Search results for: Gene Signature
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 340

Search results for: Gene Signature

310 A Computer Proven Application of the Discrete Logarithm Problem

Authors: Sebastian Kusch, Markus Kaiser

Abstract:

In this paper we analyze the application of a formal proof system to the discrete logarithm problem used in publickey cryptography. That means, we explore a computer verification of the ElGamal encryption scheme with the formal proof system Isabelle/HOL. More precisely, the functional correctness of this algorithm is formally verified with computer support. Besides, we present a formalization of the DSA signature scheme in the Isabelle/HOL system. We show that this scheme is correct what is a necessary condition for the usefulness of any cryptographic signature scheme.

Keywords: Formal proof system, higher-order logic, formal verification, cryptographic signature scheme.

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309 A New Approach to Predicting Physical Biometrics from Behavioural Biometrics

Authors: Raid R. O. Al-Nima, S. S. Dlay, W. L. Woo

Abstract:

A relationship between face and signature biometrics is established in this paper. A new approach is developed to predict faces from signatures by using artificial intelligence. A multilayer perceptron (MLP) neural network is used to generate face details from features extracted from signatures, here face is the physical biometric and signatures is the behavioural biometric. The new method establishes a relationship between the two biometrics and regenerates a visible face image from the signature features. Furthermore, the performance efficiencies of our new technique are demonstrated in terms of minimum error rates compared to published work.

Keywords: Behavioural biometric, Face biometric, Neural network, Physical biometric, Signature biometric.

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308 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.

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307 Alternative Key Exchange Algorithm Based on Elliptic Curve Digital Signature Algorithm Certificate and Usage in Applications

Authors: A. Andreasyan, C. Connors

Abstract:

The Elliptic Curve Digital Signature algorithm-based X509v3 certificates are becoming more popular due to their short public and private key sizes. Moreover, these certificates can be stored in Internet of Things (IoT) devices, with limited resources, using less memory and transmitted in network security protocols, such as Internet Key Exchange (IKE), Transport Layer Security (TLS) and Secure Shell (SSH) with less bandwidth. The proposed method gives another advantage, in that it increases the performance of the above-mentioned protocols in terms of key exchange by saving one scalar multiplication operation.

Keywords: Cryptography, elliptic curve digital signature algorithm, key exchange, network security protocols.

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306 Study of the S-Bend Intake Hammershock Based on Improved Delayed Detached Eddy Simulation

Authors: Qun-Feng Zhang, Pan-Pan Yan, Jun Li, Jun-Qing Lei

Abstract:

Numerical investigation of hammershock propagation in the S-bend intake caused by engine surge has been conducted by using Improved Delayed Detach-Eddy Simulation (IDDES). The effects of surge signatures on hammershock characteristics are obtained. It was shown that once the hammershock is produced, it moves upward to the intake entrance quickly with constant speed, however, the strength of hammershock keeps increasing. Meanwhile, being influenced by the centrifugal force, the hammershock strength on the larger radius side is much larger. Hammershock propagation speed and strength are sensitive to the ramp upgradient of surge signature. A larger ramp up gradient results in higher propagation speed and greater strength. Nevertheless, ramp down profile of surge signature have no obvious effect on the propagation speed and strength of hammershock. Increasing the maximum value of surge signature leads to enhance in the intensity of hammershock, they approximately match quadratic function distribution law.

Keywords: Hammershock, IDDES, S-bend, surge signature.

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305 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.

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304 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.

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303 Implementing Fault Tolerance with Proxy Signature on the Improvement of RSA System

Authors: H. El-Kamchouchi, Heba Gaber, Fatma Ahmed, Dalia H. El-Kamchouchi

Abstract:

Fault tolerance and data security are two important issues in modern communication systems. During the transmission of data between the sender and receiver, errors may occur frequently. Therefore, the sender must re-transmit the data to the receiver in order to correct these errors, which makes the system very feeble. To improve the scalability of the scheme, we present a proxy signature scheme with fault tolerance over an efficient and secure authenticated key agreement protocol based on the improved RSA system. Authenticated key agreement protocols have an important role in building a secure communications network between the two parties.

