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Article ; Online: Transcriptomic analysis of insecticide resistance in the lymphatic filariasis vector Culex quinquefasciatus.

Silva Martins, Walter Fabricio / Wilding, Craig Stephen / Isaacs, Alison Taylor / Rippon, Emily Joy / Megy, Karine / Donnelly, Martin James

Scientific reports

2019 Volume 9, Issue 1, Page(s) 11406

Abstract: Culex quinquefasciatus plays an important role in transmission of vector-borne diseases of public health importance, including lymphatic filariasis (LF), as well as many arboviral diseases. Currently, efforts to tackle C. quinquefasciatus vectored ... ...

Abstract	Culex quinquefasciatus plays an important role in transmission of vector-borne diseases of public health importance, including lymphatic filariasis (LF), as well as many arboviral diseases. Currently, efforts to tackle C. quinquefasciatus vectored diseases are based on either mass drug administration (MDA) for LF, or insecticide-based interventions. Widespread and intensive insecticide usage has resulted in increased resistance in mosquito vectors, including C. quinquefasciatus. Herein, the transcriptome profile of Ugandan bendiocarb-resistant C. quinquefasciatus was explored to identify candidate genes associated with insecticide resistance. High levels of insecticide resistance were observed for five out of six insecticides tested, with the lowest mortality (0.97%) reported to permethrin, while for DDT, lambdacyhalothrin, bendiocarb and deltamethrin the mortality rate ranged from 1.63-3.29%. Resistance to bendiocarb in exposed mosquitoes was marked, with 2.04% mortality following 1 h exposure and 58.02% after 4 h. Genotyping of the G119S Ace-1 target site mutation detected a highly significant association (p < 0.0001; OR = 25) between resistance and Ace1-119S. However, synergist assays using the P450 inhibitor PBO, or the esterase inhibitor TPP resulted in markedly increased mortality (to ≈80%), suggesting a role of metabolic resistance in the resistance phenotype. Using a novel, custom 60 K whole-transcriptome microarray 16 genes significantly overexpressed in resistant mosquitoes were detected, with the P450 Cyp6z18 showing the highest differential gene expression (>8-fold increase vs unexposed controls). These results provide evidence that bendiocarb resistance in Ugandan C. quinquefasciatus is mediated by both target-site mechanisms and over-expression of detoxification enzymes.
MeSH term(s)	Acetylcholinesterase/genetics ; Animals ; Culex/drug effects ; Culex/genetics ; Culex/parasitology ; Elephantiasis, Filarial/parasitology ; Elephantiasis, Filarial/prevention & control ; Elephantiasis, Filarial/transmission ; Female ; Gene Expression Profiling ; Genes, Insect/genetics ; Genotyping Techniques ; Humans ; Insect Proteins/genetics ; Insecticide Resistance/genetics ; Insecticides/pharmacology ; Mosquito Control/methods ; Mosquito Vectors/drug effects ; Mosquito Vectors/genetics ; Mosquito Vectors/parasitology ; Mutation ; Oligonucleotide Array Sequence Analysis ; Uganda ; Wuchereria bancrofti/pathogenicity
Chemical Substances	Insect Proteins ; Insecticides ; Acetylcholinesterase (EC 3.1.1.7)
Language	English
Publishing date	2019-08-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-019-47850-w
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Article ; Online: Positional clustering of differentially expressed genes on human chromosomes 20, 21 and 22.

Mégy, Karine / Audic, Stéphane / Claverie, Jean-Michel

Genome biology

2003 Volume 4, Issue 2, Page(s) P1

Abstract: Background: Clusters of genes co-expressed are known in prokaryotes (operons) and were recently described in several eukaryote organisms, including Human. According to some studies, these clusters consist of housekeeping genes, whereas other studies ... ...

