Multiple Testing Corrections
... Multiple testing corrections adjust p-values derived from multiple statistical tests to correct for occurrence of false positives. In microarray data analysis, false positives are genes that are found to be statistically different between conditions, but are not in reality. B. Importance of Multiple ...
... Multiple testing corrections adjust p-values derived from multiple statistical tests to correct for occurrence of false positives. In microarray data analysis, false positives are genes that are found to be statistically different between conditions, but are not in reality. B. Importance of Multiple ...
Reliable classification of two-class cancer data using evolutionary
... in the cell cycle and to assign probable functions to newly discovered genes with the expression patterns of known genes. Moreover, the DNA microarray provides a global perspective of gene expression levels, which can be used in gene clustering tools (Alon et al., 1999), tissue classification method ...
... in the cell cycle and to assign probable functions to newly discovered genes with the expression patterns of known genes. Moreover, the DNA microarray provides a global perspective of gene expression levels, which can be used in gene clustering tools (Alon et al., 1999), tissue classification method ...
CpG Mutation Rates in the Human Genome Are
... Throughout the Human Genome The analysis in figure 2 was limited to single-copy DNA sequences on two chromosomes (see Methods) and further required inferences based on sequence comparisons to the chimpanzee. We, therefore, sought to confirm whether this same pattern of CpG turnover could be discerne ...
... Throughout the Human Genome The analysis in figure 2 was limited to single-copy DNA sequences on two chromosomes (see Methods) and further required inferences based on sequence comparisons to the chimpanzee. We, therefore, sought to confirm whether this same pattern of CpG turnover could be discerne ...
Defects in Protein Glycosylation Cause SHO1-Dependent
... response to osmotic stress, requires Ste20 and Ste11 (O’Rourke and Herskowitz 1998). To learn more about regulation of the pheromone pathway and its possible interface with other pathways, we have sought mutants that showed increased expression of FUS1, a pheromone-responsive gene. A substantial num ...
... response to osmotic stress, requires Ste20 and Ste11 (O’Rourke and Herskowitz 1998). To learn more about regulation of the pheromone pathway and its possible interface with other pathways, we have sought mutants that showed increased expression of FUS1, a pheromone-responsive gene. A substantial num ...
- eScholarship@UMMS - University of Massachusetts
... fibroblast cell lines were used in this study: an HGPS patient fibroblast (HGPS), a normal cell line from the father of the HGPS patient (Father), and an age-matched normal fibroblast line (Age Control). Two biological replicates were performed at different passages, since some changes in HGPS may p ...
... fibroblast cell lines were used in this study: an HGPS patient fibroblast (HGPS), a normal cell line from the father of the HGPS patient (Father), and an age-matched normal fibroblast line (Age Control). Two biological replicates were performed at different passages, since some changes in HGPS may p ...
Epigenetic Inactivation of Chalcone Synthase-A
... revertant; the mechanism of the reversion is unknown. The CHS-A mRNA levels differ greatly in the two lines, as demonstrated by RNA gel-blot analysis and reverse transcription–PCR (RT–PCR) (Metzlaff et al. 1997). The levels of CHS-A mRNA from both the CHS-A transgene and the endogenous CHS-A gene (C ...
... revertant; the mechanism of the reversion is unknown. The CHS-A mRNA levels differ greatly in the two lines, as demonstrated by RNA gel-blot analysis and reverse transcription–PCR (RT–PCR) (Metzlaff et al. 1997). The levels of CHS-A mRNA from both the CHS-A transgene and the endogenous CHS-A gene (C ...
Simple Sequence Repeats as Advantageous Mutators
... rodent species, while montane and meadow voles (M. montanus and M. pennsylvanicus) are asocial and non-monogamous. These differing social behaviors depend on the pattern of expression for the vasopressin receptor avpr1a gene, with higher levels of expression in the ventral forebrain of the social vo ...
... rodent species, while montane and meadow voles (M. montanus and M. pennsylvanicus) are asocial and non-monogamous. These differing social behaviors depend on the pattern of expression for the vasopressin receptor avpr1a gene, with higher levels of expression in the ventral forebrain of the social vo ...
Leukaemia Section T-lineage acute lymphoblastic leukemia (T-ALL) Atlas of Genetics and Cytogenetics
... TRG@ (7p14) The TRG@(TCRG) locus (7p14) may be restricted to T-cell tumors in patients with ataxia telangiectasia. The TRG@ locus is not involved in translocations in TALL. Historically, it was thought that the inv(7)(p15;q34) or t(7;7)(p15;q34) juxtaposed TRB@ to TRG@, but recently it was shown tha ...
... TRG@ (7p14) The TRG@(TCRG) locus (7p14) may be restricted to T-cell tumors in patients with ataxia telangiectasia. The TRG@ locus is not involved in translocations in TALL. Historically, it was thought that the inv(7)(p15;q34) or t(7;7)(p15;q34) juxtaposed TRB@ to TRG@, but recently it was shown tha ...
