Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 556

Search results for: gene pair ranking.

556 An SVM based Classification Method for Cancer Data using Minimum Microarray Gene Expressions

Authors: R. Mallika, V. Saravanan

Abstract:

This paper gives a novel method for improving classification performance for cancer classification with very few microarray Gene expression data. The method employs classification with individual gene ranking and gene subset ranking. For selection and classification, the proposed method uses the same classifier. The method is applied to three publicly available cancer gene expression datasets from Lymphoma, Liver and Leukaemia datasets. Three different classifiers namely Support vector machines-one against all (SVM-OAA), K nearest neighbour (KNN) and Linear Discriminant analysis (LDA) were tested and the results indicate the improvement in performance of SVM-OAA classifier with satisfactory results on all the three datasets when compared with the other two classifiers.

Keywords: Support vector machines-one against all, cancerclassification, Linear Discriminant analysis, K nearest neighbour, microarray gene expression, gene pair ranking.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2293
555 A Systems Approach to Gene Ranking from DNA Microarray Data of Cervical Cancer

Authors: Frank Emmert Streib, Matthias Dehmer, Jing Liu, Max Mühlhauser

Abstract:

In this paper we present a method for gene ranking from DNA microarray data. More precisely, we calculate the correlation networks, which are unweighted and undirected graphs, from microarray data of cervical cancer whereas each network represents a tissue of a certain tumor stage and each node in the network represents a gene. From these networks we extract one tree for each gene by a local decomposition of the correlation network. The interpretation of a tree is that it represents the n-nearest neighbor genes on the n-th level of a tree, measured by the Dijkstra distance, and, hence, gives the local embedding of a gene within the correlation network. For the obtained trees we measure the pairwise similarity between trees rooted by the same gene from normal to cancerous tissues. This evaluates the modification of the tree topology due to progression of the tumor. Finally, we rank the obtained similarity values from all tissue comparisons and select the top ranked genes. For these genes the local neighborhood in the correlation networks changes most between normal and cancerous tissues. As a result we find that the top ranked genes are candidates suspected to be involved in tumor growth and, hence, indicates that our method captures essential information from the underlying DNA microarray data of cervical cancer.

Keywords: Graph similarity, DNA microarray data, cancer.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1449
554 University Ranking Systems – From League Table to Homogeneous Groups of Universities

Authors: M. Jarocka

Abstract:

The paper contains a review of the literature in terms of the critical analysis of methodologies of university ranking systems. Furthermore, the initiatives supported by the European Commission (U-Map, U-Multirank) and CHE Ranking are described. Special attention is paid to the tendencies in the development of ranking systems. According to the author, the ranking organizations should abandon the classic form of ranking, namely a hierarchical ordering of universities from “the best" to “the worse". In the empirical part of this paper, using one of the method of cluster analysis called k-means clustering, the author presents university classifications of the top universities from the Shanghai Jiao Tong University-s (SJTU) Academic Ranking of World Universities (ARWU).

Keywords: Classification, cluster analysis, ranking, university.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2397
553 A Combination of Similarity Ranking and Time for Social Research Paper Searching

Authors: P. Jomsri

Abstract:

Nowadays social media are important tools for web resource discovery. The performance and capabilities of web searches are vital, especially search results from social research paper bookmarking. This paper proposes a new algorithm for ranking method that is a combination of similarity ranking with paper posted time or CSTRank. The paper posted time is static ranking for improving search results. For this particular study, the paper posted time is combined with similarity ranking to produce a better ranking than other methods such as similarity ranking or SimRank. The retrieval performance of combination rankings is evaluated using mean values of NDCG. The evaluation in the experiments implies that the chosen CSTRank ranking by using weight score at ratio 90:10 can improve the efficiency of research paper searching on social bookmarking websites.