Abstract	Background: Clusters of genes co-expressed are known in prokaryotes (operons) and were recently described in several eukaryote organisms, including Human. According to some studies, these clusters consist of housekeeping genes, whereas other studies suggest that these clustered genes exhibit similar tissue specificity. Here we further explore the relationship between co-expression and chromosomal co-localization in the human genome by analyzing the expression status of the genes along the best-annotated chromosomes 20, 21 and 22. Methods: Gene expression levels were estimated according to their publicly available ESTs and gene differential expressions were assessed using a previously described and validated statistical test. Gene sequences for chromosomes 20, 21 and 22 were taken from the Ensembl annotation. Results: We identified clusters of genes specifically expressed in similar tissues along chromosomes 20, 21 and 22. These co-expression clusters occurred more frequently than expected by chance and may thus be biologically significant. Conclusion: The co-expression of co-localized genes might be due to higher chromatin structures influencing the gene availability for transcription in a given tissue or cell type.
MeSH term(s)	Chromosomes, Human, Pair 20/genetics ; Chromosomes, Human, Pair 21/genetics ; Chromosomes, Human, Pair 22/genetics ; Expressed Sequence Tags ; Gene Expression Profiling ; Humans
Language	English
Publishing date	2003-01-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6914 ; 1465-6906
ISSN (online)	1474-760X ; 1465-6914
ISSN	1465-6906
DOI	10.1186/gb-2003-4-2-p1
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Article: Heart-specific genes revealed by expressed sequence tag (EST) sampling

Mégy, Karine / Audic, Stéphane / Claverie, Jean-Michel

Genome biology. 2002 Dec., v. 3, no. 12

2002

Abstract: BACKGROUND: Cardiovascular diseases are the primary cause of death worldwide; the identification of genes specifically expressed in the heart is thus of major biomedical interest. We carried out a comprehensive analysis of gene-expression profiles using ... ...

Abstract	BACKGROUND: Cardiovascular diseases are the primary cause of death worldwide; the identification of genes specifically expressed in the heart is thus of major biomedical interest. We carried out a comprehensive analysis of gene-expression profiles using expressed sequence tags (ESTs) to identify genes overexpressed in the human adult heart. The initial set of genes expressed in the heart was constructed by clustering and assembling ESTs from heart cDNA libraries. Expression profiles were then generated for each gene by counting their cognate ESTs in all libraries. Differential expression was assessed by applying a previously published statistical procedure to these profiles. RESULTS: We identified 35 cardiac-specific genes overexpressed in the heart, some of which displayed significant coexpression. Some genes had no previously recognized cardiac function. Of the 35 genes, 32 were mapped back onto the human genome sequence. According to Online Mendelian Inheritance in Man (OMIM), five genes were previously known as heart-disease genes and one gene was located in the locus of a bleeding disorder. Analysis of the promoter regions of this collection of genes provides the first list of putative regulatory elements associated with differential cardiac expression. CONCLUSION: This study shows that ESTs are still a powerful tool to identify differentially expressed genes. We present a list of genes specifically expressed in the human heart, one of which is a candidate for a bleeding disorder. In addition, we provide the first set of putative regulatory elements, the combination of which appears correlated with heart-specific gene expression.
Keywords	loci ; cardiovascular diseases ; Mendelian inheritance ; complementary DNA ; gene overexpression ; humans ; hemorrhage ; expressed sequence tags ; cardiac output ; cDNA libraries ; death ; heart ; gene expression regulation ; promoter regions ; adults
Language	English
Dates of publication	2002-12
Size	p. 411.
Publishing place	Springer-Verlag
Document type	Article
Note	2019-12-04
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6906
ISSN (online)	1474-760X
ISSN	1465-6906
DOI	10.1186/gb-2002-3-12-research0074
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Article ; Online: Heart specific genes revealed by EST sampling.

