MODELING GENE EXPRESSION FROM MICROARRAY
... Substantial effort is being made to build models to analyze it. Non-hierarchical clustering techniques such as k-means clustering are a class of mixture model-based approaches4. They group genes with similar expression patterns and have already proven useful in identifying genes that contribute to c ...
... Substantial effort is being made to build models to analyze it. Non-hierarchical clustering techniques such as k-means clustering are a class of mixture model-based approaches4. They group genes with similar expression patterns and have already proven useful in identifying genes that contribute to c ...
Package `tmod`
... module), and each column corresponds to the time points or conditions for which a given analysis was run. Each significant result is shown as a red dot. Size of the dot corresponds to the effect size (or any arbitrary value), and intensity of the color corresponds to the log10 of p-value. Just like ...
... module), and each column corresponds to the time points or conditions for which a given analysis was run. Each significant result is shown as a red dot. Size of the dot corresponds to the effect size (or any arbitrary value), and intensity of the color corresponds to the log10 of p-value. Just like ...
Results - Hal Cirad
... resulted from a natural hybridization between two wild diploids Coffea species (Carvalho, 1952). Polyploids are common in certain plant and animal taxa, and the genetic and evolutionary consequences of genome duplication have been recently reviewed (Comai, 2005). In particular for allotetrapolyploid ...
... resulted from a natural hybridization between two wild diploids Coffea species (Carvalho, 1952). Polyploids are common in certain plant and animal taxa, and the genetic and evolutionary consequences of genome duplication have been recently reviewed (Comai, 2005). In particular for allotetrapolyploid ...
Robust Prediction of Expression Differences among Human
... genes and genotype data. However, since their goal was to identify statistically significant associations of single SNPs, they do not consider multiple-SNP models, where combinations of SNPs and SNPs with small effects could play a role in generating the predictive model. One work attempted to devis ...
... genes and genotype data. However, since their goal was to identify statistically significant associations of single SNPs, they do not consider multiple-SNP models, where combinations of SNPs and SNPs with small effects could play a role in generating the predictive model. One work attempted to devis ...
Heritable genome-wide variation of gene expression and promoter methylation between
... To verify the results of the array-based methylation analysis, we arbitrarily selected four genes, which were DM on the tiling arrays in either parents or offspring, FUCA1, PCDHAC1, TXNDC16, and RUFY3, and replicated the findings for those, using a different technique and a different animal material ...
... To verify the results of the array-based methylation analysis, we arbitrarily selected four genes, which were DM on the tiling arrays in either parents or offspring, FUCA1, PCDHAC1, TXNDC16, and RUFY3, and replicated the findings for those, using a different technique and a different animal material ...
Altering gene expression by aminocoumarins: the role of DNA
... To obtain a more comprehensive overview on the effect of GyrB inhibition, and thus relaxation of supercoiling, we performed microarray analysis. Bacteria were grown to OD600 = 0.6 followed by one hour of incubation with or without novobiocin. Microarray analysis confirmed that recA and arlRS express ...
... To obtain a more comprehensive overview on the effect of GyrB inhibition, and thus relaxation of supercoiling, we performed microarray analysis. Bacteria were grown to OD600 = 0.6 followed by one hour of incubation with or without novobiocin. Microarray analysis confirmed that recA and arlRS express ...
Molecular bases of Down syndrome: differential gene
... responsible for the overproduction of ROS have not been fully elucidated. The up-regulation of the SOD1 gene, located on human chr 21 (Torsdottir et al., 2001; Sinha, 2005), has been proposed as a potential culprit. However, an animal model of DS, the TS1Cje mouse, carrying a subset of triplicated h ...
... responsible for the overproduction of ROS have not been fully elucidated. The up-regulation of the SOD1 gene, located on human chr 21 (Torsdottir et al., 2001; Sinha, 2005), has been proposed as a potential culprit. However, an animal model of DS, the TS1Cje mouse, carrying a subset of triplicated h ...
