Dissecting gene regulatory networks in vertebrate development using genomic and proteomic approaches

... also involves studying gene interactions at the transcriptional regulatory level and at protein interaction level GRNs for certain lineage specification have been mapped in detail in invertebrate ... urchin and in certain in vitro model systems for vertebrates Studying GRNs in vertebrate development poses various challenges, arising from the complexity of the genome and the body plans of vertebrates ... the development of novel approaches to study GRNs in development Developments in transgenic methods, genomic and proteomic technologies have opened new vistas for exploring gene regulatory networks...

Using computational approach in understanding gene regulatory networks for antimicrobial peptide coding genes

... promoter data for (Chapter 7) a) detection of new co-regulated genes, and b) deciphering parts of gene networks of which AMP genes are members 1.4 Contribution of this thesis AMP -coding genes and ... region analysis to find new AMP genes and co-regulated genes is a first of its kind approach in the field of antimicrobial peptides The results of this analysis can guide the way for experimental ... these groups of genes, gene discovery efforts have been undertaken by many groups For example, efforts were directed to the computational discovery of beta defensin producing genes (Scheetz et...

Báo cáo y học: "Construction of Gene Regulatory Networks using biclustering and Bayesian networks" docx

... Construction of Gene Regulatory Networks using biclustering and Bayesian networks Fadhl M Alakwaa1*§, Nahed H Solouma and Yasser M Kadah3* University of Science and Technology, Sana'a, Yemen Department of ... supported by a grant from the University of Science & Technology, Yemen The authors would like to thank Prof Dana Pe'er, Columbia University; Dr Kevien Yip, Yale University and Prof G Stolovitzky, IBM ... Figure ROC and PR curves of different biclustering networks that have learned using Bayesian networks [29] A performance comparison of networks generated from learning corresponding biclustering...

Báo cáo hóa học: " Probabilistic polynomial dynamical systems for reverse engineering of gene regulatory networks" docx

... introduce a stochastic generalization of polynomial dynamical systems, namely, probabilistic polynomial dynamical systems, which is also a generalization of the above-mentioned probabilistic Boolean ... models In the next section, we present our method for the reverse engineering of gene regulatory networks as probabilistic polynomial dynamical systems Then we demonstrate this method using the ... provide a systematic method for the reverse engineering of gene regulatory networks as probabilistic Boolean nested canalyzing networks Appendices Polynomial dynamical systems Definition 1.1 Let...

Báo cáo hóa học: " Research Article Inference of Gene Regulatory Networks Based on a Universal Minimum Description Length" pot

... Inference, Morgan Kaufmann, San Francisco, Calif, USA, 1988 [2] N Friedman, M Linial, I Nachman, and D Pe’er, “Using Bayesian networks to analyze expression data,” Journal of Computational Biology, ... O Yli-Harja, and J Astola, Inference of genetic regulatory networks via best-ﬁt extensions,” in Computational and Statistical Approaches to Genomics, pp 197–210, chapter 11, Kluwer Academic ... 147–167, 2003 [15] A A Margolin, I Nemenman, K Basso, et al., “ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context,” BMC Bioinformatics, vol 7,...

Báo cáo hóa học: " Research Article Reverse Engineering of Gene Regulatory Networks: A Comparative Study" ppt

... Island of Hawaii, Hawaii, USA, January 1999 [6] K Basso, A A Margolin, G Stolovitzky, U Klein, R DallaFavera, and A Califano, Reverse engineering of regulatory networks in human B cells,” Nature ... Unfortunately, there are not enough gold standard networks and appropriate experimental data available for a large comparative study For such a study one needs a sufficiently large amount of data of different ... simulated data and presented a framework for testing microarray data analysis tools An artificial data generator has to be independent of the reverse engineering algorithms to avoid a bias in the test...

Báo cáo hóa học: " Research Article Uncovering Gene Regulatory Networks from Time-Series Microarray Data with Variational Bayesian Structural Expectation Maximization" doc

... dynamic Bayesian networks formulation, our work has two objectives First, given a set of time-series data from a single experiment, we aim at uncovering the underlying gene regulatory networks ... inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks, ” Bioinformatics, vol 19, no 17, pp 2271–2282, 2003 [23] K P Murphy, Dynamic Bayesian networks: ... e Bayesian networks, ” Bioinformatics, vol 19, supplement 2, pp ii138–ii148, 2003 [18] S Y Kim, S Imoto, and S Miyano, “Inferring gene networks from time series microarray data using dynamic Bayesian...