Mégy, Karine / Audic, Stéphane / Claverie, Jean-Michel

Genome biology

2002 Volume 3, Issue 9, Page(s) PREPRINT0008

Abstract: Background: Cardio-vascular diseases are the first cause of death worldwide, particularly in the developed countries; the identification of genes specifically expressed in the cardiac muscle is thus of major biomedical interest. In this study, we ... ...

Abstract	Background: Cardio-vascular diseases are the first cause of death worldwide, particularly in the developed countries; the identification of genes specifically expressed in the cardiac muscle is thus of major biomedical interest. In this study, we performed a comprehensive analysis of the expression profiles to identify genes over-expressed in the human adult heart using the public Expressed Sequence Tags (ESTs) database. The initial set of genes expressed in the heart was constructed by clustering and assembling ESTs from human adult heart cDNA libraries. Expression profiles were then generated for each of these genes by counting their cognate ESTs in all libraries. Differential expression was assessed by applying to these profiles a previously published statistical procedure. Results: We identified 35 "cardiac specific" genes significantly over-expressed in the heart, some of them exhibiting significant co-expressions. Some genes had clear functional association with the heart, and others had no previously recognized cardiac function. Of the 35 genes, 32 were mapped back onto the human genome sequence. According to OMIM, 5 genes were previously known as heart disease genes and one gene was located in the locus of a bleeding disorder. The analysis of the core promoter regions of our collection of "cardiac specific" genes provides the first list of putative regulatory elements associated with differential gene expression in the heart. Conclusion: This study shows that ESTs are still a powerful tool to identify differentially expressed genes: we presented a list of genes specifically expressed in the human heart, one of them being a candidate for a bleeding disorder. In addition, we provided the first set of putative regulatory elements, the combination of which appears correlated with heart-specific gene expression.
MeSH term(s)	Base Sequence ; Chromosome Mapping ; Escherichia coli/genetics ; Expressed Sequence Tags ; Gene Expression/genetics ; Gene Expression/physiology ; Gene Expression Profiling/methods ; Genome, Human ; Humans ; Myocardium/metabolism ; Phylogeny ; Promoter Regions, Genetic/genetics
Language	English
Publishing date	2002-08-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6914 ; 1465-6906
ISSN (online)	1474-760X ; 1465-6914
ISSN	1465-6906
DOI	10.1186/gb-2002-3-9-preprint0008
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Article ; Online: Heart-specific genes revealed by expressed sequence tag (EST) sampling.

Mégy, Karine / Audic, Stéphane / Claverie, Jean-Michel

Genome biology

2002 Volume 3, Issue 12, Page(s) RESEARCH0074

Abstract: Background: Cardiovascular diseases are the primary cause of death worldwide; the identification of genes specifically expressed in the heart is thus of major biomedical interest. We carried out a comprehensive analysis of gene-expression profiles using ...

Abstract	Background: Cardiovascular diseases are the primary cause of death worldwide; the identification of genes specifically expressed in the heart is thus of major biomedical interest. We carried out a comprehensive analysis of gene-expression profiles using expressed sequence tags (ESTs) to identify genes overexpressed in the human adult heart. The initial set of genes expressed in the heart was constructed by clustering and assembling ESTs from heart cDNA libraries. Expression profiles were then generated for each gene by counting their cognate ESTs in all libraries. Differential expression was assessed by applying a previously published statistical procedure to these profiles. Results: We identified 35 cardiac-specific genes overexpressed in the heart, some of which displayed significant coexpression. Some genes had no previously recognized cardiac function. Of the 35 genes, 32 were mapped back onto the human genome sequence. According to Online Mendelian Inheritance in Man (OMIM), five genes were previously known as heart-disease genes and one gene was located in the locus of a bleeding disorder. Analysis of the promoter regions of this collection of genes provides the first list of putative regulatory elements associated with differential cardiac expression. Conclusion: This study shows that ESTs are still a powerful tool to identify differentially expressed genes. We present a list of genes specifically expressed in the human heart, one of which is a candidate for a bleeding disorder. In addition, we provide the first set of putative regulatory elements, the combination of which appears correlated with heart-specific gene expression.
MeSH term(s)	Adult ; Chromosome Mapping/methods ; Cluster Analysis ; Contig Mapping/methods ; Contig Mapping/statistics & numerical data ; Databases, Genetic ; Expressed Sequence Tags ; Gene Expression Profiling/methods ; Gene Expression Profiling/statistics & numerical data ; Gene Expression Regulation/genetics ; Gene Expression Regulation/physiology ; Gene Library ; Heart Diseases/genetics ; Humans ; Muscle, Smooth, Vascular/chemistry ; Muscle, Smooth, Vascular/metabolism ; Myocardium/chemistry ; Myocardium/metabolism ; Organ Specificity/genetics ; Promoter Regions, Genetic/genetics
Language	English
Publishing date	2002-11-25
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6914 ; 1465-6906
ISSN (online)	1474-760X ; 1465-6914
ISSN	1465-6906
DOI	10.1186/gb-2002-3-12-research0074
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Article ; Online: VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics.