Keywords: Proxy signature, fault tolerance, improved RSA, key agreement.

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302 A New Design Partially Blind Signature Scheme Based on Two Hard Mathematical Problems

Authors: Nedal Tahat

Abstract:

Recently, many existing partially blind signature scheme based on a single hard problem such as factoring, discrete logarithm, residuosity or elliptic curve discrete logarithm problems. However sooner or later these systems will become broken and vulnerable, if the factoring or discrete logarithms problems are cracked. This paper proposes a secured partially blind signature scheme based on factoring (FAC) problem and elliptic curve discrete logarithms (ECDL) problem. As the proposed scheme is focused on factoring and ECDLP hard problems, it has a solid structure and will totally leave the intruder bemused because it is very unlikely to solve the two hard problems simultaneously. In order to assess the security level of the proposed scheme a performance analysis has been conducted. Results have proved that the proposed scheme effectively deals with the partial blindness, randomization, unlinkability and unforgeability properties. Apart from this we have also investigated the computation cost of the proposed scheme. The new proposed scheme is robust and it is difficult for the malevolent attacks to break our scheme.

Keywords: Cryptography, Partially Blind Signature, Factoring, Elliptic Curve Discrete Logarithms.

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301 A Watermarking Signature Scheme with Hidden Watermarks and Constraint Functions in the Symmetric Key Setting

Authors: Yanmin Zhao, Siu Ming Yiu

Abstract:

To claim the ownership for an executable program is a non-trivial task. An emerging direction is to add a watermark to the program such that the watermarked program preserves the original program’s functionality and removing the watermark would heavily destroy the functionality of the watermarked program. In this paper, the first watermarking signature scheme with the watermark and the constraint function hidden in the symmetric key setting is constructed. The scheme uses well-known techniques of lattice trapdoors and a lattice evaluation. The watermarking signature scheme is unforgeable under the Short Integer Solution (SIS) assumption and satisfies other security requirements such as the unremovability security property.

Keywords: Short integer solution problem, signatures, the symmetric-key setting, watermarking schemes.

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300 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.

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299 Hybrid Authentication Scheme for Graphical Password Using QR Code and Integrated Sound Signature

Authors: Salim Istyaq, Mohammad Sarosh Umar

Abstract:

Today, the mankind is in the stage of development, every day comes with new proposal of technology, in order to secure these types of technology, we also prepare high yielding security modules to conserve these resources. The capacity of human brain to recognize anything is far more than any species; this is all due to our developing cycle of curiosity. In this paper, we proposed a scheme based on graphical password using QR Code which provides more security to the recent online system. It also contains a supportive sound signature. In this system, authentication is done using sequence of images in QR code form. Users select one click-point per image with the help of QR scanner or recognizer. The encoded phrase in a QR code emphasizes the minimum probability of attacking via shoulder surfing or other attacks.

Keywords: Graphical password, QR code, sound signature, image authentication, cued click point.

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298 UTMGO: A Tool for Searching a Group of Semantically Related Gene Ontology Terms and Application to Annotation of Anonymous Protein Sequence

Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias

Abstract:

Gene Ontology terms have been actively used to annotate various protein sets. SWISS-PROT, TrEMBL, and InterPro are protein databases that are annotated according to the Gene Ontology terms. However, direct implementation of the Gene Ontology terms for annotation of anonymous protein sequences is not easy, especially for species not commonly represented in biological databases. UTMGO is developed as a tool that allows the user to quickly and easily search for a group of semantically related Gene Ontology terms. The applicability of the UTMGO is demonstrated by applying it to annotation of anonymous protein sequence. The extended UTMGO uses the Gene Ontology terms together with protein sequences associated with the terms to perform the annotation task. GOPET, GOtcha, GoFigure, and JAFA are used to compare the performance of the extended UTMGO.

