events were identified. ITGB4 and PYCR1 were top genes that showed significant tumor specific splice variants. Conclusion: In conclusion, RNA-seq data identified novel potential fusion transcripts and splice variants. Further evaluation of their functional significance in the pathogenesis of lung cancer is required.

• Genomics & Informatics
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• v.17 no.1
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• pp.3.1-3.4
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• 2019

Intratumor heterogeneity within a single tumor mass is one of the hallmarks of malignancy and has been reported in various tumor types. The molecular characterization of intratumor heterogeneity in breast cancer is a significant challenge for effective treatment. Using single-cell RNA sequencing (RNA-seq) data from a public resource, an ERBB pathway activated triple-negative cell population was identified. The differential expression of three subtyping marker genes (ERBB2, ESR1, and PGR) was not changed in the bulk RNA-seq data, but the single-cell transcriptomes showed intratumor heterogeneity. This result shows that ERBB signaling is activated using an indirect route and that the molecular subtype is changed on a single-cell level. Our data propose a different view on breast cancer subtypes, clarifying much confusion in this field and contributing to precision medicine.

• Proceedings of the Korean Society of Tribologists and Lubrication Engineers Conference
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• 1996.04b
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• pp.121-125
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• 1996

자동차의 환경규제, 고성증화에 맞추어 새로이 규격이 제정된 ILSAC GF-2 가솔린엔지유는 SEQ VI와 SEQ VIA를 통한 연비시험 결과 ILSAC GF-1엔지유에 비해서 연비성능이 향상되었으며, phosphorous함량 규제에 따라 ZnDDP의 첨가량을 줄였음에도 불구하고 다른 산화방지제와 마모방지제를 투입함으로써 규격엔진시험을 통과하였고 실파를 이용한 시험에서는 ILSAC GF-1에 비해서 우수한 마모방지성능과 산화안정성을 보였다.

• Proceedings of the Korea Information Processing Society Conference
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• 2020.11a
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• pp.912-915
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• 2020

최근 자연어 처리 기술은 지속적으로 발전하고 있으며, 많은 분야에서 활용되고 있다. 그 중 번역 기술은 가장 널리 사용되고 있는 자연어 처리 기술 중 하나이다. 본 논문에서는 기존의 seq2seq 모델의 단점을 극복하기 위해 개발된 Transformer 를 통해 영어-한국어 번역기를 만드는 것의 가능성을 제시한다.

• KIPS Transactions on Software and Data Engineering
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• v.10 no.11
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• pp.535-540
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• 2021

Multi-document refers to a document consisting of various topics, not a single topic, and a typical example is online reviews. There have been several attempts to summarize online reviews because of their vast amounts of information. However, collective summarization of reviews through existing summary models creates a problem of losing the various topics that make up the reviews. Therefore, in this paper, we present method to summarize the review with minimal loss of the topic. The proposed method classify reviews through processes such as preprocessing, importance evaluation, embedding substitution using BERT, and embedding clustering. Furthermore, the classified sentences generate the final summary using the trained Transformer summary model. The performance evaluation of the proposed model was compared by evaluating the existing summary model, seq2seq model, and the cosine similarity with the ROUGE score, and performed a high performance summary compared to the existing summary model.

• Journal of the Korea Society of Computer and Information
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• v.25 no.8
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• pp.1-8
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• 2020

In this paper, we propose a gene family based RNA-seq read distribution method in means to accelerate the overal transcriptome assembly computation time. To measure the performance of our transcriptome sequence data distribution method, we evaluated the performance by testing four types of data sets of the Arabidopsis thaliana genome (Whole Unclassified Reads, Family-Classified Reads, Model-Classified Reads, and Randomly Classified Reads). As a result of de novo transcript assembly in distributed nodes using model classification data, the generated gene contigs matched 95% compared to the contig generated by WUR, and the execution time was reduced by 4.2 times compared to a single node environment using the same resources.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.102-102
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• 2017

In this study, QTL analysis of allelopathy was conducted. A total of 171 of F8 RILs developed from the cross between Nongan(low allelopathic cultivar) and Sathi(high allelopathic cultivar) were used . the performance of allelopathy were evaluated using 'ECAM(Equal Compartment Agar Method)', where the root length of lettuce cultivated with the RILs were measured. The distribution of the performance was followed as normal distribution. In order to identify the location of QTLs related to allelopathy, QTL-seq with BSA(Bulked-segregant analysis) was performed with 20 highest and 10 lowest RILs. As a result, Two Sliding window coordinate region of candidate QTLs were detected on Chr4 (5,050,001 - 14,800,000, 18,650,001 - 22,500,000), Chr8 (2,550,001 - 8,250,000, 21,150,001 - 26,800,000) and One region on Chr7 (1 - 3,300,000), Chr9 (1 - 13,300,000) respectively.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.3
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• pp.343-351
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• 2016

