当前位置： SCI文献检索 > GENOME RESEARCH期刊下所有文献 > Detecting genetic variation in microarray expression data.

Detecting genetic variation in microarray expression data.

Abstract：

:The use of high-density oligonucleotide arrays to measure the expression levels of thousands of genes in parallel has become commonplace. To take further advantage of the growing body of data, we developed a method, termed "GeSNP," to mine the detailed hybridization patterns in oligonucleotide array expression data for evidence of genetic variation. To demonstrate the performance of the algorithm, the hybridization patterns in data obtained previously from SAMP8/Ta, SAMP10/Ta, and SAMR1/Ta inbred mice and from humans and chimpanzees were analyzed. Genes with consistent strain-specific and species-specific hybridization pattern differences were identified, and approximately 90% of the candidate genes were independently confirmed to harbor sequence differences. Importantly, the quality of gene expression data was also improved by masking the probes of regions with putative sequence differences between species and strains. To illustrate the application to human disease groups, data from an inflammatory bowel disease study were analyzed. GeSNP identified sequence differences in candidate genes previously discovered in independent association and linkage studies and uncovered many promising new candidates. This approach enables the opportunistic extraction of genetic variation information from new or pre-existing gene expression data obtained with high-density oligonucleotide arrays.

journal_name

Genome Res

journal_title

Genome research

authors

Greenhall JA,Zapala MA,Cáceres M,Libiger O,Barlow C,Schork NJ,Lockhart DJ

doi

10.1101/gr.6307307

subject

Has Abstract

pub_date

2007-08-01 00:00:00

pages

1228-35

issue

8

eissn

1088-9051

issn

1549-5469

pii

gr.6307307

journal_volume

17

pub_type

杂志文章

相关文献

GENOME RESEARCH文献大全
  • Natural genetic variation in C. elegans identified genomic loci controlling metabolite levels.

    abstract：:Metabolic homeostasis is sustained by complex biological networks that respond to nutrient availability. Genetic and environmental factors may disrupt this equilibrium, leading to metabolic disorders, including obesity and type 2 diabetes. To identify the genetic factors controlling metabolism, we performed quantitati...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.232322.117

    authors： Gao AW,Sterken MG,Uit de Bos J,van Creij J,Kamble R,Snoek BL,Kammenga JE,Houtkooper RH

    更新日期：2018-09-01 00:00:00

  • Genomic analysis identifies association of Fusobacterium with colorectal carcinoma.

    abstract：:The tumor microenvironment of colorectal carcinoma is a complex community of genomically altered cancer cells, nonneoplastic cells, and a diverse collection of microorganisms. Each of these components may contribute to carcinogenesis; however, the role of the microbiota is the least well understood. We have characteri...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.126573.111

    authors： Kostic AD,Gevers D,Pedamallu CS,Michaud M,Duke F,Earl AM,Ojesina AI,Jung J,Bass AJ,Tabernero J,Baselga J,Liu C,Shivdasani RA,Ogino S,Birren BW,Huttenhower C,Garrett WS,Meyerson M

    更新日期：2012-02-01 00:00:00

  • Novel susceptibility locus for mouse hepatomas: evidence for a conserved tumor suppressor gene.

    abstract：:We have identified previously a putative tumor suppressor gene (TSG) locus at human chromosome (hchr) 7q31 showing that it is altered in a variety of human epithelial tumors. To determine whether this TSG is conserved in mice, we studied loss of heterozygosity (LOH) in chemically induced mouse liver adenomas. The LOH ...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.6.11.1070

    authors： Zenklusen JC,Rodriguez LV,LaCava M,Wang Z,Goldstein LS,Conti CJ

    更新日期：1996-11-01 00:00:00

  • Phenotypically distinct female castes in honey bees are defined by alternative chromatin states during larval development.

    abstract：:The capacity of the honey bee to produce three phenotypically distinct organisms (two female castes; queens and sterile workers, and haploid male drones) from one genotype represents one of the most remarkable examples of developmental plasticity in any phylum. The queen-worker morphological and reproductive divide is...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.236497.118

    authors： Wojciechowski M,Lowe R,Maleszka J,Conn D,Maleszka R,Hurd PJ

    更新日期：2018-10-01 00:00:00

  • Population genetic inference from genomic sequence variation.

    abstract：:Population genetics has evolved from a theory-driven field with little empirical data into a data-driven discipline in which genome-scale data sets test the limits of available models and computational analysis methods. In humans and a few model organisms, analyses of whole-genome sequence polymorphism data are curren...

