A MySQL dump of a database of transcript and protein haplotypes generated by combining the Ensembl 83 (GRCh37) gene set with 1000 Genomes phase 3 phased genotype data.
Abstract Genes potentially involved in the pathology of canine atopic dermatitis (AD) were identified using gene expression microarrays. Total RNA extracted from skin biopsies was hybridized to an Agilent Technologies custom‐designed 22K canine array. The arrays were analysed using Genedata Analyst software. Data were corrected for multiple hypothesis testing and tested for significance using the National Institute on Aging array analysis tool. For comparison, data were divided into separate groups: lesional atopic ( n = 16), nonlesional atopic ( n = 17) and healthy controls ( n = 9). Fifty‐four genes were differentially expressed at a significance level of 0.05 in canine AD compared to healthy controls. Sixteen genes were differentially expressed in both nonlesional and lesional atopic skin, 26 genes only in nonlesional skin and 12 only in lesional skin. These genes were associated with innate immune and inflammatory responses, cell cycle, apoptosis, barrier formation and transcriptional regulation. The most dysregulated gene in lesional skin was S100A8, which showed an almost 23‐fold increase in expression. This is a pro‐inflammatory cytokine located in the epidermal differentiation complex. Microarray analysis is a novel technique in canine AD. Significant changes in gene expression were identified in atopic skin. These were relevant to skin barrier formation and the immune response, suggesting that they both participate in AD. Gene expression restricted to lesional skin may be involved in inflammatory changes, whereas those shared or restricted to nonlesional skin may reflect the atopic phenotype. Investigating gene polymorphisms in the targets identified in this study will help improve our understanding of the genetic basis of this disease.
Aim: The aim of this study was to test chromosomes carrying the same DRB1–DQA1–DQB1 haplotype for single nucleotide polymorphisms (SNPs) in the major histocompatibility complex (MHC) that might mark subgroups of the haplotype with different risks for type 1 diabetes (T1D). Methods: Chromosomes from T1D children, their parents and non‐diabetic siblings in families of the Type 1 Diabetes Genetics Consortium (T1DGC) were analysed by two haplotype‐based methods: (i) logistic regression analysis restricted to phased chromosomes carrying the same DRB1–DQA1–DQB1 haplotype but differentiated by the two alleles at MHC SNPs, which were individually tested for association with T1D and (ii) homozygous parent transmission disequilibrium test (TDT) for biased transmission of a SNP allele to diabetic children from parents who are heterozygous at the SNP but homozygous for the specific DRB1–DQA1–DQB1 haplotype being evaluated. Results: A number of SNPs gave nominally significant (p < 0.05) evidence of marking two subsets of the 301–501–201 haplotype that might differ with respect to their diabetogenic potency. However, none of the SNPs achieved experiment‐wide significance and hence may be false‐positive associations. Conclusions: We discuss limitations and possible deficiencies of our study suggesting further work that might yield more robust SNP associations marking two subgroups of a DRB1–DQA1–DQB1 haplotype with different T1D risks.
Ensembl(http://www.ensembl.org)integrates genomic information for a comprehensive set of chordate genomes with a particular focus on resources for human, mouse, rat, zebrafish and other high-value sequenced genomes.We provide complete gene annotations for all supported species in addition to specific resources that target genome variation, function and evolution.Ensembl data is accessible in a variety of formats including via our genome browser, API and BioMart.This year marks the tenth anniversary of Ensembl and in that time the project has grown with advances in genome technology.As of release 56 (September 2009), Ensembl supports 51 species including marmoset, pig, zebra finch, lizard, gorilla and wallaby, which were added in the past year.Major additions and improvements to Ensembl since our previous report include the incorporation of the human GRCh37 assembly, enhanced visualisation and data-mining options for the Ensembl regulatory features and continued development of our software infrastructure.
The genome of the zebra finch — a songbird and a model for the study of vertebrate brain, behaviour and evolution — has been sequenced. Its comparison with the chicken genome, the only other bird genome available, shows that genes with neural function and implicated in cognitive processing of song have been rapidly evolving in the finch lineage. The study also shows that vocal communication engages much of the zebra finch brain transcriptome and identifies a potential integrator of microRNA signals linked to vocal communication. The genome of the zebra finch — a songbird and a model for studying the vertebrate brain, behaviour and evolution — has been sequenced. Comparison with the chicken genome, the only other bird genome available, shows that genes that have neural function and are implicated in the cognitive processing of song have been evolving rapidly in the finch lineage. Moreover, vocal communication engages much of the transcriptome of the zebra finch brain. The zebra finch is an important model organism in several fields1,2 with unique relevance to human neuroscience3,4. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken5—the only bird with a sequenced genome until now6. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes7. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.
The Ensembl project (http://www.ensembl.org) provides genome resources for chordate genomes with a particular focus on human genome data as well as data for key model organisms such as mouse, rat and zebrafish. Five additional species were added in the last year including gibbon (Nomascus leucogenys) and Tasmanian devil (Sarcophilus harrisii) bringing the total number of supported species to 61 as of Ensembl release 64 (September 2011). Of these, 55 species appear on the main Ensembl website and six species are provided on the Ensembl preview site (Pre!Ensembl; http://pre.ensembl.org) with preliminary support. The past year has also seen improvements across the project.
The Ensembl Variant Effect Predictor is a powerful toolset for the analysis, annotation, and prioritization of genomic variants in coding and non-coding regions. It provides access to an extensive collection of genomic annotation, with a variety of interfaces to suit different requirements, and simple options for configuring and extending analysis. It is open source, free to use, and supports full reproducibility of results. The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.
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