Megy, Karine / Emrich, Scott J / Lawson, Daniel / Campbell, David / Dialynas, Emmanuel / Hughes, Daniel S T / Koscielny, Gautier / Louis, Christos / Maccallum, Robert M / Redmond, Seth N / Sheehan, Andrew / Topalis, Pantelis / Wilson, Derek

Nucleic acids research

2011 Volume 40, Issue Database issue, Page(s) D729–34

Abstract: VectorBase (http://www.vectorbase.org) is a NIAID-supported bioinformatics resource for invertebrate vectors of human pathogens. It hosts data for nine genomes: mosquitoes (three Anopheles gambiae genomes, Aedes aegypti and Culex quinquefasciatus), tick ( ...

Abstract	VectorBase (http://www.vectorbase.org) is a NIAID-supported bioinformatics resource for invertebrate vectors of human pathogens. It hosts data for nine genomes: mosquitoes (three Anopheles gambiae genomes, Aedes aegypti and Culex quinquefasciatus), tick (Ixodes scapularis), body louse (Pediculus humanus), kissing bug (Rhodnius prolixus) and tsetse fly (Glossina morsitans). Hosted data range from genomic features and expression data to population genetics and ontologies. We describe improvements and integration of new data that expand our taxonomic coverage. Releases are bi-monthly and include the delivery of preliminary data for emerging genomes. Frequent updates of the genome browser provide VectorBase users with increasing options for visualizing their own high-throughput data. One major development is a new population biology resource for storing genomic variations, insecticide resistance data and their associated metadata. It takes advantage of improved ontologies and controlled vocabularies. Combined, these new features ensure timely release of multiple types of data in the public domain while helping overcome the bottlenecks of bioinformatics and annotation by engaging with our user community.
MeSH term(s)	Animals ; Culicidae/genetics ; Databases, Genetic ; Genetic Variation ; Genome, Insect ; Genomics ; Insect Vectors/genetics ; Insecticide Resistance ; Ixodes/genetics ; Pediculus/genetics ; Rhodnius/genetics ; Tsetse Flies/genetics
Language	English
Publishing date	2011-12-01
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkr1089
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Article ; Online: Expression Atlas update--an integrated database of gene and protein expression in humans, animals and plants.

Petryszak, Robert / Keays, Maria / Tang, Y Amy / Fonseca, Nuno A / Barrera, Elisabet / Burdett, Tony / Füllgrabe, Anja / Fuentes, Alfonso Muñoz-Pomer / Jupp, Simon / Koskinen, Satu / Mannion, Oliver / Huerta, Laura / Megy, Karine / Snow, Catherine / Williams, Eleanor / Barzine, Mitra / Hastings, Emma / Weisser, Hendrik / Wright, James /

Jaiswal, Pankaj / Huber, Wolfgang / Choudhary, Jyoti / Parkinson, Helen E / Brazma, Alvis

Nucleic acids research

2015 Volume 44, Issue D1, Page(s) D746–52

Abstract: Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. It consists of selected ... ...

