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An integrated approach to identify the microRNAs regulation network modulating autophagy and cancer prognosis

An integrated approach to identify the microRNAs regulation ...

第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Fengji Liang Xionghui Zhou Wcnyan Qiao Xingyi Hang Ling Yin Juan Liu Yinghui Li Shanguang Chen Jianghui Xiong Bioinformatics Group and Data Coordination Center State Key Lab of Space Medicine Fundamentals and Application(SMFA)China Astronaut Research and Training Center(ACC) School of Computer Science Wuhan University430072China National Scientific Data Sharing Platform for Population and Health Telemedicine Center Institute of Medical InformaticsGeneral Hospital of Chinese PLA

A core task of drug discovery study is to identify the dependency between the genetic/ molecular makeups of the human body and disease *** we proposed a novel method for systematically screening the microRNAs regulating cancer prognosis via driving a specific ppi(protein-protein interaction) *** this method,we integrated information from microRNAs expression,mRNAs expression and patient outcome,and tried to mine the in vivo dependency between microRNAs and ppi *** conditional dependency of the mRNAs expression(G),microRNAs expression(M) and phenotype(P) was calculated, and the permutation was conduct to screen the significant Conditional Mutual Information I (G,P|M).In this study we test the proposed method on autophagy protein networks in ovarian cancer as *** is a cellular process involved the degradation of cell's own components,in which cytoplasmic contents are sequestered into a double-membrane called autophagosome and then subsequently delivered to lysosome for *** identified a group of microRNAs,which could regulate the hub nodes of autophagy ppi *** experimentally demonstrated that the transfection of the mimics of these microRNAs could inhibit autophagy via inhibiting the target gene:***,the miRNA-target gene pair is significantly associated with prognosis in a cohort of ovarian cancer patients.

关键词： microRNAs An integrated approach to identify the microRNAs regulation network modulating autophagy and cancer prognosis

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An integrated approach to identify the microRNAs regulation network modulating autophagy and cancer prognosis

An integrated approach to identify the microRNAs regulation ...

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第五届全国生物信息学与系统生物学学术大会

作者： Fengji Liang Xionghui Zhou Wenyan Qiao Xingyi Hang Ling Yin Juan Liu Yinghui Li Shanguang Chen Jianghui Xiong Telemedicine Center Institute of Medical Informatics General Hospital of Chinese PLA Beijing China School of Computer Science Wuhan University 430072 China Bioinformatics Group and Data Coordination Center State Key Lab of Space Medicine Fundamentals and Application (SMFA) China Astronaut Research and Training Center (ACC) Beijing China School of Computer Science Wuhan University 430072 China Bioinformatics Group and Data Coordination Center State Key Lab of Space Medicine Fundamentals and Application (SMFA) China Astronaut Research and Training Center (ACC) Beijing China National Scientific Data Sharing Platform for Population and Health Beijing China

A core task of drug discovery study is to identify the dependency between the genetic/ molecular makeups of the human body and disease *** we proposed a novel method for systematically screening the microRNAs regulating cancer prognosis via driving a specific ppi (protein-protein interaction) *** this method, we integrated information from microRNAs expression, mRNAs expression and patient outcome, and tried to mine the in vivo dependency between microRNAs and ppi *** conditional dependency of the mRNAs expression (G), microRNAs expression (M) and phenotype (P) was calculated, and the permutation was conduct to screen the significant Conditional Mutual Information Ⅰ (G, P|M).In this study we test the proposed method on autophagy protein networks in ovarian cancer as *** is a cellular process involved the degradation of cell's own components, in which cytoplasmic contents are sequestered into a double-membrane called autophagosome and then subsequently delivered to lysosome for *** identified a group of microRNAs, which could regulate the hub nodes of autophagy ppi *** experimentally demonstrated that the transfection of the mimics of these microRNAs could inhibit autophagy via inhibiting the target gene: ***, the miRNA-target gene pair is significantly associated with prognosis in a cohort of ovarian cancer patients .

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Predicting bone metastasis of breast cancer using context-specific miRNA regulation modules

Predicting bone metastasis of breast cancer using context-sp...

