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5. Analysis of HLA gene polymorphisms in East Africans reveals evidence of gene flow in two Semitic populations from Sudan

Author

Aamer, W., Hassan, H.Y., Nakaoka, H., Hosomichi, K., Jaeger, M., Tahir, H., Abdelraheem, M.H., Netea, M.G., Inoue, I., Aamer, W., Hassan, H.Y., Nakaoka, H., Hosomichi, K., Jaeger, M., Tahir, H., Abdelraheem, M.H., Netea, M.G., and Inoue, I.

Abstract

Item does not contain fulltext, Sudan, a northeastern African country, is characterized by high levels of cultural, linguistic, and genetic diversity, which is believed to be affected by continuous migration from neighboring countries. Consistent with such demographic effect, genome-wide SNP data revealed a shared ancestral component among Sudanese Afro-Asiatic speaking groups and non-African populations, mainly from West Asia. Although this component is shared among all Afro-Asiatic speaking groups, the extent of this sharing in Semitic groups, such as Sudanese Arab, is still unknown. Using genotypes of six polymorphic human leukocyte antigen (HLA) genes (i.e., HLA-A, -C, -B, -DRB1, -DQB1, and -DPB1), we examined the genetic structure of eight East African ethnic groups with origins in Sudan, South Sudan, and Ethiopia. We identified informative HLA alleles using principal component analysis, which revealed that the two Semitic groups (Gaalien and Shokrya) constituted a distinct cluster from the other Afro-Asiatic speaking groups in this study. The HLA alleles that distinguished Semitic Arabs co-exist in the same extended HLA haplotype, and those alleles are in strong linkage disequilibrium. Interestingly, we find the four-locus haplotype "C*12:02-B*52:01-DRB1*15:02-DQB1*06:01" exclusively in non-African populations and it is widely spread across Asia. The identification of this haplotype suggests a gene flow from Asia, and likely these haplotypes were brought to Africa through back migration from the Near East. These findings will be of interest to biomedical and anthropological studies that examine the demographic history of northeast Africa.

Published
2021

8. The use of link provider data to improve national genetic evaluation across weakly connected subpopulations

Author

Nakaoka, H., Gaillard, C., Fujinaka, K., Watanabe, N., Ito, M., Kawada, K., Ibi, T., Sasae, Y., and Sasaki, Y.

Subjects
Cattle -- Genetic aspects, Zoology and wildlife conservation
Abstract

Data from 3 prefectures and a nationwide farming corporation were used to assess the usefulness of the 'link provider data' in providing indirect genetic links for the national genetic evaluation for carcass weight across weakly connected subpopulations of the Japanese Black cattle. The data from the farming corporation provided genetic links to those of all prefectures and was therefore used as the link provider data. Two national genetic evaluation strategies under an animal model were compared, based on the generalized coefficient of determination (CD) of contrasts between mean EBV of sires or maternal grandsires (MGS) from different prefectures: strategy PA-1 was a pooled analysis of the data sets of the 3 prefectures, and strategy PA-2 was a pooled analysis of the data sets of the 3 prefectures and the farming corporation. The CD of the contrasts were greater for PA-2 than for PA-1. Under PA-2, the CD of the contrasts between mean EBV of sires or MGS ranged from 0.67 to 0.78 or from 0.61 to 0.70, respectively. Pooling the data from the 3 prefectures and the farming corporation increased the degree of connectedness through the link provider data rather than the amount of information by adding more data, thus improving the accuracy of prediction. The differences between mean EBV of sires or MGS from different prefectures were smaller for PA-1 than for PA-2. This finding suggests that genetic differences in carcass weight among prefectures are present, but that they would be confused with the environmental differences under PA-1 because of the lack of genetic connectedness among the prefectures. On the other hand, the genetic differences among the prefectures would be predicted precisely under PA-2 because the genetic connectedness among the prefectures was improved by using the link provider data. The results demonstrate that the link provider data could be used to unify within-prefecture evaluation to form a Japanese national genetic evaluation across weakly connected subpopulations. Key words: beef cattle, connectedness, genetic evaluation, link provider data, mixed linear model, precision

Published
2009

9. Effectiveness of adjusting for heterogeneity of variance in genetic evaluation of Japanese Black cattle

Author

Nakaoka, H., Narita, A., Ibi, T., Sasae, Y., Miyake, T., Yamada, T., and Sasaki, Y.