Keywords: Anonymous protein sequence, Gene Ontology, Protein sequence annotation, Protein sequence alignment

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297 A Secure Proxy Signature Scheme with Fault Tolerance Based on RSA System

Authors: H. El-Kamchouchi, Heba Gaber, Fatma Ahmed, Dalia H. El-Kamchouchi

Abstract:

Due to the rapid growth in modern communication systems, fault tolerance and data security are two important issues in a secure transaction. During the transmission of data between the sender and receiver, errors may occur frequently. Therefore, the sender must re-transmit the data to the receiver in order to correct these errors, which makes the system very feeble. To improve the scalability of the scheme, we present a secure proxy signature scheme with fault tolerance over an efficient and secure authenticated key agreement protocol based on RSA system. Authenticated key agreement protocols have an important role in building a secure communications network between the two parties.

Keywords: Proxy signature, fault tolerance, RSA, key agreement protocol.

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296 Computation of Probability Coefficients using Binary Decision Diagram and their Application in Test Vector Generation

Authors: Ashutosh Kumar Singh, Anand Mohan

Abstract:

This paper deals with efficient computation of probability coefficients which offers computational simplicity as compared to spectral coefficients. It eliminates the need of inner product evaluations in determination of signature of a combinational circuit realizing given Boolean function. The method for computation of probability coefficients using transform matrix, fast transform method and using BDD is given. Theoretical relations for achievable computational advantage in terms of required additions in computing all 2n probability coefficients of n variable function have been developed. It is shown that for n ≥ 5, only 50% additions are needed to compute all probability coefficients as compared to spectral coefficients. The fault detection techniques based on spectral signature can be used with probability signature also to offer computational advantage.

Keywords: Binary Decision Diagrams, Spectral Coefficients, Fault detection

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295 Cryptographic Attack on Lucas Based Cryptosystems Using Chinese Remainder Theorem

Authors: Tze Jin Wong, Lee Feng Koo, Pang Hung Yiu

Abstract:

Lenstra’s attack uses Chinese remainder theorem as a tool and requires a faulty signature to be successful. This paper reports on the security responses of fourth and sixth order Lucas based (LUC4,6) cryptosystem under the Lenstra’s attack as compared to the other two Lucas based cryptosystems such as LUC and LUC3 cryptosystems. All the Lucas based cryptosystems were exposed mathematically to the Lenstra’s attack using Chinese Remainder Theorem and Dickson polynomial. Result shows that the possibility for successful Lenstra’s attack is less against LUC4,6 cryptosystem than LUC3 and LUC cryptosystems. Current study concludes that LUC4,6 cryptosystem is more secure than LUC and LUC3 cryptosystems in sustaining against Lenstra’s attack.

Keywords: Lucas sequence, Dickson Polynomial, faulty signature, corresponding signature, congruence.

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294 Dynamical Analysis of Circadian Gene Expression

Authors: Carla Layana Luis Diambra

Abstract:

Microarrays technique allows the simultaneous measurements of the expression levels of thousands of mRNAs. By mining this data one can identify the dynamics of the gene expression time series. By recourse of principal component analysis, we uncover the circadian rhythmic patterns underlying the gene expression profiles from Cyanobacterium Synechocystis. We applied PCA to reduce the dimensionality of the data set. Examination of the components also provides insight into the underlying factors measured in the experiments. Our results suggest that all rhythmic content of data can be reduced to three main components.

Keywords: circadian rhythms, clustering, gene expression, PCA.

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293 A Hybrid Gene Selection Technique Using Improved Mutual Information and Fisher Score for Cancer Classification Using Microarrays

Authors: M. Anidha, K. Premalatha

Abstract:

Feature Selection is significant in order to perform constructive classification in the area of cancer diagnosis. However, a large number of features compared to the number of samples makes the task of classification computationally very hard and prone to errors in microarray gene expression datasets. In this paper, we present an innovative method for selecting highly informative gene subsets of gene expression data that effectively classifies the cancer data into tumorous and non-tumorous. The hybrid gene selection technique comprises of combined Mutual Information and Fisher score to select informative genes. The gene selection is validated by classification using Support Vector Machine (SVM) which is a supervised learning algorithm capable of solving complex classification problems. The results obtained from improved Mutual Information and F-Score with SVM as a classifier has produced efficient results.