Keywords: combination ranking, information retrieval, time, similarity ranking, static ranking, weight score

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1415
552 Identification of Complex Sense-antisense Gene's Module on 17q11.2 Associated with Breast Cancer Aggressiveness and Patient's Survival

Authors: O. Grinchuk, E. Motakis, V. Kuznetsov

Abstract:

Sense-antisense gene pair (SAGP) is a pair of two oppositely transcribed genes sharing a common region on a chromosome. In the mammalian genomes, SAGPs can be organized in more complex sense-antisense gene architectures (CSAGA) in which at least one gene could share loci with two or more antisense partners. Many dozens of CSAGAs can be found in the human genome. However, CSAGAs have not been systematically identified and characterized in context of their role in human diseases including cancers. In this work we characterize the structural-functional properties of a cluster of 5 genes –TMEM97, IFT20, TNFAIP1, POLDIP2 and TMEM199, termed TNFAIP1 / POLDIP2 module. This cluster is organized as CSAGA in cytoband 17q11.2. Affymetrix U133A&B expression data of two large cohorts (410 atients, in total) of breast cancer patients and patient survival data were used. For the both studied cohorts, we demonstrate (i) strong and reproducible transcriptional co-regulatory patterns of genes of TNFAIP1/POLDIP2 module in breast cancer cell subtypes and (ii) significant associations of TNFAIP1/POLDIP2 CSAGA with amplification of the CSAGA region in breast cancer, (ii) cancer aggressiveness (e.g. genetic grades) and (iv) disease free patient-s survival. Moreover, gene pairs of this module demonstrate strong synergetic effect in the prognosis of time of breast cancer relapse. We suggest that TNFAIP1/ POLDIP2 cluster can be considered as a novel type of structural-functional gene modules in the human genome.

Keywords: Sense-antisense gene pair, complex genome architecture, TMEM97, IFT20, TNFAIP1, POLDIP2, TMEM199, 17q11.2, breast cancer, transcription regulation, survival analysis, prognosis.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1380
551 Inhibiting Gene for a Late-Heading Gene Responsible for Photoperiod Sensitivity in Rice (Oryza sativa)

Authors: Amol Dahal, Shunsuke Hori, Haruki Nakazawa, Kazumitsu Onishi, Toshio Kawano, Masayuki Murai

Abstract:

Two indica varieties, IR36 and ‘Suweon 258’ (“S”) are middle-heading in southern Japan. 36U, also middle-heading, is an isogenic line of IR36 carrying Ur1 (Undulate rachis-1) gene. However, late-heading plants segregated in the F2 population from the F1 of S × 36U, and so did in the following generations. The concerning lateness gene is designated as Ex. From the F8 generation, isogenic-line pair of early-heading and late-heading lines, denoted by “E” (ex/ex) and “L” (Ex/Ex), were developed. Genetic analyses of heading time were conducted, using F1s and F2s among L, E, S and 36U. The following inferences were drawn from the experimental results: 1) L, and both of E and 36U harbor Ex and ex, respectively; 2) Besides Ex, S harbors an inhibitor gene to it, i.e. I-Ex which is a novel finding of the present study. 3) Ex is a dominant allele at the E1 locus.

Keywords: Basic vegetative phase, heading time, lateness gene, photoperiod-sensitive phase.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1035
550 All Types of Base Pair Substitutions Induced by γ-Rays in Haploid and Diploid Yeast Cells

Authors: Natalia Koltovaya, Nadezhda Zhuchkina, Ksenia Lyubimova

Abstract:

We study the biological effects induced by ionizing radiation in view of therapeutic exposure and the idea of space flights beyond Earth's magnetosphere. In particular, we examine the differences between base pair substitution induction by ionizing radiation in model haploid and diploid yeast Saccharomyces cerevisiae cells. Such mutations are difficult to study in higher eukaryotic systems. In our research, we have used a collection of six isogenic trp5-strains and 14 isogenic haploid and diploid cyc1-strains that are specific markers of all possible base-pair substitutions. These strains differ from each other only in single base substitutions within codon-50 of the trp5 gene or codon-22 of the cyc1 gene. Different mutation spectra for two different haploid genetic trp5- and cyc1-assays and different mutation spectra for the same genetic cyc1-system in cells with different ploidy — haploid and diploid — have been obtained. It was linear function for dose-dependence in haploid and exponential in diploid cells. We suggest that the differences between haploid yeast strains reflect the dependence on the sequence context, while the differences between haploid and diploid strains reflect the different molecular mechanisms of mutations.

