53306687
Identifying the combination of genetic factors that determine susceptibility to cervical cancer
Cervical cancer is common among women all over the world. Although infection with high-risk types of human papillomavirus (HPV) has been identified as the primary cause of cervical cancer, only some of those infected go on to develop cervical cancer. Obviously, the progression from HPV infection to cancer involves other environmental and host factors. Recent population-based twin and family studies have demonstrated the importance of the hereditary component of cervical cancer, associated with genetic susceptibility. Consequently, SNP markers and microsatellites should be considered genetic factors for determining what combinations of genetic factors are involved in precancerous changes to cervical cancer. This study employs a Bayesian network and four different decision tree algorithms, and compares the performance of these learning algorithms. The results of this study raise the possibility of investigations that could identify combinations of genetic factors, such as SNPs and microsatellites, that influence the risk associated with common complex multifactorial diseases, such as cervical cancer. The web site associated with this study is http://dblab8.csie.ncu.edu.tw/FactorAnalysis/.
1404678
SpliceInfo: an information repository for mRNA alternative splicing in human genome
We have developed an information repository named SpliceInfo to collect the occurrences of the four major alternative-splicing (AS) modes in human genome; these include exon skipping, 5′-alternative splicing, 3′-alternative splicing and intron retention. The dataset is derived by comparing the nucleotide and protein sequences available for a given gene for evidence of AS. Additional features such as the tissue specificity of the mRNA, the protein domain contained by exons, the GC-ratio of exons, the repeats contained within the exons, and the Gene Ontology are annotated computationally for each exonic region that is alternatively spliced. Motivated by a previous investigation of AS-related motifs such as exonic splicing enhancer and exonic splicing silencer, this resource also provides a means of identifying motifs candidates and this should help to identify potential regulatory mechanisms within a particular exonic sequence set and its two flanking intronic sequence sets. This is carried out using motif discovery tools to identify motif candidates related to alternative splicing regulation and together with a secondary structure prediction tool, will help in the identification of the structural properties of such regulatory motifs. The integrated resource is now available on http://SpliceInfo.mbc.NCTU.edu.tw/.
13750244
A database to aid probe design for virus identification
FENG-MAO LIN, HSIEN-DA HUANG, YU-CHUNG CHANG, PAK-LEONG CHAN, JORNG-TZONG HORNG, MING-TAT KO Department of Computer Science and Information Engineering, National Central University, No.300, Jungda Rd, Jhongli City, Taoyuan, Taiwan 320 ChungLi, 320, Taiwan Department of Biological Science and Technology & Institute of Bioinformatic, National ChiaoTung University, 1001 Ta Hsueh Road, Hsinchu, Taiwan 300 Hsin-Chu, 300, Taiwan Department of Biotechnology, Ming Chuan University, 250 Chung Shan North Road, Section 5, Taipei, 111, Taiwan Institute of Information Science, Academia Sinica, 128 Sec. 2, Academia Rd, Nankangm, Taipei, 115, Taiwan
5048088
KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites
KinasePhos is a novel web server for computationally identifying catalytic kinase-specific phosphorylation sites. The known phosphorylation sites from public domain data sources are categorized by their annotated protein kinases. Based on the profile hidden Markov model, computational models are learned from the kinase-specific groups of the phosphorylation sites. After evaluating the learned models, the model with highest accuracy was selected from each kinase-specific group, for use in a web-based prediction tool for identifying protein phosphorylation sites. Therefore, this work developed a kinase-specific phosphorylation site prediction tool with both high sensitivity and specificity. The prediction tool is freely available at .
7391844
Database of repetitive elements in complete genomes and data mining using transcription factor binding sites
Approximately 43% of the human genome is occupied by repetitive elements. Even more, around 51% of the rice genome is occupied by repetitive elements. The analysis presented here indicates that repetitive elements in complete genomes may have been very important in the evolutionary genomics. In this study, a database, called the Repeat Sequence Database, is first designed and implemented to store complete and comprehensive repetitive sequences. See http://rsdb.csie.ncu.edu.tw for more information. The database contains direct, inverted and palindromic repetitive sequences, and each repetitive sequence has a variable length ranging from seven to many hundred nucleotides. The repetitive sequences in the database are explored using a mathematical algorithm to mine rules on how combinations of individual binding sites are distributed among repetitive sequences in the database. Combinations of transcription factor binding sites in the repetitive sequences are obtained and then data mining techniques are applied to mine association rules from these combinations. The discovered associations are further pruned to remove insignificant associations and obtain a set of associations. The mined association rules facilitate efforts to identify gene classes regulated by similar mechanisms and accurately predict regulatory elements. Experiments are performed on several genomes including C. elegans, human chromosome 22, and yeast.