Subjects
Genetic research -- Methods, Cattle -- Genetic aspects, Zoology and wildlife conservation
Abstract

Heterogeneity of variance among subclasses of an effect is a potential source of bias in genetic evaluation. The objectives of this study were to quantify the heterogeneity of variance in carcass weight in Japanese Black cattle, to develop an adjustment method to account for the heterogeneity, and to evaluate the effectiveness of the method. A total of 96,950 records were collected from steers and heifers slaughtered from 1997 to 2005. These records were grouped into 2,767 farm-market-year-sex subclasses. Fourteen log-linear models for the variances were set up to estimate the heterogeneous phenotypic variances within subclasses. Schwarz's Bayesian information criterion was used for model selection. The preadjustment of records to a baseline variance was based on maximum likelihood estimates obtained from the selected model. As a result of adjustment, the SD, the CV, and the Gini coefficient for the phenotypic variance decreased by 68.6, 69.8, and 70.1%, respectively. When the top 5% of sires and top 1% of dams were selected, Spearman's rank correlation coefficients between the adjusted and unadjusted data were 0.95 for the selected sires and 0.78 for the selected dams. The effectiveness of the adjustment was evaluated in terms of the ability to predict breeding values, using the results of the successive genetic evaluations. Mean squared error between the parent averages and actual predicted values of the genetic merit for the sires whose progeny had a carcass record only from 2003 to 2005 was significantly reduced by the adjustment (P < 0.05). The results suggest that the genetic evaluation becomes more accurate by adjusting the data using the procedure developed in this study. Key words: beef cattle, carcass weight, genetic evaluation, heterogeneity of variance, model selection, statistical validation

Published
2007

16. GWAS of clinically defined gout and subtypes identifies multiple susceptibility loci that include urate transporter genes

Author

Nakayama, A., Nakaoka, H., Yamamoto, K., Sakiyama, M., Shaukat, A., Toyoda, Y., Okada, Y., Kamatani, Y., Nakamura, T., Takada, T., Inoue, K., Yasujima, T., Yuasa, H., Shirahama, Y., Nakashima, H., Shimizu, S., Higashino, T., Kawamura, Y., Ogata, H., Kawaguchi, M., Ohkawa, Y., Danjoh, I., Tokumasu, A., Ooyama, K., Ito, T., Kondo, T., Wakai, K., Stiburkova, B., Pavelka, K., Stamp, L.K., Dalbeth, N., Sakurai, Y., Suzuki, H, Hosoyamada, M., Fujimori, S., Yokoo, T., Hosoya, T., Inoue, I., Takahashi, A., Kubo, M., Ooyama, H., Shimizu, T., Ichida, K., Shinomiya, N., Merriman, T.R., Matsuo, H., Andres, M, Joosten, L.A., Janssen, M.C.H., Jansen, T.L., Liote, F., Radstake, T.R., Riches, P.L., So, A., Tauches, A.K., Nakayama, A., Nakaoka, H., Yamamoto, K., Sakiyama, M., Shaukat, A., Toyoda, Y., Okada, Y., Kamatani, Y., Nakamura, T., Takada, T., Inoue, K., Yasujima, T., Yuasa, H., Shirahama, Y., Nakashima, H., Shimizu, S., Higashino, T., Kawamura, Y., Ogata, H., Kawaguchi, M., Ohkawa, Y., Danjoh, I., Tokumasu, A., Ooyama, K., Ito, T., Kondo, T., Wakai, K., Stiburkova, B., Pavelka, K., Stamp, L.K., Dalbeth, N., Sakurai, Y., Suzuki, H, Hosoyamada, M., Fujimori, S., Yokoo, T., Hosoya, T., Inoue, I., Takahashi, A., Kubo, M., Ooyama, H., Shimizu, T., Ichida, K., Shinomiya, N., Merriman, T.R., Matsuo, H., Andres, M, Joosten, L.A., Janssen, M.C.H., Jansen, T.L., Liote, F., Radstake, T.R., Riches, P.L., So, A., and Tauches, A.K.

