著者

Bharata Kalbuaji Y-H. Taguchi Akihiko Konagaya

出版者

Chem-Bio Informatics Society

雑誌

Chem-Bio Informatics Journal (ISSN:13476297)

巻号頁・発行日

vol.19, pp.32-55, 2019-09-30 (Released:2019-10-03)

参考文献数

47

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Gene expression analysis for understanding cancer cell development is a basic, but an important step, to further our knowledge in cancer research. We may also be interested in understanding gene interactions that may lead to cancer development. One of the most important interactions is a regulatory interaction that involves transcription factor genes. In this research, we are attempting to construct a new regulatory network that imitates the transcription and translation processes of mRNA. We construct this network from four different cancer types: bile-duct cancer (BDC), lung adenocarcinoma (LUAD), colorectal cancer (CRC), and hepatocyte carcinoma (HCC). We also integrate differential expression data to obtain the interactions among differentially expressed genes. We then try to find intersecting sub-networks that exist across all cancer types. We believe that the transcription factor genes found in intersection sub-networks may reveal an important mechanism that affects cancer cell growth. In this research, we found that genes, such as those in the TEAD4, IRX5, HMGA1, and E2F gene family and the SOX gene family, are found in the enrichment analysis of the intersection sub-network obtained from multiple cancer data-sets. These genes point us toward dysregulation of the cell cycle, cell division, and cell proliferation mechanisms in cancer cells. These genes may become new cancer drug targets for cancer treatment.

著者

Y-h. Taguchi

出版者

The Japanese Biochemical Society/The Molecular Biology Society of Japan

雑誌

ConBio2017

巻号頁・発行日

2017-10-31

著者

Hideaki Umeyama Mitsuo Iwadate Y-h. Taguchi

出版者

一般社団法人 情報処理学会

雑誌

IPSJ Transactions on Bioinformatics (ISSN:18826679)

巻号頁・発行日

vol.8, pp.14-20, 2015 (Released:2015-08-19)

参考文献数

31

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Background: Spleen tyrosine kinase (SYK) is a protein related to various diseases. Aberrant SYK expression often causes the progression and initiation of several diseases including cancer and autoimmune diseases. Despite the importance of inhibiting SYK and identifying candidate inhibitors, no clinically effective inhibitors have been reported to date. Therefore, there is a need for novel SYK inhibitors. Results: Candidate compounds were investigated using in silico screening by chooseLD, which simulates ligand docking to proteins. Using this system, known inhibitors were correctly recognized as compounds with high affinity to SYK. Furthermore, many compounds in the DrugBank database were newly identified as having high affinity to the ATP-binding sites in the kinase domain with a similar affinity to previously reported inhibitors. Conclusions: Many drug candidate compounds from the DrugBank database were newly identified as inhibitors of SYK. Because compounds registered in the DrugBank are expected to have fewer side effects than currently available compounds, these newly identified compounds may be clinically useful inhibitors of SYK for the treatment of various diseases.

著者

Yuuichi Nakano Mitsuo Iwadate Hideaki Umeyama Y-h. Taguchi

出版者

一般社団法人 情報処理学会

雑誌

IPSJ Transactions on Bioinformatics (ISSN:18826679)

巻号頁・発行日

vol.7, pp.2-15, 2014 (Released:2014-01-17)

参考文献数

15

被引用文献数

1

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Type III secretion system (T3SS) effector protein is a part of bacterial secretion systems. T3SS exists in the pathogenic and symbiotic bacteria. How the T3SS effector proteins in these two classes differ from each other should be interesting. In this paper, we successfully discriminated T3SS effector proteins between plant pathogenic, animal pathogenic and plant symbiotic bacteria based on feature vectors inferred computationally by Yahara et al. only from amino acid sequences. This suggests that these three classes of bacteria employ distinct T3SS effector proteins. We also hypothesized that the feature vector proposed by Yahara et al. represents protein structure, possibly protein folds defined in Structural Classification of Proteins (SCOP) database.