3255925
A data mining method to predict transcriptional regulatory sites based on differentially expressed genes in human genome
Very large-scale gene expression analysis, i.e., UniGene and dbEST, are provided to find those genes with significantly differential expression in specific tissues. The differentially expressed genes in a specific tissue are potentially regulated concurrently by a combination of transcription factors. This study attempts to mine putative binding sites on how combinations of the known regulatory sites homologs and over-represented repetitive elements are distributed in the promoter regions of considered groups of differentially expressed genes. We propose a data mining approach to statistically discover the significantly tissue-specific combinations of known site homologs and over-represented repetitive sequences, which are distributed in the promoter regions of differential gene groups. The association rules mined would facilitate to predict putative regulatory elements and identify genes potentially co-regulated by the putative regulatory elements.
13572740
Image Texture Segmentation with Ant Colony Systems
A new scheme for texture segmentation based on ant colony systems (ACS) is proposed in this paper. Texture segmentation is one of the important branches in image pattern recognition, which provides usefulness in many applications. Until now, how to find an effective way for accomplishing texture segmentation in practical applications is still a major task. In this paper, we employ wavelet coefficients and characteristics of different subbands to serve as the basis of characteristic vectors, and we use three feature-extraction elements, namely, the extrema, entropy, and energy, to compose the characteristic vector. To alleviate segmentation fragments caused from the information in high frequency bands of texture images, we integrate the fourth element, the mean variance, into the characteristic vector. Finally, we use ACS to find a trade-off between texture segmentation and fragments. Simulation results demonstrate the effectiveness and practicability of the proposed algorithm
7392928
Finding short DNA motifs using permuted markov models
Many short DNA motifs such as transcription factor binding sites (TFBS) and splice sites exhibit strong local as well as non-local dependence. We introduce permuted variable length Markov models (PVLMM) which could capture the potentially important dependencies among positions, and apply them to the problem of detecting splice and TFB sites. They have been satisfactory from the viewpoint of prediction performance, and also give ready biological interpretations of the sequence dependence observed. The issue of model selection is also studied.
35266077
VQ-Based Gray Watermark Hiding Scheme and Genetic Index Assignment
A vector quantisation (VQ) based watermarking scheme for hiding the gray watermark is presented. It expands the watermark size, and employs VQ index assignment procedure with genetic algorithm, called genetic index assignment (GIA), for watermarking. The gray watermark is coded by VQ, and obtained indices are translated into a binary bitstream with a much smaller size. We partition the codebook into two sub-codebooks, and use either one of them based on the value of the bit for embedding. Next, GIA is employed to find better imperceptibility of watermarked image. Experimental results show that the proposed method possesses advantages over other related methods in literature.
35235754
Gene Family Identification Network Design for Protein Sequence Analysis
With the exponential accumulation of sequence data, continued progress in the Human Genome Project will depend increasingly on advanced computational tools to manage and analyze the data. Utilizing information embedded within families of homologous sequences, a gene family identification approach may facilitate the understanding of gene functions. We have developed a GeneFIND (Gene Family Identification Network Design) system for database searching against gene families. It provides rapid and accurate protein family identification by combining global and motif sequence similarities and incorporating ProClass family information. Multi-level filters are used, starting with the MOTIFIND neural networks and BLAST search, followed by SSEARCH alignment, motif pattern match, hidden Markov modeling of motifs and ClustalW motif alignment. GeneFIND has been implemented as a full-scale system for the classification of more than 1200 ProSite and 6000 PIR families. It has been used to identify thousands of new family members and is well suited for genomic sequence analysis. The system is available for on-line family identification from our WWW server ().
17310261
Cross-cultural influences on women in the IT workforce
A review of 862 papers published in SIGMIS/CPR proceedings over the past 44 years revealed only 29 articles that focused on gender and the IT workforce or gender and IT education, the majority of which were presented at the 2003 conference whose theme was diversity in the IT workforce. Therefore, in response to the call for papers to extend our understanding of topics central to computer personnel research, we present data from our field study of gender and IT that is directed at understanding differing cross-cultural influences on female experiences in the IT workforce. Four themes emerged from analysis of data from four separate studies of women in the IT workforces in Australia, Ireland, New Zealand and the United States: motherhood and careers, career choice, family dynamics and gender stereotypes. Analysis of interviews with 167 women reveals a wide range of influences on women's choice of an IT career. These results lend empirical support to the individual differences theory of gender and IT as an alternative to essentialist or social construction theories.