Abstract

Contains fulltext : 182552.pdf (publisher's version ) (Open Access), OBJECTIVE: A genome-wide association study (GWAS) of gout and its subtypes was performed to identify novel gout loci, including those that are subtype-specific. METHODS: Putative causal association signals from a GWAS of 945 clinically defined gout cases and 1213 controls from Japanese males were replicated with 1396 cases and 1268 controls using a custom chip of 1961 single nucleotide polymorphisms (SNPs). We also first conducted GWASs of gout subtypes. Replication with Caucasian and New Zealand Polynesian samples was done to further validate the loci identified in this study. RESULTS: In addition to the five loci we reported previously, further susceptibility loci were identified at a genome-wide significance level (p<5.0x10(-8)): urate transporter genes (SLC22A12 and SLC17A1) and HIST1H2BF-HIST1H4E for all gout cases, and NIPAL1 and FAM35A for the renal underexcretion gout subtype. While NIPAL1 encodes a magnesium transporter, functional analysis did not detect urate transport via NIPAL1, suggesting an indirect association with urate handling. Localisation analysis in the human kidney revealed expression of NIPAL1 and FAM35A mainly in the distal tubules, which suggests the involvement of the distal nephron in urate handling in humans. Clinically ascertained male patients with gout and controls of Caucasian and Polynesian ancestries were also genotyped, and FAM35A was associated with gout in all cases. A meta-analysis of the three populations revealed FAM35A to be associated with gout at a genome-wide level of significance (p meta =3.58x10(-8)). CONCLUSIONS: Our findings including novel gout risk loci provide further understanding of the molecular pathogenesis of gout and lead to a novel concept for the therapeutic target of gout/hyperuricaemia.

Published
2017

17. Widespread Coronary Dysfunction in the Absence of HDL Receptor SR-B1 in an Ischemic Cardiomyopathy Mouse Model

Author

Pearson, JT, Yoshimoto, M, Chen, YC, Sultani, R, Edgley, AJ, Nakaoka, H, Nishida, M, Umetani, K, Waddingham, MT, Jin, H-L, Zhang, Y, Kelly, DJ, Schwenke, DO, Inagaki, T, Tsuchimochi, H, Komuro, I, Yamashita, S, Shirai, M, Pearson, JT, Yoshimoto, M, Chen, YC, Sultani, R, Edgley, AJ, Nakaoka, H, Nishida, M, Umetani, K, Waddingham, MT, Jin, H-L, Zhang, Y, Kelly, DJ, Schwenke, DO, Inagaki, T, Tsuchimochi, H, Komuro, I, Yamashita, S, and Shirai, M

Abstract

Reduced clearance of lipoproteins by HDL scavenger receptor class B1 (SR-B1) plays an important role in occlusive coronary artery disease. However, it is not clear how much microvascular dysfunction contributes to ischemic cardiomyopathy. Our aim was to determine the distribution of vascular dysfunction in vivo in the coronary circulation of male mice after brief exposure to Paigen high fat diet, and whether this vasomotor dysfunction involved nitric oxide (NO) and or endothelium derived hyperpolarization factors (EDHF). We utilised mice with hypomorphic ApoE lipoprotein that lacked SR-B1 (SR-B1-/-/ApoER61h/h, n = 8) or were heterozygous for SR-B1 (SR-B1+/-/ApoER61h/h, n = 8) to investigate coronary dilator function with synchrotron microangiography. Partially occlusive stenoses were observed in vivo in SR-B1 deficient mice only. Increases in artery-arteriole calibre to acetylcholine and sodium nitroprusside stimulation were absent in SR-B1 deficient mice. Residual dilation to acetylcholine following L-NAME (50 mg/kg) and sodium meclofenamate (3 mg/kg) blockade was present in both mouse groups, except at occlusions, indicating that EDHF was not impaired. We show that SR-B1 deficiency caused impairment of NO-mediated dilation of conductance and microvessels. Our findings also suggest EDHF and prostanoids are important for global perfusion, but ultimately the loss of NO-mediated vasodilation contributes to atherothrombotic progression in ischemic cardiomyopathy.

