Browsing by Author "Chang, Nai-Wen"

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Analyze fluorescent characteristic of cancer cell using hyperspectroscopic imaging system (HIS)
(2012-01-01)
Hsieh, Yao-Fang
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Chen, Chih-Hsien
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Mang, Ou-Yang
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Duann, Jeng-Ren
;
Chiou, Jin-Chern
Currently, the cancer was examined by diagnosing the pathological changes of tumor. If the examination of cancer can diagnose the tumor before the cell occur the pathological changes, the cure rate of cancer will increase. This research develops a human-machine interface for hyper-spectral microscope. The hyper-spectral microscope can scan the specific area of cell and records the data of spectrum and intensity. These data is helpful to diagnose tumor. This study finds the hyper-spectral imaging have two higher intensity points at 550nm and 700nm, and one lower point at 640nm between the two higher points. For analyzing the hyper-spectral imaging, the intensity at the 550nm peak divided by the intensity at 700nm peak. Finally, we determine the accuracy of detection by Gaussian distribution. The accuracy of detecting normal cells achieves 89%, and the accuracy of cancer cells achieves 81%.
miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database
(2016-01-04)
Chou, Chih-Hung
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Chang, Nai-Wen
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Shrestha, Sirjana
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Hsu, Sheng-Da
;
Lin, Yu-Ling
MicroRNAs (miRNAs) are small non-coding RNAs of approximately 22 nucleotides, which negatively regulate the gene expression at the post-transcriptional level. This study describes an update of the miRTarBase (http://miRTarBase.mbc.nctu.edu.tw/) that provides information about experimentally validated miRNA-target interactions (MTIs). The latest update of the miRTarBase expanded it to identify systematically Argonaute-miRNA-RNA interactions from 138 crosslinking and immunoprecipitation sequencing (CLIP-seq) data sets that were generated by 21 independent studies. The database contains 4966 articles, 7439 strongly validated MTIs (using reporter assays or western blots) and 348 007 MTIs from CLIP-seq. The number of MTIs in the miRTarBase has increased around 7-fold since the 2014 miRTarBase update. The miRNA and gene expression profiles from The Cancer Genome Atlas (TCGA) are integrated to provide an effective overview of this exponential growth in the miRNA experimental data. These improvements make the miRTarBase one of the more comprehensively annotated, experimentally validated miRNA-target interactions databases and motivate additional miRNA research efforts.
miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database
(2020-01-08)
Huang, Hsi-Yuan
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Lin, Yang-Chi-Dung
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Li, Jing
;
Huang, Kai-Yao
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Shrestha, Sirjana
MicroRNAs (miRNAs) are small non-coding RNAs (typically consisting of 18-25 nucleotides) that negatively control expression of target genes at the post-transcriptional level. Owing to the biological significance of miRNAs, miRTarBase was developed to provide comprehensive information on experimentally validated miRNA-target interactions (MTIs). To date, the database has accumulated >13,404 validated MTIs from 11,021 articles from manual curations. In this update, a text-mining system was incorporated to enhance the recognition of MTI-related articles by adopting a scoring system. In addition, a variety of biological databases were integrated to provide information on the regulatory network of miRNAs and its expression in blood. Not only targets of miRNAs but also regulators of miRNAs are provided to users for investigating the up- and downstream regulations of miRNAs. Moreover, the number of MTIs with high-throughput experimental evidence increased remarkably (validated by CLIP-seq technology). In conclusion, these improvements promote the miRTarBase as one of the most comprehensively annotated and experimentally validated miRNA-target interaction databases.
miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions
(2018-01-04)
Chou, Chih-Hung
;
Shrestha, Sirjana
;
Yang, Chi-Dung
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Chang, Nai-Wen
;
Lin, Yu-Ling
MicroRNAs (miRNAs) are small non-coding RNAs of similar to 22 nucleotides that are involved in negative regulation of mRNA at the post-transcriptional level. Previously, we developed miRTarBase which provides information about experimentally validated miRNA-target interactions (MTIs). Here, we describe an updated database containing 422 517 curated MTIs from 4076 miRNAs and 23 054 target genes collected from over 8500 articles. The number of MTIs curated by strong evidence has increased similar to 1.4-fold since the last update in 2016. In this updated version, target sites validated by reporter assay that are available in the literature can be downloaded. The target site sequence can extract new features for analysis via a machine learning approach which can help to evaluate the performance of miRNA-target prediction tools. Furthermore, different ways of browsing enhance user browsing specific MTIs. With these improvements, miRTarBase serves as more comprehensively annotated, experimentally validated miRNA-target interactions databases in the field of miRNA related research. miRTarBase is available at http://miRTarBase.mbc.nctu.edu.tw/.
The new hyperspectral microscopic system for cancer diagnosis
(2011-01-01)
Hsieh, Yao-Fang
;
Mang, Ou-Yang
;
Chiou, Jin-Chern
;
Lin, Yung-Jiun
;
Tsai, Ming-Hsui
Until now, the cancer was examined by diagnosing the pathological changes of tumor. If the examination of cancer can diagnose the tumor before the cell occur the pathological changes, the cure rate of cancer will increase. This research develops a human-machine interface for hyper-spectral microscope. The hyper-spectral microscope can scan the specific area of cell and records the data of spectrum and intensity. These data is helpful to diagnose tumor. This research aims to develop a new system and a human-machine interface to control the hyper-spectral microscope. The interface can control the moving speed of motor, the exposure-time of hyper-spectrum, real-time focus, image of fluorescence, and record the data of spectral intensity and position.