AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis(WGCNA) is applied to investigate the gene expression lev...AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis(WGCNA) is applied to investigate the gene expression levels and patient clinic features. Uveal melanoma is the most common primary eye tumor in adults. Although many studies have identified some important genes and pathways that were relevant to progress of uveal melanoma, the relationship between co-expression and clinic traits in systems level of uveal melanoma is unclear yet. We employ WGCNA to investigate the relationship underlying molecular and phenotype in this study.METHODS: Gene expression profile of uveal melanoma and patient clinic traits were collected from the Gene Expression Omnibus(GEO) database. The gene co-expression is calculated by WGCNA that is the R package software. The package is used to analyze the correlation between pairs of expression levels of genes.The function of the genes were annotated by gene ontology(GO).RESULTS: In this study, we identified four co-expression modules significantly correlated with clinictraits. Module blue positively correlated with radiotherapy treatment. Module purple positively correlates with tumor location(sclera) and negatively correlates with patient age. Module red positively correlates with sclera and negatively correlates with thickness of tumor. Module black positively correlates with the largest tumor diameter(LTD). Additionally, we identified the hug gene(top connectivity with other genes) in each module. The hub gene RPS15 A, PTGDS, CD53 and MSI2 might play a vital role in progress of uveal melanoma.CONCLUSION: From WGCNA analysis and hub gene calculation, we identified RPS15 A, PTGDS, CD53 and MSI2 might be target or diagnosis for uveal melanoma.展开更多
Maize （Zea mays） is the most widely grown grain crop in the world, playing important roles in agriculture and industry. However, the functions of maize genes remain largely unknown. High-quality genome- wide transcr...Maize （Zea mays） is the most widely grown grain crop in the world, playing important roles in agriculture and industry. However, the functions of maize genes remain largely unknown. High-quality genome- wide transcriptome datasets provide important biological knowledge which has been widely and suc- cessfully used in plants not only by measuring gene expression levels but also by enabling co-expression analysis for predicting gene functions and modules related to agronomic traits. Recently, thousands of maize transcriptomic data are available across different inbred lines, development stages, tissues, and treatments, or even across different tissue sections and cell lines. Here, we integrated 701 transcriptomic and 108 epigenomic data and studied the different conditional networks with multi-dimensional omics levels. We constructed a searchable, integrative, one-stop online platform, the maize conditional co- expression network （MCENet） platform. MCENet provides 10 global/conditional co-expression net- works, 5 network accessional analysis toolkits （i.e., Network Search, Network Remodel, Module Finder, Network Comparison, and Dynamic Expression View） and multiple network functional support toolkits （e.g., motif and module enrichment analysis）. We hope that our database might help plant research communities to identify maize functional genes or modules that regulate important agronomic traits.展开更多
Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict t...Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict the prognosis of esophageal cancer. The matched microarray and RNA sequencing data of 185 patients with esophageal cancer were downloaded from The Cancer Genome Atlas(TCGA), and gene co-expression networks were built without distinguishing between squamous carcinoma and adenocarcinoma. The result showed that 12 modules were associated with one or more survival data such as recurrence status, recurrence time, vital status or vital time. Furthermore, survival analysis showed that 5 out of the 12 modules were related to progression-free survival(PFS) or overall survival(OS). As the most important module, the midnight blue module with 82 genes was related to PFS, apart from the patient age, tumor grade, primary treatment success, and duration of smoking and tumor histological type. Gene ontology enrichment analysis revealed that 'glycoprotein binding' was the top enriched function of midnight blue module genes. Additionally, the blue module was the exclusive gene clusters related to OS. Platelet activating factor receptor(PTAFR) and feline Gardner-Rasheed(FGR) were the top hub genes in both modeling datasets and the STRING protein interaction database. In conclusion, our study provides novel insights into the prognosis-associated genes and screens out candidate biomarkers for esophageal cancer.展开更多