Báo cáo hóa học: " Research Article Comparison of Gene Regulatory Networks via Steady-State Trajectories" pdf

... concentrations of mRNA and proteins induced by gene i, respectively, ci (t) is the fraction of DNA fragments committed to transcription of gene i, κi is the transcription rate of gene i, and τ ... transcriptional regulatory system (tRS) We generate networks using this model and a ﬁxed set θ of parameters We call these networks reference networks A reference network is identiﬁed by its set θ of parameters, ... straightforward simulation consists of the design of a reference network, the design of a projected network (for some value of Δx ), the generation of several trajectories for both networks from randomly...

Báo cáo y học: "Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes." potx

... is defined physically by the extent of long-range regulatory elements around its target gene Therefore, the combined synteny of HCNEs and the intertwined genes defines a minimal span of the GRB ... by a synteny- maintaining array of HCNEs [25], many of which were shown to act as the gene's regulatory inputs [6,26], often intertwined with other, unrelated (bystander) genes [9] To trace the ... that their study is inextricably bound to the WGD events in Metazoa, and that the most illuminating approach to studying their evolutionary history and the relationship between genes and their regulatory...

báo cáo khoa học: " Investigation of post-transcriptional gene regulatory networks associated with autism spectrum disorders by microRNA expression profiling of lymphoblastoid cell lines" pps

... Prediction of mammalian microRNA targets Cell 2003, 115:787-798 doi:10.1186/gm144 Cite this article as: Sarachana T, et al.: Investigation of post-transcriptional gene regulatory networks associated with ... post-transcriptional gene regulatory networks associated with autism spectrum disorders by microRNA expression profiling of lymphoblastoid cell lines Genome Medicine 2010, 2:23 ... levels of target genes that, in turn, may be associated with the underlying pathophysiology of ASD, and to provide a better understanding of the role of miRNAs as a post-transcriptional gene regulatory...

báo cáo khoa học: " Characterization of WRKY co-regulatory networks in rice and Arabidopsis" ppsx

... AtWRKY33 AtWRKY18 AtWRKY40 AtWRKY22 AtWRKY46 or AtWRKY53 AtWRKY75 AtWRKY46 or AtWRKY53 AtWRKY69 AtWRKY6 or AtWRKY31 AtWRKY46 AtWRKY54 or AtWRKY70 AtWRKY54 or AtWRKY70 AtWRKY26 or AtWRKY2 AtWRKY34 ... OsWRKY4 OsWRKY18 OsWRKY43 OsWRKY61 OsWRKY71 OsWRKY87 OsWRKY100 OsWRKY112 M oryzae BR32 OsWRKY4 OsWRKY18 OsWRKY40 OsWRKY43 OsWRKY61 OsWRKY64 OsWRKY87 OsWRKY100 OsWRKY112 M oryzae FR13 OsWRKY4 OsWRKY53 ... single zinc finger motif of a small subset of WRKY proteins is distinct from that of group and members Instead of a C2H2 pattern, their WRKY domains contain a C2HC motif As a result of this distinction,...

Báo cáo y học: " Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics" potx

... mammals and yeast, is not straightforward in plants Similarly, studying cooperative TFBSs within regulatory modules also suffers from the inclusion of potentially false-positives when selecting genes ... identified using twoway clustering Additional data file is a table giving an overview of the 139 cis -regulatory modules Additional data file is a table showing the motif order and spacing for 30 cis -regulatory ... Grad YH, Roth FP, Halfon MS, Church GM: Prediction of similarly acting cis -regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D pseudoobscura Bioinformatics...

Functional study of MicroRNA 125b in vertebrate development 1

... Biogenesis of microRNAs 1. 1.3 Targets of microRNAs 1. 2 The role of microRNAs in development 1. 2 .1 microRNA functions in embryogenesis 1. 2.2 microRNA functions in stem cell development 1. 2.3 microRNA ... functions in neurogenesis 1. 3 microRNAs in diseases 11 1. 4 The expression and known functions of miR -12 5b 14 1. 5 Motivation of the thesis 18 1. 6 Objectives of the thesis 19 1. 7 Project workflow 19 Chapter ... prospective 94 10 7 5 .1 The function of miR -12 5b in differentiation of neuronal cells 10 7 5.2 The function of miR -12 5b in regulating p53 and p53 dependentapoptosis 5.3 A global view of miR -12 5b regulatory...

