Ensembl 2006

Birney, Ewan; Andrews, Dan; Cáccamo, Mario; Chen, Y; Clarke, Laura; Coates, Guy; Cox, Tony; Cunningham, Fiona; Curwen, V.; Cutts, Tim; Down, Thomas A.; Durbin, Richard; Fernandez-Suarez, Xose M; Flicek, Paul; Gräf, Stefan; Hammond, Martin; Herrero, Javier; Howe, Kerstin; Iyer, Vivek; Jekosch, Kerstin; Kähäri, Andreas; Kasprzyk, Arek; Keefe, Damian; Kokocinski, Felix; Kulesha, Eugene; London, Darin; Longden, Ian; Melsopp, Craig; Meidl, Patrick; Overduin, Bert; Parker, Anne; Proctor, G; Prlić, Andreas; Rae, Mark; Ríos, Daniel; Redmond, Seth; Schuster, Michael; Sealy, Ian; Searle, Stephen M. J.; Severin, Jessica; Slater, Guy; Smedley, Damian; Smith, James; Stabenau, Arne; Stalker, Jim; Trevanion, Stephen J.; Ureta-Vidal, Abel; Vogel, Jan; White, Simon; Woodwark, Cara; Hubbard, Tim

doi:10.1093/nar/gkj133

Cited by 361 publications

(322 citation statements)

References 19 publications

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“…Gene prediction and phylogeny. Opossum protein-coding and non-coding RNA genes were predicted using a modified version of the Ensembl genebuild pipeline 101 , followed by several rounds of refinement using Exonerate 102 and manual curation. Orthology and paralogy were inferred using the PhyOP pipeline with all predicted opossum and human (Ensembl v40) gene transcripts as input and K S as the distance metric 11,34 .…”

Section: Methodsmentioning

confidence: 99%

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Mikkelsen¹,

Wakefield²,

Aken³

et al. 2007

Nature

664

592

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We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.

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Section: Methodsmentioning

confidence: 99%

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Mikkelsen¹,

Wakefield²,

Aken³

et al. 2007

Nature

664

592

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“…Comparison of the gene expression profiles in control cells with or without PD169316 indicated that the inhibitor by itself had a negligible impact as it resulted in the differential expression of only one gene (SERPINA1 fold change: 1.96, P ¼ 0.008). Selected differential expressed genes were annotated with GO identifiers using the biomaRt package (Durinck et al, 2005), which retrieves data from Ensembl (Birney et al, 2006). These GO terms were mapped to the generic GO slim available from the GO website (http://www.geneontology.org).…”

Section: Analysis Of Microarraysmentioning

confidence: 99%

Molecular effectors and modulators of hypericin-mediated cell death in bladder cancer cells

et al. 2007

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Photodynamic therapy (PDT) is an anticancer approach utilizing a light-absorbing molecule and visible light irradiation to generate, in the presence of O 2 , cytotoxic reactive oxygen species, which cause tumor ablation. Given that the photosensitizer hypericin is under consideration for PDT treatment of bladder cancer we used oligonucleotide microarrays in the T24 bladder cancer cell line to identify differentially expressed genes with therapeutic potential. This study reveals that the expression of several genes involved in various metabolic processes, stress-induced cell death, autophagy, proliferation, inflammation and carcinogenesis is strongly affected by PDT and pinpoints the coordinated induction of a cluster of genes involved in the unfolded protein response pathway after endoplasmic reticulum stress and in antioxidant response. Analysis of PDT-treated cells after p38 MAPK inhibition or silencing unraveled that the induction of an important subset of differentially expressed genes regulating growth and invasion, as well as adaptive mechanisms against oxidative stress, is governed by this stress-activated kinase. Moreover, p38 MAPK inhibition blocked autonomous regrowth and migration of cancer cells escaping PDT-induced cell death. This analysis identifies new molecular effectors of the cancer cell response to PDT opening attractive avenues to improve the therapeutic efficacy of hypericin-based PDT of bladder cancer.

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“…Thus ARC allows the user to find regions that are common to multiple sets as well as regions that are specific to one set and not another. Additionally, by interfacing with a local Ensembl database (Birney et al 2006), we can obtain a region's genomic annotation, which includes the sequence of the region, overlapping or nearby annotated transcripts, and other details such as the lengths and coordinates of overlapping and nearby exons. ARC also has an interface for exporting and visualizing multiple data sets via the UCSC Genome Browser, which displays sets of ARs alongside sets of genomic annotation to provide a graphical overview of the selected region.…”

Section: Active Region Comparer Toolmentioning

confidence: 99%

“…6B) annotates and filters AR data sets using a local Ensembl database (Birney et al 2006). Its options include grabbing features of the interval itself (sequence, G/C content, etc.…”

Section: Arc Toolmentioning

confidence: 99%

“…In addition, the database allows the storage of sites of transcription factor binding and modifications called BARs (binding active regions), which are important to associate with TARs. We have also constructed a set of tools (Active Region Comparer [ARC]) that can be used for the comparison of multiple sets of ARs with each other and with annotations from Ensembl (Birney et al 2006). Both the database and tools are connected with the UCSC Genome Browser for automated visualization of custom tracks.…”

mentioning

confidence: 99%

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The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci

et al. 2007

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For the ∼1% of the human genome in the ENCODE regions, only about half of the transcriptionally active regions (TARs) identified with tiling microarrays correspond to annotated exons. Here we categorize this large amount of "unannotated transcription." We use a number of disparate features to classify the 6988 novel TARs-array expression profiles across cell lines and conditions, sequence composition, phylogenetic profiles (presence/absence of syntenic conservation across 17 species), and locations relative to genes. In the classification, we first filter out TARs with unusual sequence composition and those likely resulting from cross-hybridization. We then associate some of those remaining with proximal exons having correlated expression profiles. Finally, we cluster unclassified TARs into putative novel loci, based on similar expression and phylogenetic profiles. To encapsulate our classification, we construct a Database of Active Regions and Tools (DART.gersteinlab.org). DART has special facilities for rapidly handling and comparing many sets of TARs and their heterogeneous features, synchronizing across builds, and interfacing with other resources. Overall, we find that ∼14% of the novel TARs can be associated with known genes, while ∼21% can be clustered into ∼200 novel loci. We observe that TARs associated with genes are enriched in the potential to form structural RNAs and many novel TAR clusters are associated with nearby promoters. To benchmark our classification, we design a set of experiments for testing the connectivity of novel TARs. Overall, we find that 18 of the 46 connections tested validate by RT-PCR and four of five sequenced PCR products confirm connectivity unambiguously.

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Ensembl 2006

Cited by 361 publications

References 19 publications

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Molecular effectors and modulators of hypericin-mediated cell death in bladder cancer cells

The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci

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