    journal_title：Genome research

    pub_type： 杂志文章,评审

    doi：10.1101/gr.079509.108

    authors： Pool JE,Hellmann I,Jensen JD,Nielsen R

    更新日期：2010-03-01 00:00:00

  • Identification and analysis of internal promoters in Caenorhabditis elegans operons.

    abstract：:The current Caenorhabditis elegans genomic annotation has many genes organized in operons. Using directionally stitched promoterGFP methodology, we have conducted the largest survey to date on the regulatory regions of annotated C. elegans operons and identified 65, over 25% of those studied, with internal promoters. ...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.6824707

    authors： Huang P,Pleasance ED,Maydan JS,Hunt-Newbury R,O'Neil NJ,Mah A,Baillie DL,Marra MA,Moerman DG,Jones SJ

    更新日期：2007-10-01 00:00:00

  • Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells.

    abstract：:Spatially distinct gene expression profiles in neural stem cells (NSCs) are a prerequisite to the formation of neuronal diversity, but how these arise from the regulatory interactions between chromatin accessibility and transcription factor activity has remained unclear. Here, we demonstrate that, despite their distin...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.203513.115

    authors： Hagey DW,Zaouter C,Combeau G,Lendahl MA,Andersson O,Huss M,Muhr J

    更新日期：2016-07-01 00:00:00

  • An MCMC algorithm for haplotype assembly from whole-genome sequence data.

    abstract：:In comparison to genotypes, knowledge about haplotypes (the combination of alleles present on a single chromosome) is much more useful for whole-genome association studies and for making inferences about human evolutionary history. Haplotypes are typically inferred from population genotype data using computational met...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.077065.108

    authors： Bansal V,Halpern AL,Axelrod N,Bafna V

    更新日期：2008-08-01 00:00:00

  • Bacillus subtilis during feast and famine: visualization of the overall regulation of protein synthesis during glucose starvation by proteome analysis.

    abstract：:Dual channel imaging and warping of two-dimensional (2D) protein gels were used to visualize global changes of the gene expression patterns in growing Bacillus subtilis cells during entry into the stationary phase as triggered by glucose exhaustion. The 2D gels only depict single moments during the cells' growth cycle...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.905003

    authors： Bernhardt J,Weibezahn J,Scharf C,Hecker M

    更新日期：2003-02-01 00:00:00

  • Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs.

    abstract：:Lemurs and the other strepsirrhine primates are of great interest to the primate genomics community due to their phylogenetic placement as the sister lineage to all other primates. Previous attempts to resolve the phylogeny of lemurs employed limited mitochondrial or small nuclear data sets, with many relationships po...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.7265208

    authors： Horvath JE,Weisrock DW,Embry SL,Fiorentino I,Balhoff JP,Kappeler P,Wray GA,Willard HF,Yoder AD

    更新日期：2008-03-01 00:00:00

  • The Release 6 reference sequence of the Drosophila melanogaster genome.

    abstract：:Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and co...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.185579.114

    authors： Hoskins RA,Carlson JW,Wan KH,Park S,Mendez I,Galle SE,Booth BW,Pfeiffer BD,George RA,Svirskas R,Krzywinski M,Schein J,Accardo MC,Damia E,Messina G,Méndez-Lago M,de Pablos B,Demakova OV,Andreyeva EN,Boldyreva LV,Ma

    更新日期：2015-03-01 00:00:00

  • Strategies for mutational analysis of the large multiexon ATM gene using high-density oligonucleotide arrays.

    abstract：:Mutational analysis of large genes with complex genomic structures plays an important role in medical genetics. Technical limitations associated with current mutation screening protocols have placed increased emphasis on the development of new technologies to simplify these procedures. High-density arrays of >90,000-o...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.8.12.1245

    authors： Hacia JG,Sun B,Hunt N,Edgemon K,Mosbrook D,Robbins C,Fodor SP,Tagle DA,Collins FS

    更新日期：1998-12-01 00:00:00

  • Rapid evolution of mouse Y centromere repeat DNA belies recent sequence stability.

    abstract：:The Y centromere sequence of house mouse, Mus musculus, remains unknown despite our otherwise significant knowledge of the genome sequence of this important mammalian model organism. Here, we report the complete molecular characterization of the C57BL/6J chromosome Y centromere, which comprises a highly diverged minor...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.092080.109

    authors： Pertile MD,Graham AN,Choo KH,Kalitsis P

    更新日期：2009-12-01 00:00:00

  • Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding.

    abstract：:The regulation of gene expression is mediated at the transcriptional level by enhancer regions that are bound by sequence-specific transcription factors (TFs). Recent studies have shown that the in vivo binding sites of single TFs differ between developmental or cellular contexts. How this context-specific binding is ...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.132811.111

    authors： Yáñez-Cuna JO,Dinh HQ,Kvon EZ,Shlyueva D,Stark A

    更新日期：2012-10-01 00:00:00

  • Differential divergence of three human pseudoautosomal genes and their mouse homologs: implications for sex chromosome evolution.