Keywords: Base pair substitutions, γ-rays, haploid and diploid cells, yeast Saccharomyces cerevisiae.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 444
549 Ranking Fuzzy Numbers Based on Lexicographical Ordering

Authors: B. Farhadinia

Abstract:

Although so far, many methods for ranking fuzzy numbers have been discussed broadly, most of them contained some shortcomings, such as requirement of complicated calculations, inconsistency with human intuition and indiscrimination. The motivation of this study is to develop a model for ranking fuzzy numbers based on the lexicographical ordering which provides decision-makers with a simple and efficient algorithm to generate an ordering founded on a precedence. The main emphasis here is put on the ease of use and reliability. The effectiveness of the proposed method is finally demonstrated by including a comprehensive comparing different ranking methods with the present one.

Keywords: Ranking fuzzy numbers, Lexicographical ordering.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1560
548 On Internet Access Technology Specification Model

Authors: Samson Okwakol Ariko, Venansius Baryamureeba

Abstract:

Internet Access Technologies (IAT) provide a means through which Internet can be accessed. The choice of a suitable Internet technology is increasingly becoming an important issue to ISP clients. Currently, the choice of IAT is based on discretion and intuition of the concerned managers and the reliance on ISPs. In this paper we propose a model and designs algorithms that are used in the Internet access technology specification. In the proposed model, three ranking approaches are introduced; concurrent ranking, stepwise ranking and weighted ranking. The model ranks the IAT based on distance measures computed in ascending order while the global ranking system assigns weights to each IAT according to the position held in each ranking technique, determines the total weight of a particular IAT and ranks them in descending order. The final output is an objective ranking of IAT in descending order.

Keywords: Internet Access Technology (IAT).

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1138
547 Ranking of Performance Measures of GSCM towards Sustainability: Using Analytic Hierarchy Process

Authors: Dixit Garg, S. Luthra, A. Haleem

Abstract:

During recent years, the natural environment has become a challenging topic that business organizations must consider due to the economic and ecological impacts and increasing awareness of environment protection among society. Organizations are trying to achieve the goals of improvement in environment, low cost, high quality, flexibility and more customer satisfaction. Performance measurement frameworks are very useful to monitor the performance of any organization. The basic goal of this paper is to identify performance measures and ranking of these performance measures of GSCM performance measurement towards sustainability framework. Five perspectives (Environment, Economic, Social, Operational and Cost performances) and nineteen performance measures of GSCM performance towards sustainability have been have been identified from extensive literature review. Analytical Hierarchy Process (AHP) technique has been utilized for ranking of these performance perspectives and measures. All pair comparisons in AHP have been made on the basis on the experts’ opinions (selected from academia and industry). Ranking of these performance perspectives and measures will help to understand the importance of environmental, economic, social, operational performances and cost performances in the supply chain.

Keywords: Analytical Hierarchy Process (AHP), Green Supply Chain Management, Performance Measures (PM), Sustainability.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2915
546 Comparative Study of Universities’ Web Structure Mining

Authors: Z. Abdullah, A. R. Hamdan

Abstract:

This paper is meant to analyze the ranking of University of Malaysia Terengganu, UMT’s website in the World Wide Web. There are only few researches have been done on comparing the ranking of universities’ websites so this research will be able to determine whether the existing UMT’s website is serving its purpose which is to introduce UMT to the world. The ranking is based on hub and authority values which are accordance to the structure of the website. These values are computed using two websearching algorithms, HITS and SALSA. Three other universities’ websites are used as the benchmarks which are UM, Harvard and Stanford. The result is clearly showing that more work has to be done on the existing UMT’s website where important pages according to the benchmarks, do not exist in UMT’s pages. The ranking of UMT’s website will act as a guideline for the web-developer to develop a more efficient website.