Published
2017

18. GWAS of clinically defined gout and subtypes identifies multiple susceptibility loci that include urate transporter genes

Author

Nakayama, A., Nakaoka, H., Yamamoto, K., Sakiyama, M., Shaukat, A., Toyoda, Y., Okada, Y., Kamatani, Y., Nakamura, T., Takada, T., Inoue, K., Yasujima, T., Yuasa, H., Shirahama, Y., Nakashima, H., Shimizu, S., Higashino, T., Kawamura, Y., Ogata, H., Kawaguchi, M., Ohkawa, Y., Danjoh, I., Tokumasu, A., Ooyama, K., Ito, T., Kondo, T., Wakai, K., Stiburkova, B., Pavelka, K., Stamp, L.K., Dalbeth, N., Sakurai, Y., Suzuki, H, Hosoyamada, M., Fujimori, S., Yokoo, T., Hosoya, T., Inoue, I., Takahashi, A., Kubo, M., Ooyama, H., Shimizu, T., Ichida, K., Shinomiya, N., Merriman, T.R., Matsuo, H., Andres, M, Joosten, L.A., Janssen, M.C.H., Jansen, T.L., Liote, F., Radstake, T.R., Riches, P.L., So, A., and Tauches, A.K.

Subjects
0301 basic medicine, Male, Native Hawaiian or Other Pacific Islander, Gout, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Organic Anion Transporters, Genome-wide association study, Cell Cycle Proteins, Urate transport, Histones, chemistry.chemical_compound, 0302 clinical medicine, Japan, Immunology and Allergy, Medicine, Cation Transport Proteins, Genetics, biology, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], Middle Aged, DNA-Binding Proteins, SLC22A12, Sodium-Phosphate Cotransporter Proteins, Type I, musculoskeletal diseases, Adult, congenital, hereditary, and neonatal diseases and abnormalities, Genotype, Organic Cation Transport Proteins, Immunology, Single-nucleotide polymorphism, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, White People, 03 medical and health sciences, Rheumatology, Asian People, Gene Polymorphism, Humans, Genetic Predisposition to Disease, Aged, 030203 arthritis & rheumatology, business.industry, Arthritis, Case-control study, nutritional and metabolic diseases, Proteins, Clinical and Epidemiological Research, medicine.disease, 030104 developmental biology, chemistry, Genetic Loci, Case-Control Studies, biology.protein, Uric acid, Gene polymorphism, business, Genome-Wide Association Study
Abstract