    abstract：:The human pseudoautosomal region 1 (PAR1) is essential for meiotic pairing and recombination, and its deletion causes male sterility. Comparative studies of human and mouse pseudoautosomal genes are valuable in charting the evolution of this interesting region, but have been limited by the paucity of genes conserved b...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.197001

    authors： Gianfrancesco F,Sanges R,Esposito T,Tempesta S,Rao E,Rappold G,Archidiacono N,Graves JA,Forabosco A,D'Urso M

    更新日期：2001-12-01 00:00:00

  • Optical mapping of BAC clones from the human Y chromosome DAZ locus.

    abstract：:The accurate mapping of clones derived from genomic regions containing complex arrangements of repeated elements presents special problems for DNA sequencers. Recent advances in the automation of optical mapping have enabled us to map a set of 16 BAC clones derived from the DAZ locus of the human Y chromosome long arm...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.112100

    authors： Giacalone J,Delobette S,Gibaja V,Ni L,Skiadas Y,Qi R,Edington J,Lai Z,Gebauer D,Zhao H,Anantharaman T,Mishra B,Brown LG,Saxena R,Page DC,Schwartz DC

    更新日期：2000-09-01 00:00:00

  • PipMaker--a web server for aligning two genomic DNA sequences.

    abstract：:PipMaker (http://bio.cse.psu.edu) is a World-Wide Web site for comparing two long DNA sequences to identify conserved segments and for producing informative, high-resolution displays of the resulting alignments. One display is a percent identity plot (pip), which shows both the position in one sequence and the degree ...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.10.4.577

    authors： Schwartz S,Zhang Z,Frazer KA,Smit A,Riemer C,Bouck J,Gibbs R,Hardison R,Miller W

    更新日期：2000-04-01 00:00:00

  • Gene expression profiling in human fetal liver and identification of tissue- and developmental-stage-specific genes through compiled expression profiles and efficient cloning of full-length cDNAs.

    abstract：:Fetal liver intriguingly consists of hepatic parenchymal cells and hematopoietic stem/progenitor cells. Human fetal liver aged 22 wk of gestation (HFL22w) corresponds to the turning point between immigration and emigration of the hematopoietic system. To gain further molecular insight into its developmental and functi...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.175501

    authors： Yu Y,Zhang C,Zhou G,Wu S,Qu X,Wei H,Xing G,Dong C,Zhai Y,Wan J,Ouyang S,Li L,Zhang S,Zhou K,Zhang Y,Wu C,He F

    更新日期：2001-08-01 00:00:00

  • The genome-wide determinants of human and chimpanzee microsatellite evolution.

    abstract：:Mutation rates of microsatellites vary greatly among loci. The causes of this heterogeneity remain largely enigmatic yet are crucial for understanding numerous human neurological diseases and genetic instability in cancer. In this first genome-wide study, the relative contributions of intrinsic features and regional g...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.7113408

    authors： Kelkar YD,Tyekucheva S,Chiaromonte F,Makova KD

    更新日期：2008-01-01 00:00:00

  • High-throughput plasmid purification for capillary sequencing.

    abstract：:The need for expeditious and inexpensive methods for high-throughput DNA sequencing has been highlighted by the accelerated pace of genome DNA sequencing over the past year. At the Joint Genome Institute, the throughput in terms of high-quality bases per day has increased over 20-fold during the past 18 mo, reaching a...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.167801

    authors： Elkin CJ,Richardson PM,Fourcade HM,Hammon NM,Pollard MJ,Predki PF,Glavina T,Hawkins TL

    更新日期：2001-07-01 00:00:00

  • The human phosphotyrosine signaling network: evolution and hotspots of hijacking in cancer.

    abstract：:Phosphotyrosine (pTyr) signaling, which plays a central role in cell-cell and cell-environment interactions, has been considered to be an evolutionary innovation in multicellular metazoans. However, neither the emergence nor the evolution of the human pTyr signaling system is currently understood. Tyrosine kinase (TK)...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.128819.111

    authors： Li L,Tibiche C,Fu C,Kaneko T,Moran MF,Schiller MR,Li SS,Wang E

    更新日期：2012-07-01 00:00:00

  • The human obese (OB) gene: RNA expression pattern and mapping on the physical, cytogenetic, and genetic maps of chromosome 7.