Keywords: Algorithm, ranking, website, web structure mining.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1270
545 Comparative Analysis of Different Page Ranking Algorithms

Authors: S. Prabha, K. Duraiswamy, J. Indhumathi

Abstract:

Search engine plays an important role in internet, to retrieve the relevant documents among the huge number of web pages. However, it retrieves more number of documents, which are all relevant to your search topics. To retrieve the most meaningful documents related to search topics, ranking algorithm is used in information retrieval technique. One of the issues in data miming is ranking the retrieved document. In information retrieval the ranking is one of the practical problems. This paper includes various Page Ranking algorithms, page segmentation algorithms and compares those algorithms used for Information Retrieval. Diverse Page Rank based algorithms like Page Rank (PR), Weighted Page Rank (WPR), Weight Page Content Rank (WPCR), Hyperlink Induced Topic Selection (HITS), Distance Rank, Eigen Rumor, Distance Rank Time Rank, Tag Rank, Relational Based Page Rank and Query Dependent Ranking algorithms are discussed and compared.

Keywords: Information Retrieval, Web Page Ranking, search engine, web mining, page segmentations.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 3757
544 Solutions of Fuzzy Transportation Problem Using Best Candidates Method and Different Ranking Techniques

Authors: M. S. Annie Christi

Abstract:

Transportation Problem (TP) is based on supply and demand of commodities transported from one source to the different destinations. Usual methods for finding solution of TPs are North-West Corner Rule, Least Cost Method Vogel’s Approximation Method etc. The transportation costs tend to vary at each time. We can use fuzzy numbers which would give solution according to this situation. In this study the Best Candidate Method (BCM) is applied. For ranking Centroid Ranking Technique (CRT) and Robust Ranking Technique have been adopted to transform the fuzzy TP and the above methods are applied to EDWARDS Vacuum Company, Crawley, in West Sussex in the United Kingdom. A Comparative study is also given. We see that the transportation cost can be minimized by the application of CRT under BCM.

Keywords: Best candidates method, centroid ranking technique, robust ranking technique, transportation problem, fuzzy transportation problem.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 951
543 A New Approach For Ranking Of Generalized Trapezoidal Fuzzy Numbers

Authors: Amit Kumar, Pushpinder Singh, Parampreet Kaur, Amarpreet Kaur

Abstract:

Ranking of fuzzy numbers play an important role in decision making, optimization, forecasting etc. Fuzzy numbers must be ranked before an action is taken by a decision maker. In this paper, with the help of several counter examples it is proved that ranking method proposed by Chen and Chen (Expert Systems with Applications 36 (2009) 6833-6842) is incorrect. The main aim of this paper is to propose a new approach for the ranking of generalized trapezoidal fuzzy numbers. The main advantage of the proposed approach is that the proposed approach provide the correct ordering of generalized and normal trapezoidal fuzzy numbers and also the proposed approach is very simple and easy to apply in the real life problems. It is shown that proposed ranking function satisfies all the reasonable properties of fuzzy quantities proposed by Wang and Kerre (Fuzzy Sets and Systems 118 (2001) 375-385).