ObjectiveA genome-wide association study (GWAS) of gout and its subtypes was performed to identify novel gout loci, including those that are subtype-specific.MethodsPutative causal association signals from a GWAS of 945 clinically defined gout cases and 1213 controls from Japanese males were replicated with 1396 cases and 1268 controls using a custom chip of 1961 single nucleotide polymorphisms (SNPs). We also first conducted GWASs of gout subtypes. Replication with Caucasian and New Zealand Polynesian samples was done to further validate the loci identified in this study.ResultsIn addition to the five loci we reported previously, further susceptibility loci were identified at a genome-wide significance level (p−8): urate transporter genes (SLC22A12andSLC17A1) andHIST1H2BF-HIST1H4Efor all gout cases, andNIPAL1andFAM35Afor the renal underexcretion gout subtype. WhileNIPAL1encodes a magnesium transporter, functional analysis did not detect urate transport via NIPAL1, suggesting an indirect association with urate handling. Localisation analysis in the human kidney revealed expression of NIPAL1 and FAM35A mainly in the distal tubules, which suggests the involvement of the distal nephron in urate handling in humans. Clinically ascertained male patients with gout and controls of Caucasian and Polynesian ancestries were also genotyped, andFAM35Awas associated with gout in all cases. A meta-analysis of the three populations revealedFAM35Ato be associated with gout at a genome-wide level of significance (pmeta=3.58×10−8).ConclusionsOur findings including novel gout risk loci provide further understanding of the molecular pathogenesis of gout and lead to a novel concept for the therapeutic target of gout/hyperuricaemia.

Published
2016

20. Mint3-mediated L1CAM expression in fibroblasts promotes cancer cell proliferation via integrin α5β1 and tumour growth

Author

Nakaoka, H J, primary, Tanei, Z, additional, Hara, T, additional, Weng, J S, additional, Kanamori, A, additional, Hayashi, T, additional, Sato, H, additional, Orimo, A, additional, Otsuji, K, additional, Tada, K, additional, Morikawa, T, additional, Sasaki, T, additional, Fukayama, M, additional, Seiki, M, additional, Murakami, Y, additional, and Sakamoto, T, additional

Published
2017
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21. Shared Genetic Risk Factors of Intracranial, Abdominal, and Thoracic Aneurysms

Author

Hof, F.N. van 't, Ruigrok, Y.M., Lee, C.H., Ripke, S., Anderson, G., Baas, A.F., Blankensteijn, J.D., Bottinger, E.P., Bown, M.J., Broderick, J., Bijlenga, P., Carrell, D.S., Crawford, D.C., Crosslin, D.R., Ebeling, C., Eriksson, J.G., Fornage, M., Foroud, T., von Und Zu Fraunberg, M., Friedrich, C.M., Gaal, E.I., Gottesman, O., Guo, D.C., Harrison, S.C., Hernesniemi, J., Hofman, A., Inoue, I., Jaaskelainen, J.E., Jones, G.T., Kiemeney, L.A., Kivisaari, R., Ko, N., Koskinen, S., Kubo, M., Kullo, I.J., Kuivaniemi, H., Kurki, M.I., Laakso, A., Lai, D., Leal, S.M., Lehto, H., Lemaire, S.A., Low, S.K., Malinowski, J., McCarty, C.A., Milewicz, D.M., Mosley, T.H., Nakamura, Y., Nakaoka, H., Niemela, M., Pacheco, J., Peissig, P.L., Pera, J., Rasmussen-Torvik, L., Ritchie, M.D., Rivadeneira, F., Rij, A.M. van, Santos-Cortez, R.L., Saratzis, A., Slowik, A., Takahashi, A., Tromp, G., Uitterlinden, A.G., Verma, S.S., Vermeulen, S.H., Wang, G.T., Han, B., Rinkel, G.J., Bakker, P.I. de, Graaf, J. de, et al., Hof, F.N. van 't, Ruigrok, Y.M., Lee, C.H., Ripke, S., Anderson, G., Baas, A.F., Blankensteijn, J.D., Bottinger, E.P., Bown, M.J., Broderick, J., Bijlenga, P., Carrell, D.S., Crawford, D.C., Crosslin, D.R., Ebeling, C., Eriksson, J.G., Fornage, M., Foroud, T., von Und Zu Fraunberg, M., Friedrich, C.M., Gaal, E.I., Gottesman, O., Guo, D.C., Harrison, S.C., Hernesniemi, J., Hofman, A., Inoue, I., Jaaskelainen, J.E., Jones, G.T., Kiemeney, L.A., Kivisaari, R., Ko, N., Koskinen, S., Kubo, M., Kullo, I.J., Kuivaniemi, H., Kurki, M.I., Laakso, A., Lai, D., Leal, S.M., Lehto, H., Lemaire, S.A., Low, S.K., Malinowski, J., McCarty, C.A., Milewicz, D.M., Mosley, T.H., Nakamura, Y., Nakaoka, H., Niemela, M., Pacheco, J., Peissig, P.L., Pera, J., Rasmussen-Torvik, L., Ritchie, M.D., Rivadeneira, F., Rij, A.M. van, Santos-Cortez, R.L., Saratzis, A., Slowik, A., Takahashi, A., Tromp, G., Uitterlinden, A.G., Verma, S.S., Vermeulen, S.H., Wang, G.T., Han, B., Rinkel, G.J., Bakker, P.I. de, Graaf, J. de, and et al.