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第五届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会高通量时代的生物信息学与系统生物学

作者： Xionghui Zhou Fengji Liang Juan Liu Yinghui Li Shanguang Chen Jianghui Xiong School of Computer Science Wuhan University Bioinformatics Group and Data Coordination Center State Key Lab of Space Medicine Fundamentals and Application(SMFA)China Astronaut Research and Training Center(ACC) School of Computer Science Wuhan University.WuhanChina

Background:The bone is the most frequent target of metastatic breast ***, the underlying molecular mechanisms are *** many microarray studies have reported gene signatures that can predict metastasis in breast cancer,predicting cancer metastasis to a specific organ,such as to bone,remains a challenge in cancer study. Methods:Previously we proposed a concept CoMi(Context Specific miRNA activity), which could quantify the regulation activity of miRNA on specific context(CoMi activity) by calculating the statistical difference of the expression level between the miRNA targets and non-targets in a given context(GO term biological process),and demonstrated its application on predicting *** we extend this concept to CoMi module and use it to predict whether the cancer will metastasize to ***,CoMi features which are significant associated with the bone metastasis are identified by Cox proportional hazards regression. Based on the significant CoMi features,miRNAs regulate on the same context are regarded as a significant miRNA regulation *** each significant CoMi module is used to predict bone metastasis of breast cancer patients by sum up all the risk scores(Cox proportional hazards regression) of CoMi features in the module. Results:We tested the proposed method on a breast cancer cohort contain 855 samples' gene expression profiles together with bone metastasis *** bone metastasis specific CoMi modules are identified,such as module 'hemopoiesis',which has a log rank p value of 9.05e-07 in train dataset,0.0075 in test dataset and 0.0031 in independent test dataset. Considering the hematopoietic stem cell niche is a potential therapeutic target for bone metastatic tumors,our results might facilitate to identify the miRNAs regulation modules involved in hematopoietic stem cell niche. Conclusions:We proposed the concept of CoMi activity module,and identified some CoMi activity modules which could predict bone metas

关键词： Context specific miRNA activity metastasis organ prediction miRNA regulation network

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[Correlations between clusters of protein-DNA binding sites and the binding experimental data allow to predict a structure of regulatory modules].

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Biofizika 2012年第2期57卷 212-214页

作者： Nikulova, A.A. Polishchuk, M.S. Tumanian, V.G. Makeev, V.I. Mironov, A.A. Favorov, A.V. Department of Bioengineering and Bioinformatics Moscow State University Moscow Russia Institute of Problems of Data Transmission Russian Academy of Sciences Moscow Russia Engelhardt Institute of Molecular Biology Russian Academy of Sciences Moscow Russia University of California Berkeley Berkeley USA Vavilov Institute of General Genetics Russian Academy of Sciences Moscow Russia State Research Institute for Genetics and Selection of Industrial Microorganisms «GosNIIgenetika» Moscow Russia The Sidney Kimmel Cancer Center at Johns Hopkins University Baltimore Baltimore USA

Here we analyzed an option to predict the structure of cis-regulatory modules that consist of binding sites of different proteins (heterogeneous cis-regulatory modules) using mutual positional correlations between protein-DNA binding experimental data and computationally identified clusters of binding sites for each of the proteins.

关键词： binding site cluster ChIP-chip ChIP-Seq cis-regulatory module CORE-CLUST CRM GenometriCorr PatternClust

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Allogeneic Hematopoietic Stem Cell Transplantation Is Feasible After Solid Organ Transplantation: A Retrospective Analysis By The Early Complications Subcommittee Of The Complications and Quality Of Life Working Party, EBMT

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BLOOD 2013年第21期122卷 2110-2110页

作者： Basak, Grzegorz W. Jedrzejczak, Wieslaw W. Schoemans, Helene Ljungman, Per T. Kobbe, Guido Beguin, Yves Lang, Peter Sykora, Karl-Walter te Boome, Liane C. J. van Biezen, Anja van der Werf, Steffie Mohty, Mohamad de Witte, Theo Marsh, Judith Dreger, Peter Kroeger, Nicolaus Duarte, Rafael F. Ruutu, Tapani Department of Hematology Oncology and Internal Diseases Medical University of Warsaw Warsaw Poland Hem./Onc. & Internal Diseases The Medical University of Warsaw Warsaw Poland University Hospital Gasthuisberg Leuven Belgium Centre for Allogeneic Stem Cell Transplantation Karolinska University Hospital Huddinge Stockholm Sweden Heinrich Heine Universität Düsseldorf Germany Service d'Hématologie Clinique CHU de Liège Liège Belgium Department of Pediatric Oncology University Children´s Hospital Tuebingen Germany Department of Pediatric Hematology/Oncology Hannover Medical School Hannover Germany Hematology UMCU Utrecht Netherlands Department of Medical Statistics and Bioinformatics Leiden University Medical Centre Leiden Netherlands EBMT Data Office Leiden Netherlands EBMT Acute Leukemia Working Party and Registry Hospital Saint-Antoine Paris University Paris France University Medical Centre St. Radboud Nijmegen Netherlands Hematological Medicine King's College Hospital NHS Foundation Trust London United Kingdom Medizinische Klinik und Poliklinik V Universitätsklinikum Heidelberg Germany Center of Oncology - Bone Marrow Transplantation Unit Chairman of CMWP University Medical Center Hamburg-Eppendorf Hamburg Germany Clinical Hematology Catalan Institute of Oncology Barcelona Spain University Hospital Helsinki Finland

2110

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Whole Genome Gene Discovery in the Pathogenic Oomycete Pythium insidiosum by 454 Sequencing Technology

Whole Genome Gene Discovery in the Pathogenic Oomycete Pythi...