著者

Y-h. Taguchi

出版者

The Molecular Biology Society of Japan

雑誌

The 39th Annual Meeting of the Molecular Biology Society of Japan

巻号頁・発行日

2016-11-08

著者

Yoshiki Murakami Toshihito Tanahashi Rika Okada Hidenori Toyoda Takashi Kumada Masaru Enomoto Akihiro Tamori Norifumi Kawada Y-H. Taguchi Takeshi Azuma

出版者

一般社団法人情報処理学会

雑誌

研究報告バイオ情報学(BIO) (ISSN:09196072)

巻号頁・発行日

vol.2014, no.2, pp.1-5, 2014-12-11

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Although microarray has been an important tool that can perform extensive gene expression analyses, next generation sequencing (NGS) has recently arisen as an alternative methodology that can measure gene expression. In this paper, we have compared microarray and NGS quantitatively using microRNA measurements in hepatocellular carcinoma (HCC) and found that these two are coincident with each other. NGS also turned out to be used for biomarker between HCC and normal tissue if the recently proposed principal component analysis based unsupervised feature extraction was applied.Although microarray has been an important tool that can perform extensive gene expression analyses, next generation sequencing (NGS) has recently arisen as an alternative methodology that can measure gene expression. In this paper, we have compared microarray and NGS quantitatively using microRNA measurements in hepatocellular carcinoma (HCC) and found that these two are coincident with each other. NGS also turned out to be used for biomarker between HCC and normal tissue if the recently proposed principal component analysis based unsupervised feature extraction was applied.

著者

Yuuichi Nakano Mitsuo Iwadate Hideaki Umeyama Y-h. Taguchi

出版者

Information and Media Technologies 編集運営会議

雑誌

Information and Media Technologies (ISSN:18810896)

巻号頁・発行日

vol.9, no.1, pp.141-154, 2014 (Released:2014-03-15)

参考文献数

15

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Type III secretion system (T3SS) effector protein is a part of bacterial secretion systems. T3SS exists in the pathogenic and symbiotic bacteria. How the T3SS effector proteins in these two classes differ from each other should be interesting. In this paper, we successfully discriminated T3SS effector proteins between plant pathogenic, animal pathogenic and plant symbiotic bacteria based on feature vectors inferred computationally by Yahara et al. only from amino acid sequences. This suggests that these three classes of bacteria employ distinct T3SS effector proteins. We also hypothesized that the feature vector proposed by Yahara et al. represents protein structure, possibly protein folds defined in Structural Classification of Proteins (SCOP) database.

著者

Hisamitsu Akiba Y-h. Taguchi

出版者

一般社団法人 情報処理学会

雑誌

IPSJ Transactions on Bioinformatics (ISSN:18826679)

巻号頁・発行日

vol.1, pp.35-41, 2008 (Released:2008-11-28)

参考文献数

12

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The Barcode of Life (BOL) project aims to identify species with no other information than DNA sequence. We assume that BOL includes information on higher taxa. In the present study, we compute nonmetric distance from BOL barcodes by using rank order of pairwise distance for 3 distinct examples, namely, Ant Diversity in Northern Madagascar, Survey of Chelicerates, and Birds of North America. This enables us to recognize higher taxa, i.e., genus, family, and order, more easily. For example, the ratio of mean inner taxa nonmetric distance to the intertaxa distance is smaller than that for raw (metric) distance. Furthermore, for most pairs of higher taxa, the mean intertaxa distance is more than twice larger than intrataxa distances. The nonmetric multidimensional scaling method enables to discriminate higher taxa compared to tree construction by the neighbor-joining method or the maximum parsimony method with raw distance measure, when each species is embedded into more than 40 dimensional space with an accuracy of 90% even after leave-one-out-cross-validation.

著者

Daichi Nogami Yuuichi Nakano Y-H.Taguchi

雑誌

研究報告バイオ情報学(BIO)

巻号頁・発行日

vol.2013-BIO-34, no.28, pp.1-2, 2013-06-20

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Inference of subcellular location only using sequence information is important. In this paper, we proposed the application of principal component analysis-based linear discriminant analysis for subcellular location information. It achieved the performance of Area Under the Curve under Receiver Operating Characteristic curve mostly more than 0.95 if less than 80% sequence identity non-redundancy was applied.

