scholarly journals Dempster-Shafer Theory for the Prediction of Auxin-Response Elements (AuxREs) in Plant Genomes

2018 ◽  
Vol 2018 ◽  
pp. 1-13 ◽  
Author(s):  
Nesrine Sghaier ◽  
Rayda Ben Ayed ◽  
Riadh Ben Marzoug ◽  
Ahmed Rebai
Keyword(s):  
Data Fusion ◽  
Transcriptional Activation ◽  
False Positive ◽  
Fuzzy Theory ◽  
Regulation Of Gene Expression ◽  
Evidence Theory ◽  
Regulatory Elements ◽  
Auxin Response ◽  
Shafer Theory ◽  
Comparison Of The Results

Auxin is a major regulator of plant growth and development; its action involves transcriptional activation. The identification of Auxin-response element (AuxRE) is one of the most important issues to understand the Auxin regulation of gene expression. Over the past few years, a large number of motif identification tools have been developed. Despite these considerable efforts provided by computational biologists, building reliable models to predict regulatory elements has still been a difficult challenge. In this context, we propose in this work a data fusion approach for the prediction of AuxRE. Our method is based on the combined use of Dempster-Shafer evidence theory and fuzzy theory. To evaluate our model, we have scanning the DORNRÖSCHEN promoter by our model. All proven AuxRE present in the promoter has been detected. At the 0.9 threshold we have no false positive. The comparison of the results of our model and some previous motifs finding tools shows that our model can predict AuxRE more successfully than the other tools and produce less false positive. The comparison of the results before and after combination shows the importance of Dempster-Shafer combination in the decrease of false positive and to improve the reliability of prediction. For an overall evaluation we have chosen to present the performance of our approach in comparison with other methods. In fact, the results indicated that the data fusion method has the highest degree of sensitivity (Sn) and Positive Predictive Value (PPV).

scholarly journals A revised model for promoter competition based on multi-way chromatin interactions at the α-globin locus

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
A. Marieke Oudelaar ◽  
Caroline L. Harrold ◽  
Lars L. P. Hanssen ◽  
Jelena M. Telenius ◽  
Douglas R. Higgs ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Regulation Of Gene Expression ◽  
Regulatory Elements ◽  
Chromatin Domain ◽  
Gene Promoters ◽  
Multiple Promoters ◽  
Chromatin Interactions ◽  
Technological Advances ◽  
Single Complex ◽  
Membrane Bound

AbstractSpecific communication between gene promoters and enhancers is critical for accurate regulation of gene expression. However, it remains unclear how specific interactions between multiple regulatory elements contained within a single chromatin domain are coordinated. Recent technological advances which can detect multi-way chromatin interactions at single alleles can provide insights into how multiple regulatory elements cooperate or compete for transcriptional activation. Here, we use such an approach to investigate how interactions of the α-globin enhancers are distributed between multiple promoters in a mouse model in which the α-globin domain is extended to include several additional genes. Our data show that gene promoters do not form mutually exclusive interactions with enhancers, but all interact simultaneously in a single complex. These findings suggest that promoters do not structurally compete for interactions with enhancers, but form a regulatory hub structure, which is consistent with recent models of transcriptional activation occurring in non-membrane bound nuclear compartments.

Application of the Data Fusion Method Based on Fuzzy Theory and Evidence Theory in Vehicle Recognition

2012 ◽  
Vol 546-547 ◽  
pp. 661-665
Author(s):  
Yu Xin Liu ◽  
Xu Jia
Keyword(s):  
Data Fusion ◽  
Fuzzy Theory ◽  
Evidence Theory ◽  
Experimental Results ◽  
Identification Accuracy ◽  
Fusion Method ◽  
Simulation Research ◽  
Vehicle Recognition ◽  
Vehicle Type ◽  
Single Sensor

A data fusion method which based on fuzzy theory and evidence theory was discussed in this paper， and it is applied to the vehicle type recognition simulation research using some multi-sensor characteristics such as the appearance and the length of the vehicle. The experimental results show that this method can avoid the limitation of single sensor, reduce the sensors uncertainty, and improve the identification accuracy.

scholarly journals A revised model for promoter competition based on multi-way chromatin interactions