Testis specific protein Y-encoded（TSPY） is a Y-located proto-oncogene predominantly expressed in normal male germ cells and various types of germ cell tumor. Significantly, TSPY is frequently expressed in somatic ca...Testis specific protein Y-encoded（TSPY） is a Y-located proto-oncogene predominantly expressed in normal male germ cells and various types of germ cell tumor. Significantly, TSPY is frequently expressed in somatic cancers including liver cancer but not in adjacent normal tissues, suggesting that ectopic TSPY expression could be associated with oncogenesis in non-germ cell cancers. Various studies demonstrated that TSPY expression promotes growth and proliferation in cancer cells; however, its relationship to other oncogenic events in TSPY-positive cancers remains unknown. The present study seeks to correlate TSPY expression with other molecular features in clinical cancer samples, by analyses of RNA-seq transcriptome and DNA methylation data in the Cancer Genome Atlas（TCGA） database. A total of 53 genes,including oncogenic lineage protein 28 homolog B（LIN28B） gene and RNA-binding motif protein Y-linked（RBMY） gene, are identified to be consistently co-expressed with TSPY, and have been collectively designated as the TSPY co-expression network（TCN）. TCN genes were simultaneously activated in subsets of liver hepatocellular carcinoma（30%） and lung adenocarcinoma（10%） regardless of pathological stage, but only minimally in other cancer types. Further analysis revealed that the DNA methylation level was globally lower in the TCN-active than TCN-silent cancers. The specific expression and methylation patterns of TCN genes suggest that they could be useful as biomarkers for the diagnosis,prognosis and clinical management of cancers, especially those for liver and lung cancers, associated with TSPY co-expression network genes.展开更多
To handle the handover challenge in Express Train Access Networks(ETAN).mobility fading effects in high speed railway environments should be addressed first.Based on the investigation of fading effects in this paper,w...To handle the handover challenge in Express Train Access Networks(ETAN).mobility fading effects in high speed railway environments should be addressed first.Based on the investigation of fading effects in this paper,we obtain two theoretical bounds:HOTiming upper bound and HO-Margin lower bound,which are helpful guidelines to study the handover challenge today and in the future.Then,we apply them to analyze performance of conventional handover technologies and our proposal in ETAN.This follow-up theory analyses and simulation experiment results demonstrate that the proposed handover solution can minimize handover time up to 4ms(which is the fastest one so far),and reduce HO-Margin to 0.16 dB at a train speed of 350km/h.展开更多
Objective: To identify module genes that are closely related to clinical features of hepatocellular carcinoma (HCC) by weighted gene co‑expression network analysis, and to provide a reference for early clinical diagno...Objective: To identify module genes that are closely related to clinical features of hepatocellular carcinoma (HCC) by weighted gene co‑expression network analysis, and to provide a reference for early clinical diagnosis and treatment. Methods: GSE84598 chip data were downloaded from the GEO database, and module genes closely related to the clinical features of HCC were extracted by comprehensive weighted gene co‑expression network analysis. Hub genes were identified through protein interaction network analysis by the maximum clique centrality (MCC) algorithm;Finally, the expression of hub genes was validated by TCGA database and the Kaplan Meier plotter online database was used to evaluate the prognostic relationship between hub genes and HCC patients. Results: By comparing the gene expression data between HCC tissue samples and normal liver tissue samples, a total of 6 262 differentially expressed genes were obtained, of which 2 207 were upregulated and 4 055 were downregulated. Weighted gene co‑expression network analysis was applied to identify 120 genes of key modules. By intersecting with the differentially expressed genes, 115 candidate hub genes were obtained. The results of enrichment analysis showed that the candidate hub genes were closely related to cell mitosis, p53 signaling pathway and so on. Further application of the MCC algorithm to the protein interaction network of 115 candidate hub genes identified five hub genes, namely NUF2, RRM2, UBE2C, CDC20 and MAD2L1. Validation of hub genes by TCGA database revealed that all five hub genes were significantly upregulated in HCC tissues compared to normal liver tissues;Moreover, survival analysis revealed that high expression of hub genes was closely associated with poor prognosis in HCC patients. Conclusions: This study identifies five hub genes by combining multiple databases, which may provide directions for the clinical diagnosis and treatment of HCC.展开更多