Keywords: Gene selection, mutual information, Fisher score, classification, SVM.

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292 Stroke Extraction and Approximation with Interpolating Lagrange Curves

Authors: Bence Kővári, ZSolt Kertész

Abstract:

This paper proposes a stroke extraction method for use in off-line signature verification. After giving a brief overview of the current ongoing researches an algorithm is introduced for detecting and following strokes in static images of signatures. Problems like the handling of junctions and variations in line width and line intensity are discussed in detail. Results are validated by both using an existing on-line signature database and by employing image registration methods.

Keywords: Stroke extraction, spline fitting, off-line signatureverification, image registration.

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291 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.

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290 Combining Gene and Chemo Therapy using Multifunctional Polymeric Micelles

Authors: Hong Yi Huang, Wei Ti Kuo, Yi You Huang

Abstract:

Non-viral gene carriers composed of biodegradable polymers or lipids have been considered as a safer alternative for gene carriers over viral vectors. We have developed multi-functional nano-micelles for both drug and gene delivery application. Polyethyleneimine (PEI) was modified by grafting stearic acid (SA) and formulated to polymeric micelles (PEI-SA) with positive surface charge for gene and drug delivery. Our results showed that PEI-SA micelles provided high siRNA binding efficiency. In addition, siRNA delivered by PEI-SA carriers also demonstrated significantly high cellular uptake even in the presence of serum proteins. The post-transcriptional gene silencing efficiency was greatly improved by the polyplex formulated by 10k PEI-SA/siRNA. The amphiphilic structure of PEI-SA micelles provided advantages for multifunctional tasks; where the hydrophilic shell modified with cationic charges can electrostatically interact with DNA or siRNA, and the hydrophobic core can serve as payloads for hydrophobic drugs, making it a promising multifunctional vehicle for both genetic and chemotherapy application.

Keywords: polyethyleneimine, gene delivery, micelles, siRNA

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289 Application of KL Divergence for Estimation of Each Metabolic Pathway Genes

Authors: Shohei Maruyama, Yasuo Matsuyama, Sachiyo Aburatani

Abstract:

Development of a method to estimate gene functions is an important task in bioinformatics. One of the approaches for the annotation is the identification of the metabolic pathway that genes are involved in. Since gene expression data reflect various intracellular phenomena, those data are considered to be related with genes’ functions. However, it has been difficult to estimate the gene function with high accuracy. It is considered that the low accuracy of the estimation is caused by the difficulty of accurately measuring a gene expression. Even though they are measured under the same condition, the gene expressions will vary usually. In this study, we proposed a feature extraction method focusing on the variability of gene expressions to estimate the genes' metabolic pathway accurately. First, we estimated the distribution of each gene expression from replicate data. Next, we calculated the similarity between all gene pairs by KL divergence, which is a method for calculating the similarity between distributions. Finally, we utilized the similarity vectors as feature vectors and trained the multiclass SVM for identifying the genes' metabolic pathway. To evaluate our developed method, we applied the method to budding yeast and trained the multiclass SVM for identifying the seven metabolic pathways. As a result, the accuracy that calculated by our developed method was higher than the one that calculated from the raw gene expression data. Thus, our developed method combined with KL divergence is useful for identifying the genes' metabolic pathway.

Keywords: Metabolic pathways, gene expression data, microarray, Kullback–Leibler divergence, KL divergence, support vector machines, SVM, machine learning.