2019 ◽  
Author(s):  
A. Marieke Oudelaar ◽  
Caroline L. Harrold ◽  
Lars L. P. Hanssen ◽  
Jelena M. Telenius ◽  
Douglas R. Higgs ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Regulation Of Gene Expression ◽  
Regulatory Elements ◽  
Chromatin Domain ◽  
Gene Promoters ◽  
Multiple Promoters ◽  
Chromatin Interactions ◽  
Super Enhancer ◽  
Technological Advances ◽  
Single Complex

AbstractSpecific communication between gene promoters and enhancers is critical for accurate regulation of gene expression. However, it remains unclear how specific interactions between multiple regulatory elements and genes contained within a single chromatin domain are coordinated. Recent technological advances allow for the investigation of multi-way chromatin interactions at single alleles in individual nuclei. This can provide insights into how multiple regulatory elements cooperate or compete for transcriptional activation. We have used these techniques in a mouse model in which the α-globin domain is extended to include several additional genes. This allows us to determine how the interactions of the α-globin super-enhancer are distributed between multiple promoters in a single domain. Our data show that gene promoters do not form mutually exclusive interactions with the super-enhancer, but all interact simultaneously in a single complex. These finding show that promoters within the same domain do not structurally compete for interactions with enhancers, but form a regulatory hub structure, consistent with the recent model of transcriptional activation in phase-separated nuclear condensates.

scholarly journals Measuring the Uncertainty in the Original and Negation of Evidence Using Belief Entropy for Conflict Data Fusion

Entropy ◽  
2021 ◽  
Vol 23 (4) ◽  
pp. 402
Author(s):  
Yutong Chen ◽  
Yongchuan Tang
Keyword(s):  
Information Processing ◽  
Data Fusion ◽  
Evidence Theory ◽  
Uncertain Information ◽  
Dempster Shafer Theory ◽  
Open World ◽  
Uncertainty Measurement ◽  
Basic Probability ◽  
Shafer Theory ◽  
Deng Entropy

Dempster-Shafer (DS) evidence theory is widely used in various fields of uncertain information processing, but it may produce counterintuitive results when dealing with conflicting data. Therefore, this paper proposes a new data fusion method which combines the Deng entropy and the negation of basic probability assignment (BPA). In this method, the uncertain degree in the original BPA and the negation of BPA are considered simultaneously. The degree of uncertainty of BPA and negation of BPA is measured by the Deng entropy, and the two uncertain measurement results are integrated as the final uncertainty degree of the evidence. This new method can not only deal with the data fusion of conflicting evidence, but it can also obtain more uncertain information through the negation of BPA, which is of great help to improve the accuracy of information processing and to reduce the loss of information. We apply it to numerical examples and fault diagnosis experiments to verify the effectiveness and superiority of the method. In addition, some open issues existing in current work, such as the limitations of the Dempster–Shafer theory (DST) under the open world assumption and the necessary properties of uncertainty measurement methods, are also discussed in this paper.

scholarly journals The role of the epidermis enhancer element in positive and negative transcriptional regulation of ebony in Drosophila melanogaster

2022 ◽  
Author(s):  
Noriyoshi Akiyama ◽  
Shoma Sato ◽  
Kentaro M Tanaka ◽  
Takaomi Sakai ◽  
Aya Takahashi
Keyword(s):  
Expression Pattern ◽  
Transcriptional Activation ◽  
Regulation Of Gene Expression ◽  
Regulatory Elements ◽  
Enhancer Element ◽  
Pigment Synthesis ◽  
Endogenous Expression ◽  
Spatiotemporal Regulation ◽  
Dark Pigmentation ◽  
In The Wild