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The Annual Oomycete Molecular Genetics Network Meeting(国际卵菌分子遗传学年会)

作者： Theerapong Krajaejun Shoba Ranganathan Rommanee Khositnithikul Tassanee Lerksuthirat Tassanee Lowhnoo Thidarat Rujirawat Wanta Yingyong Prapat Suriyaphol Sittichoke Tangphatsornruang Gagan Garg Department of Pathology Mahidol University Bangkok Department of Chemistry and Biomolecular Sciences Macquarie University Australia Molecular Medicine Program Multidisciplinary Unit Faculty of Science Mahidol University Bangkok Research Center Faculty of Medicine Ramathibodi HospitalMahidol University Bangkok Bioinformatics and Data Management for Research Office for Research and Development Faculty of Medicine Siriraj Hospital Mahidol University Bangkok Genome Sequencing Laboratory National Center for Genetic Engineering and Biotechnology National Science and Technology Development Agency PathumthaniThailand

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data decomposition in biomedical e-Science applications

Data decomposition in biomedical e-Science applications

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7th IEEE International Conference on e-Science Workshops, eScienceW 201

作者： Mohammed, Yassene Shahand, Shayan Korkhov, Vladimir Luyf, Angela C.M. Van Schaik, Barbera D.C. Caan, Matthan W.A. Van Kampen, Antoine H.C. Palmblad, Magnus Olabarriaga, Silvia D. Bioinformatics Laboratory Department of Clinical Epidemiology Biostatistics and Bioinformatics University of Amsterdam Netherlands Biomolecular Mass Spectrometry Unit Department of Parasitology Leiden University Medical Center Netherlands Regional Computing Center for Lower Saxony and L3S University of Hannover Germany Faculty of Applied Math and Control Processes St. Petersburg State University Russia Department of Radiology AMC University of Amsterdam Netherlands Biosystems Data Analysis Swammerdam Institute for Life Sciences University of Amsterdam 1098 XH Amsterdam Netherlands

ISBN: (纸本)9780769545981

As the focus of e-Science is moving toward the forth paradigm and data intensive science, data access remains dependent on the architecture of the used e-Science infrastructure. Such architecture is in general job-driven, i.e., a (grid) job is a sequence of commands that run on the same worker node. Making use of the infrastructure involves having a parallelized application. This is done foremost by data decomposition. In general practice of parallel programming, data decomposition depends on the programmer's experience and knowledge about the used data and the algorithm/application. On the other hand, data mining scientists have an established foundation for data decomposition, automatic decomposition methods are already in use, methodologies and patterns are defined. Our experience in porting biomedical applications to the Dutch e-Science infrastructure shows that the used data decomposition to gain parallelism fit to some degree a subgroup of the data mining decomposition patterns, i.e., object set decomposition. In this paper we discuss porting three biomedical packages to a grid computing environment, two for medical imaging and one for DNA sequencing. We show how the data access of the applications was reengineered around the executables to make use of the parallel capacity of e-Science infrastructure. © 2011 IEEE.

关键词： Grid computing

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Dynamic remodeling of context-specific miRNAs regulation networks facilitate in silico cancer drug screening

Dynamic remodeling of context-specific miRNAs regulation net...

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IEEE International Conference on Systems Biology

作者： Lida Zhu Fengji Liang Juan Liu Simon Rayner Yinghui Li Shanguang Chen Jianghui Xiong School of Computer Science Wuhan University Wuhan China Bioinformatics Group and Data Coordination Center State Key Laboratory of Space Medicine Fundamentals and Application (SMFA) China Astronaut Research and Training Center Beijing China Bioinformatics Group State Key Laboratory of Virology Wuhan Institute of Virology Chinese Academy of Sciences (CAS) Wuhan China