Keywords: Ranking function, Generalized trapezoidal fuzzy numbers

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2457
542 Ranking Fuzzy Numbers Based On Epsilon-Deviation Degree

Authors: Vincent F. Yu, Ha Thi Xuan Chi

Abstract:

Nejad and Mashinchi (2011) proposed a revision for ranking fuzzy numbers based on the areas of the left and the right sides of a fuzzy number. However, this method still has some shortcomings such as lack of discriminative power to rank similar fuzzy numbers and no guarantee the consistency between the ranking of fuzzy numbers and the ranking of their images. To overcome these drawbacks, we propose an epsilon-deviation degree method based on the left area and the right area of a fuzzy number, and the concept of the centroid point. The main advantage of the new approach is the development of an innovative index value which can be used to consistently evaluate and rank fuzzy numbers. Numerical examples are presented to illustrate the efficiency and superiority of the proposed method.

Keywords: Ranking fuzzy numbers, Centroid, Deviation degree.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1235
541 An Exploratory Study of Reliability of Ranking vs. Rating in Peer Assessment

Authors: Yang Song, Yifan Guo, Edward F. Gehringer

Abstract:

Fifty years of research has found great potential for peer assessment as a pedagogical approach. With peer assessment, not only do students receive more copious assessments; they also learn to become assessors. In recent decades, more educational peer assessments have been facilitated by online systems. Those online systems are designed differently to suit different class settings and student groups, but they basically fall into two categories: rating-based and ranking-based. The rating-based systems ask assessors to rate the artifacts one by one following some review rubrics. The ranking-based systems allow assessors to review a set of artifacts and give a rank for each of them. Though there are different systems and a large number of users of each category, there is no comprehensive comparison on which design leads to higher reliability. In this paper, we designed algorithms to evaluate assessors' reliabilities based on their rating/ranking against the global ranks of the artifacts they have reviewed. These algorithms are suitable for data from both rating-based and ranking-based peer assessment systems. The experiments were done based on more than 15,000 peer assessments from multiple peer assessment systems. We found that the assessors in ranking-based peer assessments are at least 10% more reliable than the assessors in rating-based peer assessments. Further analysis also demonstrated that the assessors in ranking-based assessments tend to assess the more differentiable artifacts correctly, but there is no such pattern for rating-based assessors.

Keywords: Peer assessment, peer rating, peer ranking, reliability.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 696
540 An Interval Type-2 Dual Fuzzy Polynomial Equations and Ranking Method of Fuzzy Numbers

Authors: Nurhakimah Ab. Rahman, Lazim Abdullah

Abstract:

According to fuzzy arithmetic, dual fuzzy polynomials cannot be replaced by fuzzy polynomials. Hence, the concept of ranking method is used to find real roots of dual fuzzy polynomial equations. Therefore, in this study we want to propose an interval type-2 dual fuzzy polynomial equation (IT2 DFPE). Then, the concept of ranking method also is used to find real roots of IT2 DFPE (if exists). We transform IT2 DFPE to system of crisp IT2 DFPE. This transformation performed with ranking method of fuzzy numbers based on three parameters namely value, ambiguity and fuzziness. At the end, we illustrate our approach by two numerical examples.

Keywords: Dual fuzzy polynomial equations, Interval type-2, Ranking method, Value.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1497
539 Ranking and Unranking Algorithms for k-ary Trees in Gray Code Order

Authors: Fateme Ashari-Ghomi, Najme Khorasani, Abbas Nowzari-Dalini

Abstract:

In this paper, we present two new ranking and unranking algorithms for k-ary trees represented by x-sequences in Gray code order. These algorithms are based on a gray code generation algorithm developed by Ahrabian et al.. In mentioned paper, a recursive backtracking generation algorithm for x-sequences corresponding to k-ary trees in Gray code was presented. This generation algorithm is based on Vajnovszki-s algorithm for generating binary trees in Gray code ordering. Up to our knowledge no ranking and unranking algorithms were given for x-sequences in this ordering. we present ranking and unranking algorithms with O(kn2) time complexity for x-sequences in this Gray code ordering

Keywords: k-ary Tree Generation, Ranking, Unranking, Gray Code.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1804
538 A Heat-Inducible Transgene Expression System for Gene Therapy