Abstract	Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and other conditions. It consists of selected microarray and RNA-sequencing studies from ArrayExpress, which have been manually curated, annotated with ontology terms, checked for high quality and processed using standardised analysis methods. Since the last update, Atlas has grown seven-fold (1572 studies as of August 2015), and incorporates baseline expression profiles of tissues from Human Protein Atlas, GTEx and FANTOM5, and of cancer cell lines from ENCODE, CCLE and Genentech projects. Plant studies constitute a quarter of Atlas data. For genes of interest, the user can view baseline expression in tissues, and differential expression for biologically meaningful pairwise comparisons-estimated using consistent methodology across all of Atlas. Our first proteomics study in human tissues is now displayed alongside transcriptomics data in the same tissues. Novel analyses and visualisations include: 'enrichment' in each differential comparison of GO terms, Reactome, Plant Reactome pathways and InterPro domains; hierarchical clustering (by baseline expression) of most variable genes and experimental conditions; and, for a given gene-condition, distribution of baseline expression across biological replicates.
MeSH term(s)	Animals ; Cell Line, Tumor ; Databases, Genetic ; Gene Expression Profiling ; Humans ; Plants/genetics ; Plants/metabolism ; Proteins/metabolism ; Proteomics ; User-Computer Interface
Chemical Substances	Proteins
Language	English
Publishing date	2015-10-19
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkv1045
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Article ; Online: Genomic insights into the Ixodes scapularis tick vector of Lyme disease

Gulia-Nuss, Monika / Nuss, Andrew B. / Meyer, Jason M. / Sonenshine, Daniel E. / Roe, R. Michael / Waterhouse, Robert M. / Sattelle, David B. / Fuente, José de la / Ribeiro, José Marcos Chaves / Megy, Karine / Thimmapuram, Jyothi / Miller, Jason R. / Walenz, Brian P. / Koren, Sergey / Hostetler, Jessica B. / Thiagarajan, Mathangi / Joardar, Vinita S. / Hannick, Linda I. / Bidwell, Shelby /

Hammond, Martin P. / Young, Sarah / Zeng, Qiandong / Abrudan, Jenica L. / Almeida, Francisca C. / Ayllón, Nieves / Bhide, Ketaki / Bissinger, Brooke W. / Bonzon-Kulichenko, Elena / Buckingham, Steven D. / Caffrey, Daniel R. / Caimano, Melissa J. / Croset, Vincent / Driscoll, Timothy / Gilbert, Don / Gillespie, Joseph J. / Giraldo-Calderón, Gloria I. / Grabowski, Jeffrey M. / Jiang, David / Khalil, Sayed M.S. / Kim, Donghun / Kocan, Katherine M. / Koči, Juraj / Kuhn, Richard J. / Kurtti, Timothy J. / Lees, Kristin / Lang, Emma G. / Kennedy, Ryan C. / Kwon, Hyeogsun / Perera, Rushika / Qi, Yumin / Radolf, Justin D. / Sakamoto, Joyce M. / Sánchez-Gracia, Alejandro / Severo, Maiara S. / Silverman, Neal / Šimo, Ladislav / Tojo, Marta / Tornador, Cristian / Zee, Janice P. van / Vázquez, Jesús / Vieira, Filipe G. / Villar, Margarita / Wespiser, Adam R. / Yang, Yunlong / Zhu, Jiwei / Arensburger, Peter / Pietrantonio, Patricia V. / Barker, Stephen C. / Shao, Renfu / Zdobnov, Evgeny M. / Hauser, Frank / Grimmelikhuijzen, Cornelis J.P. / Park, Yoonseong / Rozas, Julio / Benton, Richard / Pedra, Joao H.F. / Nelson, David R. / Unger, Maria F. / Tubio, Jose M.C. / Tu, Zhijian / Robertson, Hugh M. / Shumway, Martin / Sutton, Granger / Wortman, Jennifer R. / Lawson, Daniel / Wikel, Stephen K. / Nene, Vishvanath M. / Fraser, Claire M. / Collins, Frank H. / Birren, Bruce / Nelson, Karen E. / Caler, Elisabet / Hill, Catherine A.