Background: Much effort has been expended in exploring the connections between transcriptome, disease and drug, based on the premise that drug induced perturbations in the transcriptome will affect the phenotype and finally help to cure a disease. MicroRNAs (miRNAs) play a key role in the regulation of the transcriptome and have been identified as a key mediator in human disease and drug response. However, even if miRNA expression can be precisely detected, the information regarding miRNAs action on a particular part of the transcriptome is still lacking. Here, we introduced a novel concept, the Context-specific MiRNA activity (CoMi activity), to reflect a miRNA's regulation effect on a context specific gene set, by calculating the statistical difference between the distributions of its target gene expression and non-target gene expression. In this study we investigate whether CoMi activity could provide a novel perspective on miRNA mechanisms of action in disease and drug response, and facilitate in silico drug screening. Results: Using breast cancer as an example, we examined the CoMi activity based on a Gene Ontology (GO) term as context. Then we constructed a differential CoMi activity network (cancer vs. normal), based on the comi activity represents as a link between miRNAs and GO terms, (e.g. hsa-miR-27a's regulation on GO term "apoptosis"). The topological analysis of the generated network demonstrated that the cancer specific CoMi network is a scale free network. The highly connected nodes highlighted a group of known onco-miRNAs (e.g. hsa miR-183*) and tumor suppressor miRNAs (e.g. hsa-miR-34a), as well as some well-known cancer related GO biological processes (e.g. apoptosis). Interestingly, we found that chemotherapeutic drug treatment can counteract the dis regulated CoMi activity in the cancer-specific network. For instance, 100% of down-regulated CoMi activities in a "core" breast cancer network contains apoptosis-related GO terms that could be counte

关键词： Drugs Gene expression Breast cancer Libraries Silicon Indexes

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Novel network pharmacology methods for drug mechanism of action identification,pre-clinical drug screening and drug repositioning

Novel network pharmacology methods for drug mechanism of act...

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中国药理学会第十一次全国学术会议

作者： XIONG Jiang-hui Simon RAYNER TIAN Ze Bioinformatics Group and Data Coordination Center State Key Lab of Space Medicine Fundamentals and Application China Astronaut Research and Training Center Beijing China Bioinformatics Group State Key Laboratory of Virology Wuhan Institute of Virology Chinese Academy of Sciences Wuhan China Department of Medical Oncology Dana-Farber Cancer Institute Harvard Medical School Boston Massachusetts USA

The high rates of failure in oncology drug clinical trials highlight the problems of using pre-clinical data to predict the clinical effects of *** we present two methodology innovations on network pharmacology modeling.(1) We hypothesize that the gene network associated with cancer outcome in heterogeneous patient populations could serve as a reference for identifying drug *** proposed a novel in vivo genetic interaction between genes as 'synergistic outcome determination' in a similar way to 'ynthetic lethality'.We scanned above genetic interactions based on microarray profiling for cancer prognosis, and identified a cluster of important yet epigenetically regulated gene *** projecting drug sensitivity-associated genes on to this network, we could define a perturbation index for each drug based upon its characteristic perturbation ***, by using this index, we significantly discriminated successful drugs from the candidate pool, and revealed the mechanisms of drug ***, the prognosis-guided synergistic gene-gene interaction networks could serve as an efficient in silico tool for pre-clinical drug prioritization and rational design of combinatorial *** of this work was published, and we will present new results on this project.(2) MicroRNAs (miRNAs) play a key role in the regulation of the transcriptome and have been identified as a key mediator in human disease and drug *** introduced a novel concept, the Context-specific MiRNA activity (CoMi activity), to reflect a miRNA's regulation effect on a context specific gene *** breast cancer as an example, we examined the CoMi activity based on a Gene Ontology (GO) term as ***, we found that chemotherapeutic drug treatment can counteract the dis-regulated CoMi activity in the cancer-specific *** instance, 100% of down-regulated CoMi activities in a " core" breast cancer network contains apoptosis

关键词： network pharmacology microRNA in silico drug screening network biology drug repositioning

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Context-specific miRNA regulation network predicts cancer prognosis

Context-specific miRNA regulation network predicts cancer pr...

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IEEE International Conference on Systems Biology

作者： Xionghui Zhou Juan Liu Changning Liu Simon Rayner Fengji Liang Jingfang Ju Yinghui Li Shanguang Chen Jianghui Xiong School of Computer Science Wuhan University Wuhan China Bioinformatics Research Group Key Laboratory of Intelligent Information Processing Advanced Computing Research Laboratory Institute of Computing Technology Chinese Academy of Sciences (CAS) Beijing China Bioinformatics Group State Key Laboratory of Virology Wuhan Institute of Virology Chinese Academy of Sciences (CAS) Wuhan China Bioinformatics Group and Data Coordination Center State Key Laboratory of Space Medicine Fundamentals and Application China Astronaut Research and Training Center Beijing China Department of Pathology Stony Brook University Medical Center New York USA

MicroRNAs can regulate hundreds of target genes and play a pivotal role in a broad range of biological process. However, relatively little is known about how these highly connected miRNAs-target networks are remodelled in the context of various diseases. Here we examine the dynamic alteration of context-specific miRNA regulation to determine whether modified microRNAs regulation on specific biological processes is a useful information source for predicting cancer prognosis. A new concept, Context-specific miRNA activity (CoMi activity) is introduced to describe the statistical difference between the expression level of a miRNA's target genes and non-targets genes within a given gene set (context).

关键词： Breast cancer Context Correlation Biological processes Metastasis Tumors

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