Abstract The spatiotemporal regulation of gene expression is essential to ensure robust phenotypic outcomes. Pigmentation patterns in Drosophila are determined by pigments biosynthesized in the developing epidermis and the cis-regulatory elements (CREs) of the genes involved in this process are well-characterized. Here we report that the known primary epidermal enhancer (priEE) is dispensable for the transcriptional activation of ebony (involved in light-colored pigment synthesis) in the developing epidermis of D. melanogaster. The evidence was obtained by introducing an approximately 1 kbp deletion at the priEE by genome editing. The effect of the priEE deletion on pigmentation and on the endogenous expression pattern of a mCherry-fused ebony allele was examined in the abdomen. The expression levels of the mCherry-fused ebony in the priEE-deleted strains were slightly higher than that of the control strain, indicating that the sequences outside the priEE have an ability to drive an expression of this gene in the epidermis. Interestingly, the priEE deletion resulted in a derepression of this gene in the dorsal midline of the abdominal tergites, where dark pigmentation is present in the wild-type individuals. This indicated that the priEE fragment contains a silencer. Furthermore, the endogenous expression pattern of ebony in the two additional strains with partially deleted priEE revealed that the silencer resides within a 351-bp fragment in the 5' portion of the priEE. These results demonstrated that deletion assays combined with reporter assays are highly effective in detecting the presence of positively and negatively regulating sequences within and outside the focal CREs.

Decision Support System for Advanced Traffic Management Through Data Fusion

2002 ◽  
Vol 1804 (1) ◽  
pp. 173-178 ◽  
Author(s):  
Lawrence A. Klein ◽  
Ping Yi ◽  
Hualiang Teng
Keyword(s):  
Data Fusion ◽  
Traffic Management ◽  
Information Sources ◽  
Partial Information ◽  
Weather Conditions ◽  
Field Testing ◽  
Traffic Operations ◽  
Dempster Shafer Theory ◽  
Classification Technique ◽  
Shafer Theory

The Dempster–Shafer theory for data fusion and mining in support of advanced traffic management is introduced and tested. Dempste–Shafer inference is a statistically based classification technique that can be applied to detect traffic events that affect normal traffic operations. It is useful when data or information sources contribute partial information about a scenario, and no single source provides a high probability of identifying the event responsible for the received information. The technique captures and combines whatever information is available from the data sources. Dempster’s rule is applied to determine the most probable event—as that with the largest probability based on the information obtained from all contributing sources. The Dempster–Shafer theory is explained and its implementation described through numerical examples. Field testing of the data fusion technique demonstrated its effectiveness when the probability masses, which quantify the likelihood of the postulated events for the scenario, reflect current traffic and weather conditions.

scholarly journals Conflict Data Fusion in a Multi-Agent System Premised on the Base Basic Probability Assignment and Evidence Distance

Entropy ◽  
2021 ◽  
Vol 23 (7) ◽  
pp. 820
Author(s):  
Jingyu Liu ◽  
Yongchuan Tang
Keyword(s):  
Data Fusion ◽  
Evidence Theory ◽  
Multi Agent System ◽  
Agent System ◽  
Combination Rules ◽  
Probability Assignment ◽  
Basic Probability Assignment ◽  
Reasonable Evidence ◽  
Basic Probability ◽  
Multi Agent

The multi-agent information fusion (MAIF) system can alleviate the limitations of a single expert system in dealing with complex situations, as it allows multiple agents to cooperate in order to solve problems in complex environments. Dempster–Shafer (D-S) evidence theory has important applications in multi-source data fusion, pattern recognition, and other fields. However, the traditional Dempster combination rules may produce counterintuitive results when dealing with highly conflicting data. A conflict data fusion method in a multi-agent system based on the base basic probability assignment (bBPA) and evidence distance is proposed in this paper. Firstly, the new bBPA and reconstructed BPA are used to construct the initial belief degree of each agent. Then, the information volume of each evidence group is obtained by calculating the evidence distance so as to modify the reliability and obtain more reasonable evidence. Lastly, the final evidence is fused with the Dempster combination rule to obtain the result. Numerical examples show the effectiveness and availability of the proposed method, which improves the accuracy of the identification process of the MAIF system.

scholarly journals Genome-Wide Identification and Analysis of the APETALA2 (AP2) Transcription Factor in Dendrobium officinale

2021 ◽  
Vol 22 (10) ◽  
pp. 5221
Author(s):  
Danqi Zeng ◽  
Jaime A. Teixeira da Silva ◽  
Mingze Zhang ◽  
Zhenming Yu ◽  
Can Si ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Flower Development ◽  
Regulatory Elements ◽  
Negative Control ◽  
Dendrobium Officinale ◽  
Luciferase Reporter ◽  
Pcr Analysis ◽  
Luciferase Reporter Gene ◽  
Genome Wide ◽  
Ap2 Transcription Factor