Abstract

Contains fulltext : 171496.pdf (publisher's version ) (Open Access), BACKGROUND: Intracranial aneurysms (IAs), abdominal aortic aneurysms (AAAs), and thoracic aortic aneurysms (TAAs) all have a familial predisposition. Given that aneurysm types are known to co-occur, we hypothesized that there may be shared genetic risk factors for IAs, AAAs, and TAAs. METHODS AND RESULTS: We performed a mega-analysis of 1000 Genomes Project-imputed genome-wide association study (GWAS) data of 4 previously published aneurysm cohorts: 2 IA cohorts (in total 1516 cases, 4305 controls), 1 AAA cohort (818 cases, 3004 controls), and 1 TAA cohort (760 cases, 2212 controls), and observed associations of 4 known IA, AAA, and/or TAA risk loci (9p21, 18q11, 15q21, and 2q33) with consistent effect directions in all 4 cohorts. We calculated polygenic scores based on IA-, AAA-, and TAA-associated SNPs and tested these scores for association to case-control status in the other aneurysm cohorts; this revealed no shared polygenic effects. Similarly, linkage disequilibrium-score regression analyses did not show significant correlations between any pair of aneurysm subtypes. Last, we evaluated the evidence for 14 previously published aneurysm risk single-nucleotide polymorphisms through collaboration in extended aneurysm cohorts, with a total of 6548 cases and 16 843 controls (IA) and 4391 cases and 37 904 controls (AAA), and found nominally significant associations for IA risk locus 18q11 near RBBP8 to AAA (odds ratio [OR]=1.11; P=4.1x10(-5)) and for TAA risk locus 15q21 near FBN1 to AAA (OR=1.07; P=1.1x10(-3)). CONCLUSIONS: Although there was no evidence for polygenic overlap between IAs, AAAs, and TAAs, we found nominally significant effects of two established risk loci for IAs and TAAs in AAAs. These two loci will require further replication.

Published
2016

27. SAT0324 ABCG2 Dysfunction Leads to Renal Urate Underexcretion Type Hyperuricemia in Addition to Extra-Renal Urate Underexcretion Type Hyperuricemia

Author

Ichida, K., primary, Matsuo, H., additional, Nakayama, A., additional, Sakiyama, M., additional, Chiba, T., additional, Shimizu, S., additional, Nakashima, H., additional, Nakamura, T., additional, Takada, Y., additional, Takada, T., additional, Nakaoka, H., additional, Wakai, K., additional, Sakurai, Y., additional, Shimizu, T., additional, Suzuki, H., additional, and Shinomiya, N., additional

Published
2015
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30. The Rice Annotation Project Database (RAP-DB): 2008 update