著者

Shodai Katsukawa Y-H.Taguchi

雑誌

研究報告バイオ情報学(BIO)

巻号頁・発行日

vol.2013-BIO-34, no.27, pp.1-2, 2013-06-20

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Type II diabetes (T2D) was a critical symptom also related to other diseases including cancers. Thus, suppression of T2D is important. In this paper, we investigated microRNAs as candidates of drug targets and biomarkers. A recently proposed principal component analysis based linear discriminant analysis allows us to specify numerous miRNAs differently expressed between type II diabetes patients and healthy control. Type II diabetes, Impaired Fasting Glucose patients, and normal control are successfully discriminated by blood miRNAs.

著者

Yuuichi Nakano Mitsuo Iwadate Hideaki Umeyama Y-H.Taguchi

雑誌

研究報告バイオ情報学(BIO)

巻号頁・発行日

vol.2013-BIO-34, no.10, pp.1-8, 2013-06-20

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Type III secretion system (T3SS) effector protein is a part of bacterial secretion systems. T3SS exists in the pathogenic and symbiotic bacteria. How the T3SS effector proteins in these two classes differ from each other should be interesting. In this paper, we proposed the usage of principal component analysis based linear discriminant analysis that discriminates T3SS effector proteins between plant pathogenic, animal pathogenic and plant symbiotic bacteria by the accuracy of 0.77. We also hypothesized that the feature vector proposed by Yahara et al represents protein structure, possibly protein folds defined in Structural Classification of Proteins (SCOP) database.

著者

Yudai Suzuki Kazunari Yokoyama Naomi Sakuramoto Y-H.Taguchi

雑誌

研究報告バイオ情報学(BIO)

巻号頁・発行日

vol.2013-BIO-34, no.5, pp.1-2, 2013-06-20

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Soil microbiological biodiversity has recently been shown to be causally related to soil diseases. In this study, we attempted to elucidate soil microbiological interactions by numerically analyzing the carbon-resource consumption rates in soils provided by a number of domestic companies and research institutes.

著者

Miyuki Owada Y-h.Taguchi

雑誌

研究報告バイオ情報学(BIO)

巻号頁・発行日

vol.2012, no.17, pp.1-2, 2012-06-21

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Promoter methylation is an important factor for gene expression regulation. Especially, it can control target gene regulation semipermanently. Thus, for example, it is used for tissue specific gene expression regulation. Recently, brain tissue promoter methylation patterns turn out to be more personalized than those in other tissues. In this paper, we try finding which genes are specifically methylated among individuals.Promoter methylation is an important factor for gene expression regulation. Especially, it can control target gene regulation semipermanently. Thus, for example, it is used for tissue specific gene expression regulation. Recently, brain tissue promoter methylation patterns turn out to be more personalized than those in other tissues. In this paper, we try finding which genes are specifically methylated among individuals.

著者

Kohei Iijima Y-h.Taguchi

雑誌

研究報告バイオ情報学(BIO)

巻号頁・発行日

vol.2012, no.18, pp.1-2, 2012-06-21

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Gene expression development during cell differentiation is a key factor to understand the mechanism of development. However, conventional gene expression analysis cannot distinguish among individual cell expression. In this paper, we re-analyze single cell gene expression measurements obtained by next gene sequencing technology during differentiation from mouse ES cell to MEF.Gene expression development during cell differentiation is a key factor to understand the mechanism of development. However, conventional gene expression analysis cannot distinguish among individual cell expression. In this paper, we re-analyze single cell gene expression measurements obtained by next gene sequencing technology during differentiation from mouse ES cell to MEF.