E3 ubiquitin ligases are participated in numerous processes, regulating the response to biotic and abiotic stresses. Botrytis susceptible1 interactor (BOI) is a RING (Really Interesting New Gene)-type E3 ligase that m...E3 ubiquitin ligases are participated in numerous processes, regulating the response to biotic and abiotic stresses. Botrytis susceptible1 interactor (BOI) is a RING (Really Interesting New Gene)-type E3 ligase that mediates the ubiquitination of BOS1 (Botrytis susceptible1), a transcription factor involved in stress and pathogen responses. Although BOI is an E3 ligase, there are reports to show that BOI interacts with target proteins such as DELLAs or CONSTANS to repress gibberellin responses and flowering without the degradation of the target proteins. In this article, we utilize diversified methods to comprehensively analyze the expression pattern, interaction network and function of BOI gene. Firstly, 1800 bp upstream region of BOI gene from Arabidopsis thaliana (Arabidopsis) genome was isolated, and fused GUS reporter gene. The resulting expression cassette was introduced into wild-type Arabidopsis through Agrobacterium-mediated transformation. The result demonstrated that BOI gene was expressed predominantly in leaves, siliques, young roots, and flowering tissues, indicating that BOI gene may be involved in multiple processes in plant growth and development in Arabidopsis. Besides, eight candidate interacting proteins were obtained from the Arabidopsis cDNA library via yeast two-hybrid technology, including EXO70E2 (AT5G61010), WRKY7 (AT4G24240), WRKY11 (AT4G31550), WRKY17 (AT2G24570), UBP20 (AT4G17895), L5 (AT1G12290), SAUR9 (AT4G36110) and TCP21 (AT5G08330). Functional analysis of these candidate interacting proteins manifested that they related to multiple pathways, including biological and abiotic stress, programmed cell death, protein degradation, material metabolism and transcriptional regulation. In addition, the results of the transient assay proclaimed that BOI protein affects the protein stability of EXO70E2 and L5 through its E3 ubiquitin ligase activity. Our results provide novel clues for a better understanding of molecular mechanisms underlying BOI-mediated regulations.展开更多
Based on the heat flow data published in 1990 and 2001, a study of the factors influencing the terrestrial heat flow distribution in the China continent and its quantitative expression is carried out using the ＂Netli...Based on the heat flow data published in 1990 and 2001, a study of the factors influencing the terrestrial heat flow distribution in the China continent and its quantitative expression is carried out using the ＂Netlike Plastic-Flow＂ continental dynamics model and the methods of statistic analysis and optimum fitting. The result indicates that the factors influencing the heat flow distribution is classified into two groups, i.e. background and tectonic ones, in which the former mainly involves the non- uniform distribution of mantle heat flow, heat production of radioactive dements in the crust, heattransfer media and hydrothermal circulation, while the latter mainly involves plastic-flow networks and relatively-stable blocks. The plastic-flow network is a manifestation of shear localization in the netlike plastic-flow process in the lower lithosphere, which is composed of two sets of plastic-flow belts （PFBs） intersecting each other and, as one of the basic action regimes, controls the intraplate tectonic deformation. Relatively stable blocks （RSBs）, which are the tectonic units with relatively-high viscosities existing in the netlike plastic-flow field, as one of the principal origins, result in the development of large-seale compressional basins. PFB and RSB, as the active and quiet states of tectonic deformation, give rise to the higher and lower heat flow values, respectivdy. The provincial average heat flow in continent can be estimated using the expression qav = q0 ＋ a Pbt-c Pbk, where the three terms of the right side are background heat flow, PFB-positive contribution and RSB-negative contribution, Pbt and Pbk are the PFB- and RSB-coverage ratios, respectively, a is the coefficient of PFB- positive contribution depending mainly on the strain in the lower lithosphere, and c is the coefficient of RSB-negative contribution related mainly to the thickness of the lithosphere, the aseismic-area ratio and the tectonic age. For the major portion of the China continent excluding some of the southeastern region of China, the confidence interval of the provincial average background heat flow is qo=57.25±24.8 mW/m^2 and the PFB-positive- and RSB-negative-contribution coefficients are a=14.8-71.9 mW/m^2 and c=0-25.6 mW/m^2, respectively. The concepts of PFB and RSB effects and the heat flow expression suggested provide a new choice of the approach to the quantitative description of the characteristics of heat flow distribution in continent and their physical mechanisms.展开更多