Author

Tanaka, T., Antonio, B.A., Kikuchi, S., Matsumoto, T., Nagamura, Y., Numa, H., Sakai, H., Wu, J., Itoh, T., Sasaki, T., Aono, R., Fujii, Y., Habara, T., Harada, E., Kanno, M., Kawahara, Y., Kawashima, H., Kubooka, H., Matsuya, A., Nakaoka, H., Saichi, N., Sanbonmatsu, R., Sato, Y., Shinso, Y., Suzuki, M., Takeda, J.-i., Tanino, M., Todokoro, F., Yamaguchi, K., Yamamoto, N., Yamasaki, C., Imanishi, T., Okido, T., Tada, M., Ikeo, K., Tateno, Y., Gojobori, T., Lin, Y-C, Wei, F-J, Hsing, Y-i, Zhao, Q., Bin, H., Kramer, M.R., McCombie, R.W., Lonsdale, D., O’Donovan, C.C., Whitfield, E.J., Apweiler, R., Koyanagi, K.O., Khurana, J.P., Raghuvanshi, S., Singh, N.K., Tyagi, A.K., Haberer, G., Fujisawa, M., Hosokawa, S., Ito, Y., Ikawa, H., Shibata, M., Yamamoto, M., Bruskiewich, R.M., Hoen, D.R., Bureau, T.E., Namiki, N., Ohyanagi, H., Sakai, Y., Nobushima, S., Sakata, K., Barrero, R.A., Souvorov, A., Smith-White, B., Tatusova, T., An, S., An, G., OOta, S., Fuks, G., Messing, J., Christie, K.R., Lieberherr, D., Kim, H-R, Zuccolo, A., Wing, R.A., Nobuta, K., Green, P.J., Lu, C., Meyers, B.C., Chaparro, C., Piegu, B., Panaud, O., Echeverria, M., Tanaka, T., Antonio, B.A., Kikuchi, S., Matsumoto, T., Nagamura, Y., Numa, H., Sakai, H., Wu, J., Itoh, T., Sasaki, T., Aono, R., Fujii, Y., Habara, T., Harada, E., Kanno, M., Kawahara, Y., Kawashima, H., Kubooka, H., Matsuya, A., Nakaoka, H., Saichi, N., Sanbonmatsu, R., Sato, Y., Shinso, Y., Suzuki, M., Takeda, J.-i., Tanino, M., Todokoro, F., Yamaguchi, K., Yamamoto, N., Yamasaki, C., Imanishi, T., Okido, T., Tada, M., Ikeo, K., Tateno, Y., Gojobori, T., Lin, Y-C, Wei, F-J, Hsing, Y-i, Zhao, Q., Bin, H., Kramer, M.R., McCombie, R.W., Lonsdale, D., O’Donovan, C.C., Whitfield, E.J., Apweiler, R., Koyanagi, K.O., Khurana, J.P., Raghuvanshi, S., Singh, N.K., Tyagi, A.K., Haberer, G., Fujisawa, M., Hosokawa, S., Ito, Y., Ikawa, H., Shibata, M., Yamamoto, M., Bruskiewich, R.M., Hoen, D.R., Bureau, T.E., Namiki, N., Ohyanagi, H., Sakai, Y., Nobushima, S., Sakata, K., Barrero, R.A., Souvorov, A., Smith-White, B., Tatusova, T., An, S., An, G., OOta, S., Fuks, G., Messing, J., Christie, K.R., Lieberherr, D., Kim, H-R, Zuccolo, A., Wing, R.A., Nobuta, K., Green, P.J., Lu, C., Meyers, B.C., Chaparro, C., Piegu, B., Panaud, O., and Echeverria, M.

Abstract

The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.

Published
2008

35. MS54 SERUM APOLIPOPROTEIN B-48 LEVEL IS CORRELATED WITH CAROTID INTIMA-MEDIA THICKNESS (IMT) IN SUBJECTS WITH NORMAL SERUM TRIGLYCERIDE LEVEL

Author

Nakatani, K., primary, Sugimoto, T., additional, Kawase, R., additional, Nakaoka, H., additional, Inagaki, M., additional, Yuasa-Kawase, M., additional, Tsubakio-Yamamoto, K., additional, Sandoval, J.C., additional, Masuda, D., additional, Ohama, T., additional, Nakagawa-Toyama, Y., additional, Nishida, M., additional, Ishigami, M., additional, Komuro, I., additional, and Yamashita, S., additional