The APETALA2 (AP2) transcription factors (TFs) play crucial roles in regulating development in plants. However, a comprehensive analysis of the AP2 family members in a valuable Chinese herbal orchid, Dendrobium officinale, or in other orchids, is limited. In this study, the 14 DoAP2 TFs that were identified from the D. officinale genome and named DoAP2-1 to DoAP2-14 were divided into three clades: euAP2, euANT, and basalANT. The promoters of all DoAP2 genes contained cis-regulatory elements related to plant development and also responsive to plant hormones and stress. qRT-PCR analysis showed the abundant expression of DoAP2-2, DoAP2-5, DoAP2-7, DoAP2-8 and DoAP2-12 genes in protocorm-like bodies (PLBs), while DoAP2-3, DoAP2-4, DoAP2-6, DoAP2-9, DoAP2-10 and DoAP2-11 expression was strong in plantlets. In addition, the expression of some DoAP2 genes was down-regulated during flower development. These results suggest that DoAP2 genes may play roles in plant regeneration and flower development in D. officinale. Four DoAP2 genes (DoAP2-1 from euAP2, DoAP2-2 from euANT, and DoAP2-6 and DoAP2-11 from basal ANT) were selected for further analyses. The transcriptional activation of DoAP2-1, DoAP2-2, DoAP2-6 and DoAP2-11 proteins, which were localized in the nucleus of Arabidopsis thaliana mesophyll protoplasts, was further analyzed by a dual-luciferase reporter gene system in Nicotiana benthamiana leaves. Our data showed that pBD-DoAP2-1, pBD-DoAP2-2, pBD-DoAP2-6 and pBD-DoAP2-11 significantly repressed the expression of the LUC reporter compared with the negative control (pBD), suggesting that these DoAP2 proteins may act as transcriptional repressors in the nucleus of plant cells. Our findings on AP2 genes in D. officinale shed light on the function of AP2 genes in this orchid and other plant species.

scholarly journals Expression of laminin γ 1 cultured hepatocytes involves repeated CTC and GC elements in the LAMC1 promoter

1996 ◽  
Vol 313 (3) ◽  
pp. 745-752 ◽  
Author(s):  
Françoise LEVAVASSEUR ◽  
Jocelyne LIÉTARD ◽  
Kohei OGAWA ◽  
Nathalie THÉRET ◽  
Peter D. BURBELO ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Hepatoma Cell ◽  
Primary Cultures ◽  
Regulatory Elements ◽  
Hepatoma Cells ◽  
Basement Membranes ◽  
Major Protein ◽  
Cultured Hepatocytes

Laminin γ1 chain is present in all basement membranes and is expressed at high levels in various diseases, such as hepatic fibrosis. We have identified cis- and trans-acting elements involved in the regulation of this gene in normal rat liver, as well as in hepatocyte primary cultures and hepatoma cell lines. Northern-blot analyses showed that laminin γ1 mRNA was barely detectable in freshly isolated hepatocytes and expressed at high levels in hepatocyte primary cultures, as early as 4 h after liver dissociation. Actinomycin D and cycloheximide treatment in vivo and in vitro indicated that laminin γ1 overexpression in cultured hepatocytes was under the control of transcriptional mechanisms. Transfection of deletion mutants of the 5´ flanking region of murine LAMC1 gene in hepatoma cells that constitutively express laminin γ1 indicated that regulatory elements were located between -594 bp and -94 bp. This segment included GC- and CTC-containing motifs. Gel-shift analyses showed that two complexes were resolved with different affinity for the CTC sequence depending on the location of the GC box. The pattern of complex formation with nuclear factors from freshly isolated and cultured hepatocytes was different from that obtained with total liver and similar to that with hepatoma cells. Southwestern analysis indicated that several polypeptides bound the CTC-rich sequence. Affinity chromatography demonstrated that a Mr 60000 polypeptide was a major protein binding to the CTC motif. This polypeptide is probably involved in the transcriptional activation of various proto-oncogenes and extracellular matrix genes that are expressed at high levels in both hepatoma cells and early hepatocyte cultures.

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