This paper proposes a technique for synthesizing a pixel-based photo-realistic talking face animation using two-step synthesis with HMMs and DNNs. We introduce facial expression parameters as an intermediate represent...This paper proposes a technique for synthesizing a pixel-based photo-realistic talking face animation using two-step synthesis with HMMs and DNNs. We introduce facial expression parameters as an intermediate representation that has a good correspondence with both of the input contexts and the output pixel data of face images. The sequences of the facial expression parameters are modeled using context-dependent HMMs with static and dynamic features. The mapping from the expression parameters to the target pixel images are trained using DNNs. We examine the required amount of the training data for HMMs and DNNs and compare the performance of the proposed technique with the conventional PCA-based technique through objective and subjective evaluation experiments.展开更多
Module-based methods have made much progress in deconstructing biological networks.However,it is a great challenge to quantitatively compare the topological structural variations of modules(allosteric modules,AMs)unde...Module-based methods have made much progress in deconstructing biological networks.However,it is a great challenge to quantitatively compare the topological structural variations of modules(allosteric modules,AMs)under different situations.A total of 23,42 and 15co-expression modules were identified in baicalin(BA),jasminoidin(JA)and ursodeoxycholic acid(UA)in a global anti-ischemic mice network,respectively.Then,we integrated the methods of module-based consensus ratio(MCR)and modified Z summary module statistic to validate 12 BA,22 JA and 8 UA on-modules based on comparing with vehicle.The MCRs for pairwise comparisons were 1.55%(BA vs JA),1.45%(BA vs UA),and1.27%(JA vs UA),respectively.Five conserved allosteric modules(CAMs)and 17 unique allosteric modules(UAMs)were identified among these groups.In conclusion,module-centric analysis may provide us a unique approach to understand multiple pharmacological mechanisms associated with differential phenotypes in the era of modular pharmacology.展开更多
Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community.Here,we present RED（Rice Expression Database;http：//expression.ic4r.org）,an integrated dat...Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community.Here,we present RED（Rice Expression Database;http：//expression.ic4r.org）,an integrated database of rice gene expression profiles derived entirely from RNA-Seq data.RED features a comprehensive collection of 284 high-quality RNA-Seq experiments,integrates a large number of gene expression profiles and covers a wide range of rice growth stages as well as various treatments.Based on massive expression profiles,RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene（s） of interest.Besides,it provides user-friendly web interfaces for querying,browsing and visualizing expression profiles of concerned genes.Together,as a core resource in BIG Data Center,RED bears great utility for characterizing the function of rice genes and better understanding important biological processes and mechanisms underlying complex agronomic traits in rice.展开更多
基金Supported by the National Natural Science Foundation of China(No.81271019No.61463046)Gansu Province Science Foundation for Youths(No.145RJYA282)
文摘AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis(WGCNA) is applied to investigate the gene expression levels and patient clinic features. Uveal melanoma is the most common primary eye tumor in adults. Although many studies have identified some important genes and pathways that were relevant to progress of uveal melanoma, the relationship between co-expression and clinic traits in systems level of uveal melanoma is unclear yet. We employ WGCNA to investigate the relationship underlying molecular and phenotype in this study.METHODS: Gene expression profile of uveal melanoma and patient clinic traits were collected from the Gene Expression Omnibus(GEO) database. The gene co-expression is calculated by WGCNA that is the R package software. The package is used to analyze the correlation between pairs of expression levels of genes.The function of the genes were annotated by gene ontology(GO).RESULTS: In this study, we identified four co-expression modules significantly correlated with clinictraits. Module blue positively correlated with radiotherapy treatment. Module purple positively correlates with tumor location(sclera) and negatively correlates with patient age. Module red positively correlates with sclera and negatively correlates with thickness of tumor. Module black positively correlates with the largest tumor diameter(LTD). Additionally, we identified the hug gene(top connectivity with other genes) in each module. The hub gene RPS15 A, PTGDS, CD53 and MSI2 might play a vital role in progress of uveal melanoma.CONCLUSION: From WGCNA analysis and hub gene calculation, we identified RPS15 A, PTGDS, CD53 and MSI2 might be target or diagnosis for uveal melanoma.