Functional study of MicroRNA 125b in vertebrate development 2

... 95%, n = 85 m 125 bMO + p53MO m 125 bMO * * 98%, n = 1 12 100%, n = 114 * lp 125 bMO1 /2/ 3 in p53M214K mutant 100%, n = 113 * lp 125 bMO1 /2/ 3 + p53MO lp 125 bMO1 /2/ 3 Figure 20 - Rescue of miR - 125 b morphants ... Log2 fold change in miR - 125 b level 8 ** -2 -4 ** 125 b- AS NC-AS1 125 b- DP NC-DP2 -6 Mock b Log2 fold change in miR - 125 b level a Figure 14 - Validation of miR - 125 b overexpression and knockdown in ... cells in the 24 -hpf brains: embryos were injected with a standard negative control morpholino, miR - 125 b duplex ( 125 b- DP), m 125 bMO or lp 125 bMO1 /2/ 3 Two different concentrations of 125 b- DP ( 12. 5...

Detection of actual and assessment of potential plantations in Lao PDR using GIS and remote sensing technologies doc

... ii Rubber in Laos Detection of actual and assessment of potential plantations in Lao PDR using GIS and remote sensing technologies Diplomarbeit der Philosophisch-naturwissenschaftlichen ... regarding decision-making and elaboration of development strategies Using my GIS and Remote Sensing competence and my fascination for the possibilities offered by spatial data and modelling approaches, ... Analysis of land use and land cover changes 3.2 25 34 A spatial assessment of the potential development of rubber plantations in Laos 51 3.2.1 Reasons for the necessity of potential rubber mapping in...

Xem thêm

Từ khóa: using eqtls to reconstruct gene regulatory networks learning gene regulatory networks from only positive and unlabeled data analysis of transcriptional regulatory networks in cancer research regulatory considerations in product development for back of the eye reconstruction of gene regulatory networks amp gene regulatory networks practical software development using uml and java pdf production networks in the asiapacific region facts and policy implications mobile application development using html5 and javascript objectoriented software engineering practical software development using uml and java pdf web development using html5 and css3 java ee 6 development using glassfish and eclipse webservices in java example using eclipse and jboss website development using php and mysql dynamic web application development using xml and java by david parsons pdf Nghiên cứu sự hình thành lớp bảo vệ và khả năng chống ăn mòn của thép bền thời tiết trong điều kiện khí hậu nhiệt đới việt nam Nghiên cứu tổ hợp chất chỉ điểm sinh học vWF, VCAM 1, MCP 1, d dimer trong chẩn đoán và tiên lượng nhồi máu não cấp Nghiên cứu vật liệu biến hóa (metamaterials) hấp thụ sóng điện tử ở vùng tần số THz Nghiên cứu tổ chức chạy tàu hàng cố định theo thời gian trên đường sắt việt nam Biện pháp quản lý hoạt động dạy hát xoan trong trường trung học cơ sở huyện lâm thao, phú thọ Giáo án Sinh học 11 bài 13: Thực hành phát hiện diệp lục và carôtenôit Giáo án Sinh học 11 bài 13: Thực hành phát hiện diệp lục và carôtenôit Giáo án Sinh học 11 bài 13: Thực hành phát hiện diệp lục và carôtenôit NGHIÊN CỨU CÔNG NGHỆ KẾT NỐI VÔ TUYẾN CỰ LY XA, CÔNG SUẤT THẤP LPWAN SLIDE Nghiên cứu khả năng đo năng lượng điện bằng hệ thu thập dữ liệu 16 kênh DEWE 5000 Tìm hiểu công cụ đánh giá hệ thống đảm bảo an toàn hệ thống thông tin Thiết kế và chế tạo mô hình biến tần (inverter) cho máy điều hòa không khí Sở hữu ruộng đất và kinh tế nông nghiệp châu ôn (lạng sơn) nửa đầu thế kỷ XIX Chuong 2 nhận dạng rui ro Tranh tụng tại phiên tòa hình sự sơ thẩm theo pháp luật tố tụng hình sự Việt Nam từ thực tiễn xét xử của các Tòa án quân sự Quân khu (Luận văn thạc sĩ)chuong 1 tong quan quan tri rui ro Nguyên tắc phân hóa trách nhiệm hình sự đối với người dưới 18 tuổi phạm tội trong pháp luật hình sự Việt Nam (Luận văn thạc sĩ)BÀI HOÀN CHỈNH TỔNG QUAN VỀ MẠNG XÃ HỘI Chiến lược marketing tại ngân hàng Agribank chi nhánh Sài Gòn từ 2013-2015 MÔN TRUYỀN THÔNG MARKETING TÍCH HỢP