Although the chemical, physical, and nutritional properties of bovine milk have been extensively studied, only a few studies have attempted to characterize milk-synthesizing genes using RNA-seq data. RNA-seq data was collected from 21 Holstein samples, along with group information about milk production ability; milk yield; and protein, fat, and solid contents. Meta-analysis was employed in order to generally characterize genes related to milk production. In addition, we attempted to investigate the relationship between milk related traits, parity, and lactation period. We observed that milk fat is highly correlated with lactation period; this result indicates that this effect should be considered in the model in order to accurately detect milk production related genes. By employing our developed model, 271 genes were significantly (false discovery rate [FDR] adjusted p-value<0.1) detected as milk production related differentially expressed genes. Of these genes, five (albumin, nitric oxide synthase 3, RNA-binding region (RNP1, RRM) containing 3, secreted and transmembrane 1, and serine palmitoyltransferase, small subunit B) were technically validated using quantitative real-time polymerase chain reaction (qRT-PCR) in order to check the accuracy of RNA-seq analysis. Finally, 83 gene ontology biological processes including several blood vessel and mammary gland development related terms, were significantly detected using DAVID gene-set enrichment analysis. From these results, we observed that detected milk production related genes are highly enriched in the circulation system process and mammary gland related biological functions. In addition, we observed that detected genes including caveolin 1, mammary serum amyloid A3.2, lingual antimicrobial peptide, cathelicidin 4 (CATHL4), cathelicidin 6 (CATHL6) have been reported in other species as milk production related gene. For this reason, we concluded that our detected 271 genes would be strong candidates for determining milk production.

• Proceedings of the Korea Information Processing Society Conference
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• 2019.10a
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• pp.898-900
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• 2019

SPARQL(SPARQL Protocol and RDF Query Language)은 지식 베이스를 위한 표준 시맨틱 질의 언어이다. 최근 인공지능 분야에서 지식 베이스는 질의 응답 시스템, 시맨틱 검색 등 그 활용성이 커지고 있다. 그러나 SPARQL 과 같은 질의 언어를 사용하기 위해서는 질의 언어의 문법을 이해하기 때문에, 일반 사용자의 경우에는 그 활용성이 제한될 수밖에 없다. 이에 본 논문은 신경망 기반 기계 번역 기술을 활용하여 자연어 질의로부터 SPARQL 을 생성하는 방법을 제안한다. 우리는 제안하는 방법을 대규모 공개 지식 베이스인 Wikidata 를 사용해 검증하였다. 우리는 실험에서 사용할 Wikidata 에 존재하는 영화 지식을 묻는 자연어 질의-SPARQL 질의 쌍 20,000 건을 생성하였고, 여러 sequence-to-sequence 모델을 비교한 실험에서 합성곱 신경망 기반의 모델이 BLEU 96.8%의 가장 좋은 결과를 얻음을 보였다.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.10
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• pp.1565-1574
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• 2018

Objective: The aim of the present study was to identify genetic variants based on RNA-seq data, obtained via transcriptome sequencing of muscle tissue of pigs differing in muscle histological structure, and to verify the variants' effect on histological microstructure and production traits in a larger pig population. Methods: RNA-seq data was used to identify the panel of single nucleotide polymorphisms (SNPs) significantly related with percentage and diameter of each fiber type (I, IIA, IIB). Detected polymorphisms were mapped to quantitative trait loci (QTLs) regions. Next, the association study was performed on 944 animals representing five breeds (Landrace, Large White, Pietrain, Duroc, and native Puławska breed) in order to evaluate the relationship of selected SNPs and histological characteristics, meat quality and carcasses traits. Results: Mapping of detected genetic variants to QTL regions showed that chromosome 14 was the most overrepresented with the identification of four QTLs related to percentage of fiber types I and IIA. The association study performed on a 293 longissimus muscle samples confirmed a significant positive effect of transforming acidic coiled-coil-containing protein 2 (TACC2) polymorphisms on fiber diameter, while SNP within forkhead box O1 (FOXO1) locus was associated with decrease of diameter of fiber types IIA and IIB. Moreover, subsequent general linear model analysis showed significant relationship of FOXO1, delta 4-desaturase, sphingolipid 1 (DEGS1), and troponin T2 (TNNT2) genes with loin 'eye' area, FOXO1 with loin weight, as well as FOXO1 and TACC2 with lean meat percentage. Furthermore, the intramuscular fat content was positively associated (p<0.01) with occurrence of polymorphisms within DEGS1, TNNT2 genes and negatively with occurrence of TACC2 polymorphism. Conclusion: This study's results indicate that the SNP calling analysis based on RNA-seq data can be used to search candidate genes and establish the genetic basis of phenotypic traits. The presented results can be used for future studies evaluating the use of selected SNPs as genetic markers related to muscle histological profile and production traits in pig breeding.