基金supported by the National Natural Science Foundation of China (Nos. 31771467, 31571360 and 31371291)
文摘Maize （Zea mays） is the most widely grown grain crop in the world, playing important roles in agriculture and industry. However, the functions of maize genes remain largely unknown. High-quality genome- wide transcriptome datasets provide important biological knowledge which has been widely and suc- cessfully used in plants not only by measuring gene expression levels but also by enabling co-expression analysis for predicting gene functions and modules related to agronomic traits. Recently, thousands of maize transcriptomic data are available across different inbred lines, development stages, tissues, and treatments, or even across different tissue sections and cell lines. Here, we integrated 701 transcriptomic and 108 epigenomic data and studied the different conditional networks with multi-dimensional omics levels. We constructed a searchable, integrative, one-stop online platform, the maize conditional co- expression network （MCENet） platform. MCENet provides 10 global/conditional co-expression net- works, 5 network accessional analysis toolkits （i.e., Network Search, Network Remodel, Module Finder, Network Comparison, and Dynamic Expression View） and multiple network functional support toolkits （e.g., motif and module enrichment analysis）. We hope that our database might help plant research communities to identify maize functional genes or modules that regulate important agronomic traits.
文摘Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict the prognosis of esophageal cancer. The matched microarray and RNA sequencing data of 185 patients with esophageal cancer were downloaded from The Cancer Genome Atlas(TCGA), and gene co-expression networks were built without distinguishing between squamous carcinoma and adenocarcinoma. The result showed that 12 modules were associated with one or more survival data such as recurrence status, recurrence time, vital status or vital time. Furthermore, survival analysis showed that 5 out of the 12 modules were related to progression-free survival(PFS) or overall survival(OS). As the most important module, the midnight blue module with 82 genes was related to PFS, apart from the patient age, tumor grade, primary treatment success, and duration of smoking and tumor histological type. Gene ontology enrichment analysis revealed that 'glycoprotein binding' was the top enriched function of midnight blue module genes. Additionally, the blue module was the exclusive gene clusters related to OS. Platelet activating factor receptor(PTAFR) and feline Gardner-Rasheed(FGR) were the top hub genes in both modeling datasets and the STRING protein interaction database. In conclusion, our study provides novel insights into the prognosis-associated genes and screens out candidate biomarkers for esophageal cancer.
基金partially supported by a Merit-Reviewed grant from the Department of Veterans Affairsa Peer-Reviewed Cancer Research Program grant from the Department of Defense (W81XWH-16-1-0488) to Y-FCL
文摘Testis specific protein Y-encoded（TSPY） is a Y-located proto-oncogene predominantly expressed in normal male germ cells and various types of germ cell tumor. Significantly, TSPY is frequently expressed in somatic cancers including liver cancer but not in adjacent normal tissues, suggesting that ectopic TSPY expression could be associated with oncogenesis in non-germ cell cancers. Various studies demonstrated that TSPY expression promotes growth and proliferation in cancer cells; however, its relationship to other oncogenic events in TSPY-positive cancers remains unknown. The present study seeks to correlate TSPY expression with other molecular features in clinical cancer samples, by analyses of RNA-seq transcriptome and DNA methylation data in the Cancer Genome Atlas（TCGA） database. A total of 53 genes,including oncogenic lineage protein 28 homolog B（LIN28B） gene and RNA-binding motif protein Y-linked（RBMY） gene, are identified to be consistently co-expressed with TSPY, and have been collectively designated as the TSPY co-expression network（TCN）. TCN genes were simultaneously activated in subsets of liver hepatocellular carcinoma（30%） and lung adenocarcinoma（10%） regardless of pathological stage, but only minimally in other cancer types. Further analysis revealed that the DNA methylation level was globally lower in the TCN-active than TCN-silent cancers. The specific expression and methylation patterns of TCN genes suggest that they could be useful as biomarkers for the diagnosis,prognosis and clinical management of cancers, especially those for liver and lung cancers, associated with TSPY co-expression network genes.
基金supported by the National Basic Research Program of China (973 Program)(No.2012CB315606 and 2010CB328201)
文摘To handle the handover challenge in Express Train Access Networks(ETAN).mobility fading effects in high speed railway environments should be addressed first.Based on the investigation of fading effects in this paper,we obtain two theoretical bounds:HOTiming upper bound and HO-Margin lower bound,which are helpful guidelines to study the handover challenge today and in the future.Then,we apply them to analyze performance of conventional handover technologies and our proposal in ETAN.This follow-up theory analyses and simulation experiment results demonstrate that the proposed handover solution can minimize handover time up to 4ms(which is the fastest one so far),and reduce HO-Margin to 0.16 dB at a train speed of 350km/h.