Authors: Masaki Yamaguchi, Akira Ito, Noriaki Okamoto, Yoshinori Kawabe, Masamichi Kamihira

Abstract:

Heat-inducible gene expression vectors are useful for hyperthermia-induced cancer gene therapy, because the combination of hyperthermia and gene therapy can considerably improve the therapeutic effects. In the present study, we developed an enhanced heat-inducible transgene expression system in which a heat-shock protein (HSP) promoter and tetracycline-responsive transactivator were combined. When the transactivator plasmid containing the tetracycline-responsive transactivator gene was co-transfected with the reporter gene expression plasmid, a high level of heat-induced gene expression was observed compared with that using the HSP promoter without the transactivator. In vitro evaluation of the therapeutic effect using HeLa cells showed that heat-induced therapeutic gene expression caused cell death in a high percentage of these cells, indicating that this strategy is promising for cancer gene therapy.

Keywords: Inducible gene expression, Gene therapy, Hyperthermia, Heat shock protein, Tetracycline transactivator.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1820
537 A New blaVIM Gene in a Pseudomonas putida Isolated from ENT Units in Sulaimani Hospitals

Authors: Dalanya Asaad Mohammed, Dara Abdul Razaq

Abstract:

A total of twenty tensile biopsies were collected from children undergoing tonsillectomy from teaching hospital ENT department and Kurdistan private hospital in sulaimani city. All biopsies were homogenized and cultured; the obtained bacterial isolates were purified and identified by biochemical tests and VITEK 2 compact system. Among the twenty studied samples, only one Pseudomonas putida with probability of 99% was isolated. Antimicrobial susceptibility was carried out by disk diffusion method, Pseudomonas putida showed resistance to all antibiotics used except vancomycin. The isolate further subjected to PCR and DNA sequence analysis of blaVIM gene using different set of primers for different regions of VIM gene. The results were found to be PCR positive for the blaVIM gene. To determine the sequence of blaVIM gene, DNA sequencing performed. Sequence alignment of blaVIM gene with previously recorded blaVIM gene in NCBI- database showed that P. putida isolate have different blaVIM gene.

Keywords: Clinical isolates, Putida, Sulaimani, Vim gene.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1379
536 Ranking Genes from DNA Microarray Data of Cervical Cancer by a local Tree Comparison

Authors: Frank Emmert-Streib, Matthias Dehmer, Jing Liu, Max Muhlhauser

Abstract:

The major objective of this paper is to introduce a new method to select genes from DNA microarray data. As criterion to select genes we suggest to measure the local changes in the correlation graph of each gene and to select those genes whose local changes are largest. More precisely, we calculate the correlation networks from DNA microarray data of cervical cancer whereas each network represents a tissue of a certain tumor stage and each node in the network represents a gene. From these networks we extract one tree for each gene by a local decomposition of the correlation network. The interpretation of a tree is that it represents the n-nearest neighbor genes on the n-th level of a tree, measured by the Dijkstra distance, and, hence, gives the local embedding of a gene within the correlation network. For the obtained trees we measure the pairwise similarity between trees rooted by the same gene from normal to cancerous tissues. This evaluates the modification of the tree topology due to tumor progression. Finally, we rank the obtained similarity values from all tissue comparisons and select the top ranked genes. For these genes the local neighborhood in the correlation networks changes most between normal and cancerous tissues. As a result we find that the top ranked genes are candidates suspected to be involved in tumor growth. This indicates that our method captures essential information from the underlying DNA microarray data of cervical cancer.