Published
2010
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36. P343 FATTY ACIDS DERIVATIVES BY LIPID PEROXIDATION ARE SIGNIFICANTLY INCREASED IN PATIENTS WITH HIGH APOLIPOPROTEIN B-48 LEVELS, INDEPENDENT OF TRIGLYCERIDE CONCENTRATIONS

Author

Masuda, D., primary, Nakaoka, H., additional, Kawase, R., additional, Inagaki, M., additional, Yuasa-Kawase, M., additional, Nakatani, K., additional, Tsubakio-Yamamoto, K., additional, Sandocal, J.C., additional, Ohama, T., additional, Nakagawa-Toyama, Y., additional, Nishida, M., additional, Ishigami, M., additional, Ishida, N., additional, Shichiri, M., additional, Yoshida, Y., additional, Komuro, I., additional, and Yamashita, S., additional

Published
2010
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37. P300 EFFECT OF PROBUCOL ON AN ANTIOXIDANT PROPERTY OF HDL IN PATIENTS WITH HETEROZYGOUS FAMILIAL HYPERCHOLESTEROLEMIA

Author

Inagaki, M., primary, Nakagawa-Toyama, Y., additional, Kawase, R., additional, Nakaoka, H., additional, Nakatani, K., additional, Yuasa-Kawase, M., additional, Tsubakio-Yamamoto, K., additional, Sandoval, J.C., additional, Masuda, D., additional, Ohama, T., additional, Nishida, M., additional, Ishigami, M., additional, and Yamashita, S., additional

Published
2010
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38. P294 ADIPONECTIN ENHANCES DE NOVO HEPATIC HDL SYNTHESIS THROUGH LXR ALPHA- AND COUP-TFII-DEPENDENT PATHWAYS

Author

Tsubakio-Yamamoto, K., primary, Ohama, T., additional, Masuda, D., additional, Sandoval, J.C., additional, Inagaki, M., additional, Nakatani, K., additional, Yuasa-Kawase, M., additional, Kawase, R., additional, Nakaoka, H., additional, Nakagawa-Toyama, Y., additional, Nishida, M., additional, Ishigami, M., additional, Kihara, S., additional, Shimomura, I., additional, Komuro, I., additional, and Yamashita, S., additional

Published
2010
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39. P346 APOB48/TG RATIO IS A NOVEL AND USEFUL MARKER FOR THE DETECTION OF TYPE III HYPERLIPIDEMIA AFTER ANTIHYPERLIPIDEMIC INTERVENTIONS

Author

Nakaoka, H., primary, Yuasa-Kawase, M., additional, Masuda, D., additional, Kawase, R., additional, Nakatani, K., additional, Inagaki, M., additional, Sandoval, J.C., additional, Tsubakio-Yamamoto, K., additional, Ohama, T., additional, Nakagawa-Toyama, Y., additional, Nishida, M., additional, Ishigami, M., additional, Komuro, I., additional, and Yamashita, S., additional

Published
2010
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43. Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees

Author

Matsuya, A., primary, Sakate, R., additional, Kawahara, Y., additional, Koyanagi, K. O., additional, Sato, Y., additional, Fujii, Y., additional, Yamasaki, C., additional, Habara, T., additional, Nakaoka, H., additional, Todokoro, F., additional, Yamaguchi, K., additional, Endo, T., additional, OOta, S., additional, Makalowski, W., additional, Ikeo, K., additional, Suzuki, Y., additional, Hanada, K., additional, Hashimoto, K., additional, Hirai, M., additional, Iwama, H., additional, Saitou, N., additional, Hiraki, A. T., additional, Jin, L., additional, Kaneko, Y., additional, Kanno, M., additional, Murakami, K., additional, Noda, A. O., additional, Saichi, N., additional, Sanbonmatsu, R., additional, Suzuki, M., additional, Takeda, J.-i., additional, Tanaka, M., additional, Gojobori, T., additional, Imanishi, T., additional, and Itoh, T., additional

Published
2007
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