    abstract：:The recently identified mouse obese (ob) gene apparently encodes a secreted protein that may function in the signaling pathway of adipose tissue. Mutations in the mouse ob gene are associated with the early development of gross obesity. A detailed knowledge concerning the RNA expression pattern and precise genomic loc...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.5.1.5

    authors： Green ED,Maffei M,Braden VV,Proenca R,DeSilva U,Zhang Y,Chua SC Jr,Leibel RL,Weissenbach J,Friedman JM

    更新日期：1995-08-01 00:00:00

  • Closing the gaps on human chromosome 19 revealed genes with a high density of repetitive tandemly arrayed elements.

    abstract：:The reported human genome sequence includes about 400 gaps of unknown sequence that were not found in the bacterial artificial chromosome (BAC) and cosmid libraries used for sequencing of the genome. These missing sequences correspond to approximately 1% of euchromatic regions of the human genome. Gap filling is a lab...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.1929904

    authors： Leem SH,Kouprina N,Grimwood J,Kim JH,Mullokandov M,Yoon YH,Chae JY,Morgan J,Lucas S,Richardson P,Detter C,Glavina T,Rubin E,Barrett JC,Larionov V

    更新日期：2004-02-01 00:00:00

  • The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo.

    abstract：:Highly overlapping patterns of genome-wide binding of many distinct transcription factors have been observed in worms, insects, and mammals, but the origins and consequences of this overlapping binding remain unclear. While analyzing chromatin immunoprecipitation data sets from 21 sequence-specific transcription facto...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.130682.111

    authors： Satija R,Bradley RK

    更新日期：2012-04-01 00:00:00

  • Genomic analysis of primordial dwarfism reveals novel disease genes.

    abstract：:Primordial dwarfism (PD) is a disease in which severely impaired fetal growth persists throughout postnatal development and results in stunted adult size. The condition is highly heterogeneous clinically, but the use of certain phenotypic aspects such as head circumference and facial appearance has proven helpful in d...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.160572.113

    authors： Shaheen R,Faqeih E,Ansari S,Abdel-Salam G,Al-Hassnan ZN,Al-Shidi T,Alomar R,Sogaty S,Alkuraya FS

    更新日期：2014-02-01 00:00:00

  • Why do human diversity levels vary at a megabase scale?

    abstract：:Levels of diversity vary across the human genome. This variation is caused by two forces: differences in mutation rates and the differential impact of natural selection. Pertinent to the question of the relative importance of these two forces is the observation that both diversity within species and interspecies diver...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.3461105

    authors： Hellmann I,Prüfer K,Ji H,Zody MC,Pääbo S,Ptak SE

    更新日期：2005-09-01 00:00:00

  • Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis.

    abstract：:The impact of inherited genetic variation on gene expression in humans is well-established. The majority of known expression quantitative trait loci (eQTLs) impact expression of local genes (cis-eQTLs). More research is needed to identify effects of genetic variation on distant genes (trans-eQTLs) and understand their...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.216754.116

    authors： Yang F,Wang J,GTEx Consortium.,Pierce BL,Chen LS

    更新日期：2017-11-01 00:00:00

  • An EST-enriched comparative map of Brassica oleracea and Arabidopsis thaliana.

    abstract：:A detailed comparative map of Brassica oleracea and Arabidopsis thaliana has been established based largely on mapping of Arabidopsis ESTs in two Arabidopsis and four Brassica populations. Based on conservative criteria for inferring synteny, "one to one correspondence" between Brassica and Arabidopsis chromosomes acc...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.10.6.776

    authors： Lan TH,DelMonte TA,Reischmann KP,Hyman J,Kowalski SP,McFerson J,Kresovich S,Paterson AH

    更新日期：2000-06-01 00:00:00

  • Functional conservation of Rel binding sites in drosophilid genomes.

    abstract：:Evolutionary constraints on gene regulatory elements are poorly understood: Little is known about how the strength of transcription factor binding correlates with DNA sequence conservation, and whether transcription factor binding sites can evolve rapidly while retaining their function. Here we use the model of the NF...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.6490707

    authors： Copley RR,Totrov M,Linnell J,Field S,Ragoussis J,Udalova IA

    更新日期：2007-09-01 00:00:00

  • Transcriptional fates of human-specific segmental duplications in brain.

    abstract：:Despite the importance of duplicate genes for evolutionary adaptation, accurate gene annotation is often incomplete, incorrect, or lacking in regions of segmental duplication. We developed an approach combining long-read sequencing and hybridization capture to yield full-length transcript information and confidently d...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.237610.118

    authors： Dougherty ML,Underwood JG,Nelson BJ,Tseng E,Munson KM,Penn O,Nowakowski TJ,Pollen AA,Eichler EE

    更新日期：2018-10-01 00:00:00