Mapping of partially overlapping de novo deletions across an autism
... [INTLQ3—Posthuma et al., 2005] (Fig. 1) both of which are relevant to the patients described here. By means of fluorescence in situ hybridization (FISH) mapping with bacterial artificial chromosomes (BAC) clone probes along the critical chromosomal bands we define the boundaries of both deletions an ...
... [INTLQ3—Posthuma et al., 2005] (Fig. 1) both of which are relevant to the patients described here. By means of fluorescence in situ hybridization (FISH) mapping with bacterial artificial chromosomes (BAC) clone probes along the critical chromosomal bands we define the boundaries of both deletions an ...
... regulatory differences are due to divergent evolution of the target structural genes. Although several regulatory anthocyanin genes have now been isolated from Antirrhinum and Petunia spp, the data are too incomplete to exclude either of these two possibilities. Molecular analysis of the an11 locus ...
Modulation of base excision repair of 8
... always present in chromosomal DNA (28). Interestingly, genome-wide distribution of 8-oxoG shows a distinctive non-random pattern (29), thus suggesting a spatial heterogeneity of damage generation and/or repair in cells, the reasons for which are unclear. Here, we used a reporter gene approach to inv ...
... always present in chromosomal DNA (28). Interestingly, genome-wide distribution of 8-oxoG shows a distinctive non-random pattern (29), thus suggesting a spatial heterogeneity of damage generation and/or repair in cells, the reasons for which are unclear. Here, we used a reporter gene approach to inv ...
Leukaemia Section t(5;9)(q14.1;p24) SSBP2/JAK2 Atlas of Genetics and Cytogenetics in Oncology and Haematology
... a). Partial GTG-banded karyotypes showing the t(5;9)(q14.1;p24.1). b). Partial FISH analysis showing the 5'JAK2 hybridization signal on der(5), the 3'JAK2 hybridization signal on der(9) and an intact JAK2 hybridization signal on the normal chromosome 9. ...
... a). Partial GTG-banded karyotypes showing the t(5;9)(q14.1;p24.1). b). Partial FISH analysis showing the 5'JAK2 hybridization signal on der(5), the 3'JAK2 hybridization signal on der(9) and an intact JAK2 hybridization signal on the normal chromosome 9. ...
Molecular Plant-Microbe Interactions
... induced by all the mutants with a 50 to 75% recovery at day 40 on O. viciifolia plants, compared with strain N33, in which the recovery was 100%. However, fewer bacteria were recovered from nodules induced by all mutants compared with the wild type after 6 days of growth on yeast mannitol agar plate ...
... induced by all the mutants with a 50 to 75% recovery at day 40 on O. viciifolia plants, compared with strain N33, in which the recovery was 100%. However, fewer bacteria were recovered from nodules induced by all mutants compared with the wild type after 6 days of growth on yeast mannitol agar plate ...
A process for analysis of microarray comparative genomics
... and reference strains. This is determined by labelling genomic DNA from the test and reference sample with different fluorescent dyes followed by co-hybridisation to the microarray slide. If a gene is conserved in both samples the fluorescence emitted at the corresponding position on the array will ...
... and reference strains. This is determined by labelling genomic DNA from the test and reference sample with different fluorescent dyes followed by co-hybridisation to the microarray slide. If a gene is conserved in both samples the fluorescence emitted at the corresponding position on the array will ...
Genetic counseling in Angelman syndrome: The challenges of
... risk. This figure is an estimation derived from our experience [Hendrickson et al., 1991], plus the cumulative data of many large surveys of AS cases where the typical, large deletion was not associated with recurrence within the family. Although the risk is expected to be quite low in future pregna ...
... risk. This figure is an estimation derived from our experience [Hendrickson et al., 1991], plus the cumulative data of many large surveys of AS cases where the typical, large deletion was not associated with recurrence within the family. Although the risk is expected to be quite low in future pregna ...
Large-Scale Variation Among Human and Great Ape Genomes
... an organism, which may result in phenotypic variation susceptible to selection pressures. Gene loss has been proposed as an important force in driving the evolution of eukaryotic genomes in response to selective pressures such as altered growth conditions in yeast, or infectious disease in the human ...
... an organism, which may result in phenotypic variation susceptible to selection pressures. Gene loss has been proposed as an important force in driving the evolution of eukaryotic genomes in response to selective pressures such as altered growth conditions in yeast, or infectious disease in the human ...
BIOINFORMATICS
... We demonstrate our approach by creating a diagnosis model to accurately distinguish between follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL). We will use the oligonucleotide microarray gene expression data of Shipp et al. (2002) produced at the Whitehead Institute (WI data), and va ...
... We demonstrate our approach by creating a diagnosis model to accurately distinguish between follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL). We will use the oligonucleotide microarray gene expression data of Shipp et al. (2002) produced at the Whitehead Institute (WI data), and va ...