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288 Signing the First Packet in Amortization Scheme for Multicast Stream Authentication

Authors: Mohammed Shatnawi, Qusai Abuein, Susumu Shibusawa

Abstract:

Signature amortization schemes have been introduced for authenticating multicast streams, in which, a single signature is amortized over several packets. The hash value of each packet is computed, some hash values are appended to other packets, forming what is known as hash chain. These schemes divide the stream into blocks, each block is a number of packets, the signature packet in these schemes is either the first or the last packet of the block. Amortization schemes are efficient solutions in terms of computation and communication overhead, specially in real-time environment. The main effictive factor of amortization schemes is it-s hash chain construction. Some studies show that signing the first packet of each block reduces the receiver-s delay and prevents DoS attacks, other studies show that signing the last packet reduces the sender-s delay. To our knowledge, there is no studies that show which is better, to sign the first or the last packet in terms of authentication probability and resistance to packet loss. In th is paper we will introduce another scheme for authenticating multicast streams that is robust against packet loss, reduces the overhead, and prevents the DoS attacks experienced by the receiver in the same time. Our scheme-The Multiple Connected Chain signing the First packet (MCF) is to append the hash values of specific packets to other packets,then append some hashes to the signature packet which is sent as the first packet in the block. This scheme is aspecially efficient in terms of receiver-s delay. We discuss and evaluate the performance of our proposed scheme against those that sign the last packet of the block.

Keywords: multicast stream authentication, hash chain construction, signature amortization, authentication probability.

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287 Annotations of Gene Pathways Images in Biomedical Publications Using Siamese Network

Authors: Micheal Olaolu Arowolo, Muhammad Azam, Fei He, Mihail Popescu, Dong Xu

Abstract:

As the quantity of biological articles rises, so does the number of biological route figures. Each route figure shows gene names and relationships. Manually annotating pathway diagrams is time-consuming. Advanced image understanding models could speed up curation, but they must be more precise. There is rich information in biological pathway figures. The first step to performing image understanding of these figures is to recognize gene names automatically. Classical optical character recognition methods have been employed for gene name recognition, but they are not optimized for literature mining data. This study devised a method to recognize an image bounding box of gene name as a photo using deep Siamese neural network models to outperform the existing methods using ResNet, DenseNet and Inception architectures, the results obtained about 84% accuracy.

Keywords: Biological pathway, gene identification, object detection, Siamese network, ResNet.

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286 Techniques Used in String Matching for Network Security

Authors: Jamuna Bhandari

Abstract:

String matching also known as pattern matching is one of primary concept for network security. In this area the effectiveness and efficiency of string matching algorithms is important for applications in network security such as network intrusion detection, virus detection, signature matching and web content filtering system. This paper presents brief review on some of string matching techniques used for network security.

Keywords: Filtering, honeypot, network telescope, pattern, string, signature.

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285 Novel Hybrid Method for Gene Selection and Cancer Prediction

Authors: Liping Jing, Michael K. Ng, Tieyong Zeng

Abstract:

Microarray data profiles gene expression on a whole genome scale, therefore, it provides a good way to study associations between gene expression and occurrence or progression of cancer. More and more researchers realized that microarray data is helpful to predict cancer sample. However, the high dimension of gene expressions is much larger than the sample size, which makes this task very difficult. Therefore, how to identify the significant genes causing cancer becomes emergency and also a hot and hard research topic. Many feature selection algorithms have been proposed in the past focusing on improving cancer predictive accuracy at the expense of ignoring the correlations between the features. In this work, a novel framework (named by SGS) is presented for stable gene selection and efficient cancer prediction . The proposed framework first performs clustering algorithm to find the gene groups where genes in each group have higher correlation coefficient, and then selects the significant genes in each group with Bayesian Lasso and important gene groups with group Lasso, and finally builds prediction model based on the shrinkage gene space with efficient classification algorithm (such as, SVM, 1NN, Regression and etc.). Experiment results on real world data show that the proposed framework often outperforms the existing feature selection and prediction methods, say SAM, IG and Lasso-type prediction model.

Keywords: Gene Selection, Cancer Prediction, Lasso, Clustering, Classification.