Article Positive and Purifying Selection on the Drosophila Y
... content is perhaps surprising given the largely heterochromatic state of the Y and its lack of recombination, and yet it is clear that genes have moved to and from the Y at an appreciable rate. This turnover appears to be dominated by gene gains (Koerich et al. 2008) and as a consequence, most of th ...
... content is perhaps surprising given the largely heterochromatic state of the Y and its lack of recombination, and yet it is clear that genes have moved to and from the Y at an appreciable rate. This turnover appears to be dominated by gene gains (Koerich et al. 2008) and as a consequence, most of th ...
Differential Expression Analysis
... Example of the Problem Suppose that 1000 genes are represented on an array and we test each with a t test with a Type I error threshold of 0.05. We might expect 40 genes to be differentially expressed. Of the 960 non-differentially expressed genes we can expect 5% errors, or .05 × 960 = 48 false pos ...
... Example of the Problem Suppose that 1000 genes are represented on an array and we test each with a t test with a Type I error threshold of 0.05. We might expect 40 genes to be differentially expressed. Of the 960 non-differentially expressed genes we can expect 5% errors, or .05 × 960 = 48 false pos ...
the complete Genetics Booklet
... than his parents do. He has only “bb” recessive Lamellar Ichthyosis genes to pass on, that's true. But like any other parent, he will contribute only one half of his children's genes, and his child would need two “b”genes to display the disorder. That child could get another “b” gene only if his oth ...
... than his parents do. He has only “bb” recessive Lamellar Ichthyosis genes to pass on, that's true. But like any other parent, he will contribute only one half of his children's genes, and his child would need two “b”genes to display the disorder. That child could get another “b” gene only if his oth ...
18.11
... Tim Hunt Lee Hartwaell Cytoskeleton functions Paul Nurse transcription mechanisms** cell cycle** transcriptional regulation organelle biogenesis chromatin modification secretion* signal transduction Randy W. Schekman protein James E. degradation* Rothman Thomas C. Südhof protein targeting mechanisms ...
... Tim Hunt Lee Hartwaell Cytoskeleton functions Paul Nurse transcription mechanisms** cell cycle** transcriptional regulation organelle biogenesis chromatin modification secretion* signal transduction Randy W. Schekman protein James E. degradation* Rothman Thomas C. Südhof protein targeting mechanisms ...
Full-text PDF
... Let us now consider an example. It has long been hypothesized that there may be some kind of correspondence between gene transcription order and functional relationships of the encoded proteins. Dandekar et al. showed that some highly conserved gene pairs do indeed interact physically on the same me ...
... Let us now consider an example. It has long been hypothesized that there may be some kind of correspondence between gene transcription order and functional relationships of the encoded proteins. Dandekar et al. showed that some highly conserved gene pairs do indeed interact physically on the same me ...
Genome Databases and Open Access Resources
... 1997 first eukaryotic genome : Saccharomyces cerevisiae S288C; International collaboration; 16 Chromosomes; 12,057 Kb, ~6000 genes. 1998 first multicellular organism Nematode Caenorhabditis elegans; 97 Mb; ~19,000 genes. 1999: first human chromosome: Chromosome 22 (49 Mb, 673 genes). ...
... 1997 first eukaryotic genome : Saccharomyces cerevisiae S288C; International collaboration; 16 Chromosomes; 12,057 Kb, ~6000 genes. 1998 first multicellular organism Nematode Caenorhabditis elegans; 97 Mb; ~19,000 genes. 1999: first human chromosome: Chromosome 22 (49 Mb, 673 genes). ...
The Genetics of Alcohol Metabolism
... various components of the body are not just simple stretches of DNA that serve as a template from which proteins are generated. Instead, they have a complex structure involv ing, in some cases, dozens of pieces of coding sequences interspersed with noncoding sequences. The coding sequences, which a ...
... various components of the body are not just simple stretches of DNA that serve as a template from which proteins are generated. Instead, they have a complex structure involv ing, in some cases, dozens of pieces of coding sequences interspersed with noncoding sequences. The coding sequences, which a ...