Nature Communications

2023

Abstract: Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and ... ...

Abstract	Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing ∼57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick–host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host ‘questing’, prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent.
Keywords	ixodes ; vector ; ticks
Publishing date	2023-03-10T14:34:05Z
Publisher	Springer
Publishing country	fr
Document type	Article ; Online
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Article ; Online: Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.

Nucleic acids research

2013 Volume 42, Issue Database issue, Page(s) D926–32

Abstract: Expression Atlas (http://www.ebi.ac.uk/gxa) is a value-added database providing information about gene, protein and splice variant expression in different cell types, organism parts, developmental stages, diseases and other biological and experimental ... ...

Abstract	Expression Atlas (http://www.ebi.ac.uk/gxa) is a value-added database providing information about gene, protein and splice variant expression in different cell types, organism parts, developmental stages, diseases and other biological and experimental conditions. The database consists of selected high-quality microarray and RNA-sequencing experiments from ArrayExpress that have been manually curated, annotated with Experimental Factor Ontology terms and processed using standardized microarray and RNA-sequencing analysis methods. The new version of Expression Atlas introduces the concept of 'baseline' expression, i.e. gene and splice variant abundance levels in healthy or untreated conditions, such as tissues or cell types. Differential gene expression data benefit from an in-depth curation of experimental intent, resulting in biologically meaningful 'contrasts', i.e. instances of differential pairwise comparisons between two sets of biological replicates. Other novel aspects of Expression Atlas are its strict quality control of raw experimental data, up-to-date RNA-sequencing analysis methods, expression data at the level of gene sets, as well as genes and a more powerful search interface designed to maximize the biological value provided to the user.
MeSH term(s)	Databases, Genetic ; Gene Expression Profiling ; Genomics ; Humans ; Internet ; Oligonucleotide Array Sequence Analysis ; Proteins/genetics ; Proteins/metabolism ; RNA Isoforms/metabolism ; Sequence Analysis, RNA
Chemical Substances	Proteins ; RNA Isoforms
Language	English
Publishing date	2013-12-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkt1270
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Article ; Online: Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.

Nucleic acids research

2011 Volume 40, Issue Database issue, Page(s) D91–7

Abstract: Ensembl Genomes (http://www.ensemblgenomes.org) is an integrative resource for genome-scale data from non-vertebrate species. The project exploits and extends technology (for genome annotation, analysis and dissemination) developed in the context of the ( ...

Abstract	Ensembl Genomes (http://www.ensemblgenomes.org) is an integrative resource for genome-scale data from non-vertebrate species. The project exploits and extends technology (for genome annotation, analysis and dissemination) developed in the context of the (vertebrate-focused) Ensembl project and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. Since its launch in 2009, Ensembl Genomes has undergone rapid expansion, with the goal of providing coverage of all major experimental organisms, and additionally including taxonomic reference points to provide the evolutionary context in which genes can be understood. Against the backdrop of a continuing increase in genome sequencing activities in all parts of the tree of life, we seek to work, wherever possible, with the communities actively generating and using data, and are participants in a growing range of collaborations involved in the annotation and analysis of genomes.
MeSH term(s)	Animals ; Databases, Genetic ; Genome ; Genome, Bacterial ; Genome, Fungal ; Genome, Plant ; Genomics ; Invertebrates/genetics ; Molecular Sequence Annotation ; Systems Integration
Language	English
Publishing date	2011-11-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkr895
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