Keywords: Graph similarity, generalized trees, graph alignment, DNA microarray data, cervical cancer.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1488
535 A Dynamic Time-Lagged Correlation based Method to Learn Multi-Time Delay Gene Networks

Authors: Ankit Agrawal, Ankush Mittal

Abstract:

A gene network gives the knowledge of the regulatory relationships among the genes. Each gene has its activators and inhibitors that regulate its expression positively and negatively respectively. Genes themselves are believed to act as activators and inhibitors of other genes. They can even activate one set of genes and inhibit another set. Identifying gene networks is one of the most crucial and challenging problems in Bioinformatics. Most work done so far either assumes that there is no time delay in gene regulation or there is a constant time delay. We here propose a Dynamic Time- Lagged Correlation Based Method (DTCBM) to learn the gene networks, which uses time-lagged correlation to find the potential gene interactions, and then uses a post-processing stage to remove false gene interactions to common parents, and finally uses dynamic correlation thresholds for each gene to construct the gene network. DTCBM finds correlation between gene expression signals shifted in time, and therefore takes into consideration the multi time delay relationships among the genes. The implementation of our method is done in MATLAB and experimental results on Saccharomyces cerevisiae gene expression data and comparison with other methods indicate that it has a better performance.

Keywords: Activators, correlation, dynamic time-lagged correlation based method, inhibitors, multi-time delay gene network.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1346
534 Differentiation of Gene Expression Profiles Data for Liver and Kidney of Pigs

Authors: Khlopova N.S., Glazko V.I., Glazko T.T.

Abstract:

Using DNA microarrays the comparative analysis of a gene expression profiles is carried out in a liver and kidneys of pigs. The hypothesis of a cross hybridization of one probe with different cDNA sites of the same gene or different genes is checked up, and it is shown, that cross hybridization can be a source of essential errors at revealing of a key genes in organ-specific transcriptome. It is reveald that distinctions in profiles of a gene expression are well coordinated with function, morphology, biochemistry and histology of these organs.

Keywords: Microarray, gene expression profiles, key genes.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1271
533 Investments Attractiveness via Combinatorial Optimization Ranking

Authors: Ivan C. Mustakerov, Daniela I. Borissova

Abstract:

The paper proposes an approach to ranking a set of potential countries to invest taking into account the investor point of view about importance of different economic indicators. For the goal, a ranking algorithm that contributes to rational decision making is proposed. The described algorithm is based on combinatorial optimization modeling and repeated multi-criteria tasks solution. The final result is list of countries ranked in respect of investor preferences about importance of economic indicators for investment attractiveness. Different scenarios are simulated conforming to different investors preferences. A numerical example with real dataset of indicators is solved. The numerical testing shows the applicability of the described algorithm. The proposed approach can be used with any sets of indicators as ranking criteria reflecting different points of view of investors. 

Keywords: Combinatorial optimization modeling, economics investment attractiveness, economics ranking algorithm, multi-criteria problems.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1767
532 Automatic Clustering of Gene Ontology by Genetic Algorithm

Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias, Zalmiyah Zakaria, Saberi M. Mohamad

Abstract:

Nowadays, Gene Ontology has been used widely by many researchers for biological data mining and information retrieval, integration of biological databases, finding genes, and incorporating knowledge in the Gene Ontology for gene clustering. However, the increase in size of the Gene Ontology has caused problems in maintaining and processing them. One way to obtain their accessibility is by clustering them into fragmented groups. Clustering the Gene Ontology is a difficult combinatorial problem and can be modeled as a graph partitioning problem. Additionally, deciding the number k of clusters to use is not easily perceived and is a hard algorithmic problem. Therefore, an approach for solving the automatic clustering of the Gene Ontology is proposed by incorporating cohesion-and-coupling metric into a hybrid algorithm consisting of a genetic algorithm and a split-and-merge algorithm. Experimental results and an example of modularized Gene Ontology in RDF/XML format are given to illustrate the effectiveness of the algorithm.