Stamm revision
... The yeast Saccharomyces cerevisiae has been used extensively to investigate functions of RNA and protein components of the spliceosome. As many of the yeast core splicing factors are evolutionarily conserved with human counterparts, information gained in yeast can be directly applied to humans. The ...
... The yeast Saccharomyces cerevisiae has been used extensively to investigate functions of RNA and protein components of the spliceosome. As many of the yeast core splicing factors are evolutionarily conserved with human counterparts, information gained in yeast can be directly applied to humans. The ...
video slide - Saginaw Valley State University
... the distance separating the loci. The recombination frequencies used to construct a linkage map for a particular chromosome are obtained from experimental crosses, such as the cross depicted in Figure 15.6. The distances between genes are expressed as map units (centimorgans), with one map unit equi ...
... the distance separating the loci. The recombination frequencies used to construct a linkage map for a particular chromosome are obtained from experimental crosses, such as the cross depicted in Figure 15.6. The distances between genes are expressed as map units (centimorgans), with one map unit equi ...
Information Encoding in Biological Molecules: DNA and
... • Publications (listed at http://www.ensembl.org/Docs/ ...
... • Publications (listed at http://www.ensembl.org/Docs/ ...
Nitrogen Fixation In Methanogens: The Archaeal
... may contain a single nitrogenase of the molybdenum type. The presence of molybdenum nitrogenases in other methanogens is corroborated by nif gene phylogeny (26), and by the apparent absence from the nif gene clusters of a gene corresponding to vnfG or anfG, which encode the δ subunits of alternative ...
... may contain a single nitrogenase of the molybdenum type. The presence of molybdenum nitrogenases in other methanogens is corroborated by nif gene phylogeny (26), and by the apparent absence from the nif gene clusters of a gene corresponding to vnfG or anfG, which encode the δ subunits of alternative ...
Choreography of Transcriptomes and Lipidomes of
... expressed lipid metabolism–related genes (DELM) were identified. Regardless of whether the genes were subjected to upregulation, downregulation, or complex regulation, there are several noteworthy features of DELM genes. DELM gene expression patterns are extremely diverse, spreading into all clusters ...
... expressed lipid metabolism–related genes (DELM) were identified. Regardless of whether the genes were subjected to upregulation, downregulation, or complex regulation, there are several noteworthy features of DELM genes. DELM gene expression patterns are extremely diverse, spreading into all clusters ...
Exploring HLA Diversity in Brazil
... Q: What are some of the challenges you’ve encountered in your HLA research? EC: We are starting from the beginning, in the sense that there is no established methodology to evaluate all HLA gene segments and regions. Much of the genetic analysis of HLA has been focused on answering specific clinical ...
... Q: What are some of the challenges you’ve encountered in your HLA research? EC: We are starting from the beginning, in the sense that there is no established methodology to evaluate all HLA gene segments and regions. Much of the genetic analysis of HLA has been focused on answering specific clinical ...
Genome - people.iup.edu
... Orthologs: genes found in one organism that are similar to those in another organism but differ because of speciation Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Normally, orthologs retain the same function in the course of evolution. Identifica ...
... Orthologs: genes found in one organism that are similar to those in another organism but differ because of speciation Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Normally, orthologs retain the same function in the course of evolution. Identifica ...
Identification and Characterization of KLK-L4, a New Kallikrein
... 1 gene (NES1) was found to be a tumor suppressor (11) that is down-regulated during breast cancer progression. The zyme/ protease M/neurosin gene is expressed in primary breast cancers but is down-regulated at metastatic sites (4). The large size of the kallikrein gene family in other species, such ...
... 1 gene (NES1) was found to be a tumor suppressor (11) that is down-regulated during breast cancer progression. The zyme/ protease M/neurosin gene is expressed in primary breast cancers but is down-regulated at metastatic sites (4). The large size of the kallikrein gene family in other species, such ...
Basic Array Analysis
... which are significant at the 5% level, we will get hundreds of false positives. Multiplicity adjustments winnow this down so that the number of false positives is smaller ...
... which are significant at the 5% level, we will get hundreds of false positives. Multiplicity adjustments winnow this down so that the number of false positives is smaller ...