著者

Shigeharu Ishida Hideaki Umeyama Mitsuo Iwadate Y-h.Taguchi

雑誌

研究報告バイオ情報学(BIO)

巻号頁・発行日

vol.2012, no.12, pp.1-6, 2012-06-21

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Drug discovery for autoimmune diseases is recently recognized to be an important task. In this study, we try to perform structure prediction of proteins whose gene promoter regions were previous reported to be specifically methelysed or de-methylased commonly for three autoimmune diseases, systemic lupus erythematosus, rheumatoid arthritis, and dermatomyositis. FAMS were employed for this purpose and we can predict three dimensional structure with significantly small enough P-values. Most of them are suggested to be self immunology related proteins and will be important drug target candidates. We also found some proteins which form complex with each other. The possibility of a new drug target, i.e., suppression of protein complex formation is suggested.Drug discovery for autoimmune diseases is recently recognized to be an important task. In this study, we try to perform structure prediction of proteins whose gene promoter regions were previous reported to be specifically methelysed or de-methylased commonly for three autoimmune diseases, systemic lupus erythematosus, rheumatoid arthritis, and dermatomyositis. FAMS were employed for this purpose and we can predict three dimensional structure with significantly small enough P-values. Most of them are suggested to be self immunology related proteins and will be important drug target candidates. We also found some proteins which form complex with each other. The possibility of a new drug target, i.e., suppression of protein complex formation is suggested.

著者

Y-H.Taguchi Yoshiki Murakami

雑誌

研究報告バイオ情報学(BIO)

巻号頁・発行日

vol.2012-BIO-28, no.13, pp.1-6, 2012-03-21

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Disease biomarker using blood is clinically important, since blood is easy to obtain from patients, thus it requires relatively less stress. However, blood generally reflects not only targeted diseases but also whole body status of patients. Thus, it is important which contents of blood are considered. Recently, miRNAs in blood, blood-borne miRNome, turns out to be promising candidates for blood based biomarker for diseases. In this paper, we propose a new method based upon principal component analysis to identify better candidates for miRNAs as blood based biomarker using miRNA expression profiles of patients. Our method based upon principal components analysis provides us better blood-borne miRNome to discriminate diseases from healthy controls. They are hsa-miR-425,hsa-miR-15b,hsa-miR-185, hsa-miR-92a, hsa-miR-140-3p, hsamiR-320a, hsa-miR-486-5p, hsa-miR-16, hsa-miR-191, hsa-miR-106b, hsa-miR-19b, and hsa-miR-30d and are previously extensively reported to be cancer/disease related miRNAs. We have found that these common miRNAs are expressive or suppressive significantly in most of diseases/cancers, but in diseases/cancers specific combinatory manner. It enables us to discriminate cancers/diseases from healthy control well.

著者

Y-h.Taguchi Kazunari Yokoyama

雑誌

研究報告バイオ情報学(BIO)

巻号頁・発行日

vol.2012-BIO-28, no.10, pp.1-6, 2012-03-21

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Soil disease suppression is a worldwide important issue in order to realize stable food supply to people. In spite of that, no established indicators of soil disease suppression have been found out yet. This prevents us from controlling well soil state such that no diseases take place. In this paper, we have proposed a new biological indicator of soil disease suppression; the ability of bacteria to consume carbon resources, which can be automatically observed by Omunilog ID system during a duration of one or two days. This indicator turned out to distinguish disease suppressive soils from others. We have modeled these characteristic time developments of consumption of carbon resources by the simple ecological model where bacteria compete with each other for carbon resources. Measured ecological structure of soil bacteria can fit with the theoretical prediction well. In order to find characteristic features for each of soils, observed time developments are embedded into two dimensional space by non-metric multidimensional method. It results in the almost one dimensional arrangements of embedded points. By analyzing spacial distributions of each carbon resources in the embedded space, healthy soil turns out to have mostly uniform distribution along this one dimensional arrangement. Since sick soil and non-soil example have rather localized distributions, the ecological systems in more disease suppressive soil are both more diverse and more uniform. Since this indicator can be extremely easily and quickly obtained automatically, it is expected to use in order to validate many efforts to try to improve soil before any harvests very much.