Data mining techniques in gene expression data analysis

... expression analysis, supervised data mining methods include class association rule mining and classiﬁcation while unsupervised data mining methods mainly refer to the various clustering methods ... biological information from the huge and fast-growing gene expression data Essentially, data mining methods can be divided into two big categories: supervised and unsupervised Supervised data mining ... clustering methods Class association rule mining is one well-known data mining task Each row of the expression data matrix involved in class association rule mining corresponds to a sample or a condition...

Data mining methodologies for gene expression analysis application to strain improvement

... Genomic Datasets 27 2.5 Gene Expression Data for Strain Improvement 30 Overview of Proposed Data- mining Framework for Strain Improvement 32 PCA Based Methodology for ... Novel data- mining methods suitable for gene expression data mining are proposed and validated using artiﬁcial and real expression datasets In the following sections, gene expression data generation ... efﬁcient data- mining methodologies to uncover the hidden patterns and identify the genetic targets for strain improvement There are several challenges for the analysis of gene expression data Some...

Computational analysis of sexual dimorphism in gene expression under toxico pathological states

... COMPUTATIONAL ANALYSIS OF SEXUAL DIMORPHISM IN GENE EXPRESSION UNDER TOXICO- PATHOLOGICAL STATES ZHANG XUN (B.Sc & M.Sc., Lanzhou University) A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF ... review of sex-dimorphic gene expression in animals under both normal physiology and toxicopathological states The current understanding of hormonal and genetic contributions to sexual dimorphism ... analyses of sex-biased genes and their inverted expression patterns under different toxico- pathological conditions 94 Figure 23 Inverted sex-biased gene expression profiles of the zebrafish in...

Tài liệu Báo cáo khoa học: Mixed lineage leukemia: roles in gene expression, hormone signaling and mRNA processing docx

... that includes a DNA-binding domain, a ligand-binding domain and a transactivation domain The DNA-binding domain is responsible for DNA binding speciﬁcity and dimerization, and the ligand-binding ... domain involved in protein–protein interactions FYRC and FYRN domains are involved in heterodimerization between MLLN and MLLC terminal fragments High-mobility group (HMG) domains are involved in ... selective and independent roles within the hematopoietic system, maintaining quiescence in HSCs and promoting proliferation in progenitors [23] Similarly, in an independent study using a conditional...

báo cáo hóa học:" Cyclic changes in gene expression induced by Peg-interferon alfa-2b plus ribavirin in peripheral blood " pot

... 107.7 interferon, alpha-inducible protein 27 (ISG12, P27) 1.9 interferon -induced protein 35 5.0 Interferon -induced protein 44, p44 8.4 interferon -induced protein 44-like 2.2 interferon induced ... relapsed by the end of treatment Changes in Global Gene Expression Gene expression in PBMC changed dramatically and rapidly during PEG-interferon- α2b (PegIntron™) /ribavirin therapy, with major changes ... 1Fold -changes 2Fold -changes interferon, alpha-inducible protein 27 sialic acid binding Ig-like lectin 1, sialoadhesin chemokine (C-C motif) ligand radical S-adenosyl methionine domain containing interferon-induced...

Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae pdf

... further investigate the relationship between genetic variation in gene expression and phenotypic variation, we measured genome-wide mRNA transcript levels in nine strains of Saccharomyces cerevisiae ... differences in transcript abundance both within and between closely related species [4-12] In some instances, genetic variation in gene expression has been associated with phenotypic variation ... homeostasis gene involved in copper sulfide mineralization in Saccharomyces cerevisiae Mol Cell Biol 1996, 16:2464-2472 Thomas D, Surdin-Kerjan Y: Metabolism of sulfur amino acids in Saccharomyces cerevisiae...

Tracking developmental changes in gene expression pot

... of gene Birnbaum et al [5] used binary coding, principal component analysis and k-means clustering to find dominant expression patterns among the 5,712 differentially expressed genes (defined ... as coordinates, resulting in five points in a multidimensional space The Euclidian geometric distance between these points was calculated To obtain the clustering, the points closest in space ... are totipotent and maintain their identity only in the context of the organism Yet, amazingly, this approach proved successful Only a minor set of genes appeared to be induced by protoplasting and...

báo cáo khoa học: " Gene expression profile analysis of tobacco leaf trichomes" docx

... http://www.biomedcentral.com/1471-2229/11/76 Page of 10 Table The 20 most abundant ESTs in the tobacco leaf trichome library with gene annotation of their closest hit identified by Blastx No of ESTs Gene ID Gene annotation of closest ... differentially expressed genes between trichomes and leaves were compared A total of 63.7% of highly expressed genes and 70.6% of low expressed genes of trichomes were annotated http:// amigo.geneontology.org ... understanding of the effects of hormone on trichomes will help to find new ways of the regulation of chemical compounds in the leaf surface Conclusion We analyzed gene expression in the leaf trichomes...