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284 A Phenomic Algorithm for Reconstruction of Gene Networks

Authors: Rio G. L. D'Souza, K. Chandra Sekaran, A. Kandasamy

Abstract:

The goal of Gene Expression Analysis is to understand the processes that underlie the regulatory networks and pathways controlling inter-cellular and intra-cellular activities. In recent times microarray datasets are extensively used for this purpose. The scope of such analysis has broadened in recent times towards reconstruction of gene networks and other holistic approaches of Systems Biology. Evolutionary methods are proving to be successful in such problems and a number of such methods have been proposed. However all these methods are based on processing of genotypic information. Towards this end, there is a need to develop evolutionary methods that address phenotypic interactions together with genotypic interactions. We present a novel evolutionary approach, called Phenomic algorithm, wherein the focus is on phenotypic interaction. We use the expression profiles of genes to model the interactions between them at the phenotypic level. We apply this algorithm to the yeast sporulation dataset and show that the algorithm can identify gene networks with relative ease.

Keywords: Evolutionary computing, gene expression analysis, gene networks, microarray data analysis, phenomic algorithms.

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283 Analysis of OPG Gene Polymorphism T245G (rs3134069) in Slovak Postmenopausal Women

Authors: I. Boroňová, J. Bernasovská, J. Kľoc, Z. Tomková, E. Petrejčíková, S. Mačeková, J. Poráčová, M. M. Blaščáková

Abstract:

Osteoporosis is a common multifactorial disease with a strong genetic component characterized by reduced bone mass and increased risk of fractures. Genetic factors play an important role in the pathogenesis of osteoporosis. The aim of our study was to identify the genotype and allele distribution of T245G polymorphism in OPG gene in Slovak postmenopausal women. A total of 200 unrelated Slovak postmenopausal women with diagnosed osteoporosis and 200 normal controls were genotyped for T245G (rs3134069) polymorphism of OPG gene. Genotyping was performed using the Custom Taqman®SNP Genotyping assays. Genotypes and alleles frequencies showed no significant differences (p=0.5551; p=0.6022). The results of the present study confirm the importance of T245G polymorphism in OPG gene in the pathogenesis of osteoporosis.

Keywords: OPG gene, osteoporosis, Real-time PCR, T245G polymorphism.

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282 Comparative Study on Swarm Intelligence Techniques for Biclustering of Microarray Gene Expression Data

Authors: R. Balamurugan, A. M. Natarajan, K. Premalatha

Abstract:

Microarray gene expression data play a vital in biological processes, gene regulation and disease mechanism. Biclustering in gene expression data is a subset of the genes indicating consistent patterns under the subset of the conditions. Finding a biclustering is an optimization problem. In recent years, swarm intelligence techniques are popular due to the fact that many real-world problems are increasingly large, complex and dynamic. By reasons of the size and complexity of the problems, it is necessary to find an optimization technique whose efficiency is measured by finding the near optimal solution within a reasonable amount of time. In this paper, the algorithmic concepts of the Particle Swarm Optimization (PSO), Shuffled Frog Leaping (SFL) and Cuckoo Search (CS) algorithms have been analyzed for the four benchmark gene expression dataset. The experiment results show that CS outperforms PSO and SFL for 3 datasets and SFL give better performance in one dataset. Also this work determines the biological relevance of the biclusters with Gene Ontology in terms of function, process and component.

Keywords: Particle swarm optimization, Shuffled frog leaping, Cuckoo search, biclustering, gene expression data.

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281 Construction of a Fusion Gene Carrying E10A and K5 with 2A Peptide-Linked by Using Overlap Extension PCR

Authors: Tiancheng Lan

Abstract:

E10A is a kind of replication-defective adenovirus which carries the human endostatin gene to inhibit the growth of tumors. Kringle 5(K5) has almost the same function as angiostatin to also inhibit the growth of tumors since they are all the byproduct of the proteolytic cleavage of plasminogen. Tumor size increasing can be suppressed because both of the endostatin and K5 can restrain the angiogenesis process. Therefore, in order to improve the treatment effect on tumor, 2A peptide is used to construct a fusion gene carrying both E10A and K5. Using 2A peptide is an ideal strategy when a fusion gene is expressed because it can avoid many problems during the expression of more than one kind of protein. The overlap extension PCR is also used to connect 2A peptide with E10A and K5. The final construction of fusion gene E10A-2A-K5 can provide a possible new method of the anti-angiogenesis treatment with a better expression performance.

Keywords: E10A, Kringle 5, 2A peptide, overlap extension PCR.

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