Genetic Regulation of Meristem Maintenance and Organ
... Molecular genetic studies in Arabidopsis thaliana over the last 15 years have produced a wealth of information that has considerably advanced our understanding of plant development at the molecular level. Among these advances, the ABC model of floral organ specification and the negative feedback mod ...
... Molecular genetic studies in Arabidopsis thaliana over the last 15 years have produced a wealth of information that has considerably advanced our understanding of plant development at the molecular level. Among these advances, the ABC model of floral organ specification and the negative feedback mod ...
Recent and ongoing selection in the human genome
... Genome-wide scans for sweeps in humans The LCT and G6PD loci provide some of the most striking examples of ongoing selective sweeps in the human genome. These genes were identified a priori as candidate genes on the basis of functional information. Several recent papers have aimed at detecting loci ...
... Genome-wide scans for sweeps in humans The LCT and G6PD loci provide some of the most striking examples of ongoing selective sweeps in the human genome. These genes were identified a priori as candidate genes on the basis of functional information. Several recent papers have aimed at detecting loci ...
Mutations in FUS, an RNA Processing Protein, Cause Familial
... the genome-wide scan using the 10K singlenucleotide polymorphism (SNP) arrays. This confirmed linkage to chromosome 16 with a conserved haplotype containing more than 400 genes (fig. S1). Using a candidate gene approach, we sequenced 279 exons from 32 genes and expressed sequence tags (ESTs) and 10 ...
... the genome-wide scan using the 10K singlenucleotide polymorphism (SNP) arrays. This confirmed linkage to chromosome 16 with a conserved haplotype containing more than 400 genes (fig. S1). Using a candidate gene approach, we sequenced 279 exons from 32 genes and expressed sequence tags (ESTs) and 10 ...
SCAPE-IntroductionToTaverna-myExper
... SOAP/WSDL Web services REST Web services SoapLab Web services R statistical services Inline Beanshell scripts External tools and scripts (via ssh or localhost) Spreadsheet import XPath and text manipulation services SADI semantic Web services Nested workflows (workflow within workflow) BioMoby BioMa ...
... SOAP/WSDL Web services REST Web services SoapLab Web services R statistical services Inline Beanshell scripts External tools and scripts (via ssh or localhost) Spreadsheet import XPath and text manipulation services SADI semantic Web services Nested workflows (workflow within workflow) BioMoby BioMa ...
PDF - WashU Epigenome Browser
... Learn more about the supported numerical track formats bedGraph (http: //wiki.wubrowse.org/bedgraph) and bigWig (http://wiki.wubrowse.org/bigwig). ...
... Learn more about the supported numerical track formats bedGraph (http: //wiki.wubrowse.org/bedgraph) and bigWig (http://wiki.wubrowse.org/bigwig). ...
Using Risk-based Sampling to Enrich Cohorts for Endpoints, Genes
... We now consider a pure interaction scenario, where E doubles risk but only for those who carry one or two copies of the variant allele, and genotype does not affect risk in the absence of exposure. Figure 2A shows results based on comparing a saturated model for joint effects with a model with just ...
... We now consider a pure interaction scenario, where E doubles risk but only for those who carry one or two copies of the variant allele, and genotype does not affect risk in the absence of exposure. Figure 2A shows results based on comparing a saturated model for joint effects with a model with just ...
Oncogenomics
Oncogenomics is a relatively new sub-field of genomics that applies high throughput technologies to characterize genes associated with cancer. Oncogenomics is synonymous with ""cancer genomics"". Cancer is a genetic disease caused by accumulation of mutations to DNA leading to unrestrained cell proliferation and neoplasm formation. The goal of oncogenomics is to identify new oncogenes or tumor suppressor genes that may provide new insights into cancer diagnosis, predicting clinical outcome of cancers, and new targets for cancer therapies. The success of targeted cancer therapies such as Gleevec, Herceptin, and Avastin raised the hope for oncogenomics to elucidate new targets for cancer treatment.Besides understanding the underlying genetic mechanisms that initiates or drives cancer progression, one of the main goals of oncogenomics is to allow for the development of personalized cancer treatment. Cancer develops due to an accumulation of mutations in DNA. These mutations accumulate randomly, and thus, different DNA mutations and mutation combinations exist between different individuals with the same type of cancer. Thus, identifying and targeting specific mutations which have occurred in an individual patient may lead to increased efficacy of cancer therapy.The completion of the Human Genome Project has greatly facilitated the field of oncogenomics and has increased the abilities of researchers to find cancer causing genes. In addition, the sequencing technologies now available for sequence generation and data analysis have been applied to the study of oncogenomics. With the amount of research conducted on cancer genomes and the accumulation of databases documenting the mutational changes, it has been predicted that the most important cancer-causing mutations, rearrangements, and altered expression levels will be cataloged and well characterized within the next decade.Cancer research may look either on the genomic level at DNA mutations, the epigenetic level at methylation or histone modification changes, the transcription level at altered levels of gene expression, or the protein level at altered levels of protein abundance and function in cancer cells. Oncogenomics focuses on the genomic, epigenomic, and transcript level alterations in cancer.