Báo cáo sinh học: " A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series" pps

... e-CCC -Biclustering: Finding and reporting all maximal eCCC-Biclusters in polynomial time This section presents e-CCC -Biclustering, a polynomial time biclustering algorithm for finding and reporting ... Related work on biclustering algorithms for time series gene expression data Supplementary material describing related work on biclustering algorithms for time series gene expression data analysis ... co-regulated gene clusters Bioinformatics 2004, 20(16):2711-2718 Madeira SC, Oliveira AL: An Efficient Biclustering Algorithm for finding Genes with Similar Patterns in Time- Series Expression Data In...

Báo cáo y học: "Changes in gene expression during the development of mammary tumors in MMTV-Wnt-1 transgenic mice" ppt

... that the initiating pathway determines a distinctive expression phenotype in tumors In addition, using proteins as markers of cell phenotypes, we showed that initiating oncogenes determine the developmental ... discussion Mammary tumors in MMTV-Wnt-1 transgenic mice have an expression profile distinct from that seen in mammary tumors induced by MMTV-Neu Comparison of expression profiles of tumors from ... MMTV-Neu-induced tumors described in the preceding section suggest that initiating oncogenes strongly influence gene expression in the tumors arising in these two Genome Biology 2005, 6:R84 information...

Báo cáo y học: "A method for high-throughput gene expression signature analysis" ppt

... microarray technology continues to be a mainstay of biologic discovery However, the ability to measure gene expression signatures of interest with great rapidity and flexibility, and at very high ... performed with LMF in our laboratory also delivered impressive accuracies (30 -gene androgen signature, 642 wells: 98.8% accuracy; 11 -gene sarcoma signature, 766 wells: 99.6% accuracy; 21 -gene ... BADGE, Beads Array for the Detection of Gene Expression, a high-throughput diagnostic bioassay Genome Res 2001, 11:1888-1898 Yeakley JM, Fan JB, Doucet D, Luo L, Wickham E, Ye Z, Chee MS, Fu...

CELL GEOMETRIC CONSTRAINTS INDUCE ACTOMYOSIN CONTRACTILITY DEPENDENT CHANGES IN GENE EXPRESSION AND CHROMOSOME POSITIONING

... repositioning Nuclear lamina which includes lamin and lamin binding proteins mediates chromosomal positioning (125, 126) Along with chromosome positioning, gene clustering has also been considered ... by geometrical cues and how it correlates with chromatin compaction and gene expression The critical molecular intermediates involved in the geometry regulated chromatin compaction and gene expression ... activity changes during the early onset of differentiation and couple with emergence of chromosomal positioning 12 Chapter 2: Cell geometric constraints induce modular gene expression...

Báo cáo hóa học: " The Local Maximum Clustering Method and Its Application in Microarray Gene Expression Data Analysis" docx

... of N data points to be clustered The local maximum of a data point i is the data point whose magnitude is the maximum among all the data points within a certain distance from the data point i ... the clustering results of diﬀerent methods The letters L, H, K, and S stand for the LMC method, the hierarchic clustering method, the K-mean clustering method, and the self-organization map clustering ... matches to the clusters in the models than the LMC and the hierarchic clustering methods 3.2 An application to microarray gene expression data Application of the LMC method to gene expression data...

báo cáo khoa học: " Identification of tissue-specific, abiotic stressresponsive gene expression patterns in wine grape (Vitis vinifera L.) based on curation and mining of large-scale EST data sets" docx

... Tillett et al.: Identification of tissue-specific, abiotic stress-responsive gene expression patterns in wine grape (Vitis vinifera L.) based on curation and mining of large-scale EST data sets BMC ... Lund S: Generation of ESTs in Vitis vinifera wine grape (Cabernet Sauvignon) and table grape (Muscat Hamburg) and discovery of new candidate genes with potential roles in berry development Gene ... metabolites including anthocyanins and proanthocyanins [19-22] mRNA and enzyme expression profiles during development and in response to abiotic stress effects have been studied intensively in wine grape...

Báo cáo hóa học: " Research Article The Wavelet-Based Cluster Analysis for Temporal Gene Expression Data" pptx

... the localized high-frequency details of the expression signal When the wavelet is fully diluted, the length of the wavelet is more comparable to the length of the gene expression signal and therefore ... therefore it extracts the low frequency trends of the signal In order to overcome the issue in temporal gene expression data analysis we take an approach using wavelet transformation The transformation ... As for the clustering analysis with the cubic splines, especially in large scale of temporal gene expression data, further research and comparison are needed In this paper, we ﬁrstly transformed...

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