基金National Natural Science Foundation of China (No.81760851)Guangxi University Youth Promotion Program (No.2019KY0348)。
文摘Objective: To identify module genes that are closely related to clinical features of hepatocellular carcinoma (HCC) by weighted gene co‑expression network analysis, and to provide a reference for early clinical diagnosis and treatment. Methods: GSE84598 chip data were downloaded from the GEO database, and module genes closely related to the clinical features of HCC were extracted by comprehensive weighted gene co‑expression network analysis. Hub genes were identified through protein interaction network analysis by the maximum clique centrality (MCC) algorithm;Finally, the expression of hub genes was validated by TCGA database and the Kaplan Meier plotter online database was used to evaluate the prognostic relationship between hub genes and HCC patients. Results: By comparing the gene expression data between HCC tissue samples and normal liver tissue samples, a total of 6 262 differentially expressed genes were obtained, of which 2 207 were upregulated and 4 055 were downregulated. Weighted gene co‑expression network analysis was applied to identify 120 genes of key modules. By intersecting with the differentially expressed genes, 115 candidate hub genes were obtained. The results of enrichment analysis showed that the candidate hub genes were closely related to cell mitosis, p53 signaling pathway and so on. Further application of the MCC algorithm to the protein interaction network of 115 candidate hub genes identified five hub genes, namely NUF2, RRM2, UBE2C, CDC20 and MAD2L1. Validation of hub genes by TCGA database revealed that all five hub genes were significantly upregulated in HCC tissues compared to normal liver tissues;Moreover, survival analysis revealed that high expression of hub genes was closely associated with poor prognosis in HCC patients. Conclusions: This study identifies five hub genes by combining multiple databases, which may provide directions for the clinical diagnosis and treatment of HCC.
文摘E3 ubiquitin ligases are participated in numerous processes, regulating the response to biotic and abiotic stresses. Botrytis susceptible1 interactor (BOI) is a RING (Really Interesting New Gene)-type E3 ligase that mediates the ubiquitination of BOS1 (Botrytis susceptible1), a transcription factor involved in stress and pathogen responses. Although BOI is an E3 ligase, there are reports to show that BOI interacts with target proteins such as DELLAs or CONSTANS to repress gibberellin responses and flowering without the degradation of the target proteins. In this article, we utilize diversified methods to comprehensively analyze the expression pattern, interaction network and function of BOI gene. Firstly, 1800 bp upstream region of BOI gene from Arabidopsis thaliana (Arabidopsis) genome was isolated, and fused GUS reporter gene. The resulting expression cassette was introduced into wild-type Arabidopsis through Agrobacterium-mediated transformation. The result demonstrated that BOI gene was expressed predominantly in leaves, siliques, young roots, and flowering tissues, indicating that BOI gene may be involved in multiple processes in plant growth and development in Arabidopsis. Besides, eight candidate interacting proteins were obtained from the Arabidopsis cDNA library via yeast two-hybrid technology, including EXO70E2 (AT5G61010), WRKY7 (AT4G24240), WRKY11 (AT4G31550), WRKY17 (AT2G24570), UBP20 (AT4G17895), L5 (AT1G12290), SAUR9 (AT4G36110) and TCP21 (AT5G08330). Functional analysis of these candidate interacting proteins manifested that they related to multiple pathways, including biological and abiotic stress, programmed cell death, protein degradation, material metabolism and transcriptional regulation. In addition, the results of the transient assay proclaimed that BOI protein affects the protein stability of EXO70E2 and L5 through its E3 ubiquitin ligase activity. Our results provide novel clues for a better understanding of molecular mechanisms underlying BOI-mediated regulations.