Keywords: Automatic clustering, cohesion-and-coupling metric, gene ontology; genetic algorithm, split-and-merge algorithm.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1710
531 Integration of Microarray Data into a Genome-Scale Metabolic Model to Study Flux Distribution after Gene Knockout

Authors: Mona Heydari, Ehsan Motamedian, Seyed Abbas Shojaosadati

Abstract:

Prediction of perturbations after genetic manipulation (especially gene knockout) is one of the important challenges in systems biology. In this paper, a new algorithm is introduced that integrates microarray data into the metabolic model. The algorithm was used to study the change in the cell phenotype after knockout of Gss gene in Escherichia coli BW25113. Algorithm implementation indicated that gene deletion resulted in more activation of the metabolic network. Growth yield was more and less regulating gene were identified for mutant in comparison with the wild-type strain.

Keywords: Metabolic network, gene knockout, flux balance analysis, microarray data, integration.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 712
530 Quantitative Ranking Evaluation of Wine Quality

Authors: A. Brunel, A. Kernevez, F. Leclere, J. Trenteseaux

Abstract:

Today, wine quality is only evaluated by wine experts with their own different personal tastes, even if they may agree on some common features. So producers do not have any unbiased way to independently assess the quality of their products. A tool is here proposed to evaluate wine quality by an objective ranking based upon the variables entering wine elaboration, and analysed through principal component analysis (PCA) method. Actual climatic data are compared by measuring the relative distance between each considered wine, out of which the general ranking is performed.

Keywords: Wine, grape, vine, weather conditions, rating, climate, principal component analysis, metric analysis.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1579
529 Clustering Approach to Unveiling Relationships between Gene Regulatory Networks

Authors: Hiba Hasan, Khalid Raza

Abstract:

Reverse engineering of genetic regulatory network involves the modeling of the given gene expression data into a form of the network. Computationally it is possible to have the relationships between genes, so called gene regulatory networks (GRNs), that can help to find the genomics and proteomics based diagnostic approach for any disease. In this paper, clustering based method has been used to reconstruct genetic regulatory network from time series gene expression data. Supercoiled data set from Escherichia coli has been taken to demonstrate the proposed method.

Keywords: Gene expression, gene regulatory networks (GRNs), clustering, data preprocessing, network visualization.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1833
528 Fuzzy Approach for Ranking of Motor Vehicles Involved in Road Accidents

Authors: Lazim Abdullah, N orhanadiah Zam

Abstract:

Increasing number of vehicles and lack of awareness among road users may lead to road accidents. However no specific literature was found to rank vehicles involved in accidents based on fuzzy variables of road users. This paper proposes a ranking of four selected motor vehicles involved in road accidents. Human and non-human factors that normally linked with road accidents are considered for ranking. The imprecision or vagueness inherent in the subjective assessment of the experts has led the application of fuzzy sets theory to deal with ranking problems. Data in form of linguistic variables were collected from three authorised personnel of three Malaysian Government agencies. The Multi Criteria Decision Making, fuzzy TOPSIS was applied in computational procedures. From the analysis, it shows that motorcycles vehicles yielded the highest closeness coefficient at 0.6225. A ranking can be drawn using the magnitude of closeness coefficient. It was indicated that the motorcycles recorded the first rank.

Keywords: Road accidents, decision making, closeness coefficient, fuzzy number

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1284
527 Eye Location Based on Structure Feature for Driver Fatigue Monitoring

Authors: Qiong Wang

Abstract:

One of the most important problems to solve is eye location for a driver fatigue monitoring system. This paper presents an efficient method to achieve fast and accurate eye location in grey level images obtained in the real-word driving conditions. The structure of eye region is used as a robust cue to find possible eye pairs. Candidates of eye pair at different scales are selected by finding regions which roughly match with the binary eye pair template. To obtain real one, all the eye pair candidates are then verified by using support vector machines. Finally, eyes are precisely located by using binary vertical projection and eye classifier in eye pair images. The proposed method is robust to deal with illumination changes, moderate rotations, glasses wearing and different eye states. Experimental results demonstrate its effectiveness.

Keywords: eye location, structure feature, driver fatiguemonitoring

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1321