文摘Based on the heat flow data published in 1990 and 2001, a study of the factors influencing the terrestrial heat flow distribution in the China continent and its quantitative expression is carried out using the ＂Netlike Plastic-Flow＂ continental dynamics model and the methods of statistic analysis and optimum fitting. The result indicates that the factors influencing the heat flow distribution is classified into two groups, i.e. background and tectonic ones, in which the former mainly involves the non- uniform distribution of mantle heat flow, heat production of radioactive dements in the crust, heattransfer media and hydrothermal circulation, while the latter mainly involves plastic-flow networks and relatively-stable blocks. The plastic-flow network is a manifestation of shear localization in the netlike plastic-flow process in the lower lithosphere, which is composed of two sets of plastic-flow belts （PFBs） intersecting each other and, as one of the basic action regimes, controls the intraplate tectonic deformation. Relatively stable blocks （RSBs）, which are the tectonic units with relatively-high viscosities existing in the netlike plastic-flow field, as one of the principal origins, result in the development of large-seale compressional basins. PFB and RSB, as the active and quiet states of tectonic deformation, give rise to the higher and lower heat flow values, respectivdy. The provincial average heat flow in continent can be estimated using the expression qav = q0 ＋ a Pbt-c Pbk, where the three terms of the right side are background heat flow, PFB-positive contribution and RSB-negative contribution, Pbt and Pbk are the PFB- and RSB-coverage ratios, respectively, a is the coefficient of PFB- positive contribution depending mainly on the strain in the lower lithosphere, and c is the coefficient of RSB-negative contribution related mainly to the thickness of the lithosphere, the aseismic-area ratio and the tectonic age. For the major portion of the China continent excluding some of the southeastern region of China, the confidence interval of the provincial average background heat flow is qo=57.25±24.8 mW/m^2 and the PFB-positive- and RSB-negative-contribution coefficients are a=14.8-71.9 mW/m^2 and c=0-25.6 mW/m^2, respectively. The concepts of PFB and RSB effects and the heat flow expression suggested provide a new choice of the approach to the quantitative description of the characteristics of heat flow distribution in continent and their physical mechanisms.
文摘This paper proposes a technique for synthesizing a pixel-based photo-realistic talking face animation using two-step synthesis with HMMs and DNNs. We introduce facial expression parameters as an intermediate representation that has a good correspondence with both of the input contexts and the output pixel data of face images. The sequences of the facial expression parameters are modeled using context-dependent HMMs with static and dynamic features. The mapping from the expression parameters to the target pixel images are trained using DNNs. We examine the required amount of the training data for HMMs and DNNs and compare the performance of the proposed technique with the conventional PCA-based technique through objective and subjective evaluation experiments.
基金The project supported by National Natural Science Foundation of China(90209015)the Foundation of'Eleventh Five'National Key Technologies R&D Program(2006BAI08B04-06)
文摘Module-based methods have made much progress in deconstructing biological networks.However,it is a great challenge to quantitatively compare the topological structural variations of modules(allosteric modules,AMs)under different situations.A total of 23,42 and 15co-expression modules were identified in baicalin(BA),jasminoidin(JA)and ursodeoxycholic acid(UA)in a global anti-ischemic mice network,respectively.Then,we integrated the methods of module-based consensus ratio(MCR)and modified Z summary module statistic to validate 12 BA,22 JA and 8 UA on-modules based on comparing with vehicle.The MCRs for pairwise comparisons were 1.55%(BA vs JA),1.45%(BA vs UA),and1.27%(JA vs UA),respectively.Five conserved allosteric modules(CAMs)and 17 unique allosteric modules(UAMs)were identified among these groups.In conclusion,module-centric analysis may provide us a unique approach to understand multiple pharmacological mechanisms associated with differential phenotypes in the era of modular pharmacology.
基金supported by grants from Strategic Priority Research Program of the Chinese Academy of Sciences(No. XDA08020102 to Z.Z.and S.H.)International Partnership Program of the Chinese Academy of Sciences(No.153F11KYSB20160008)+3 种基金National Programs for High Technology Research and Development (863 ProgramNo.2015AA020108 to Z.Z.)National Natural Science Foundation of China(No.31100915 to LH.)the 100-Talent Program of Chinese Academy of Sciences(awarded to Z.Z.)
文摘Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community.Here,we present RED（Rice Expression Database;http：//expression.ic4r.org）,an integrated database of rice gene expression profiles derived entirely from RNA-Seq data.RED features a comprehensive collection of 284 high-quality RNA-Seq experiments,integrates a large number of gene expression profiles and covers a wide range of rice growth stages as well as various treatments.Based on massive expression profiles,RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene（s） of interest.Besides,it provides user-friendly web interfaces for querying,browsing and visualizing expression profiles of concerned genes.Together,as a core resource in BIG Data Center,RED bears great utility for characterizing the function of rice genes and better understanding important biological processes and mechanisms underlying complex agronomic traits in rice.
