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96
Reactome: a database of reactions, pathways and biological processes.Nucl Acids Res 39: D691–7
, 2011
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eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids. Res. 40: D284– D289
, 2012
"... Orthologous relationships form the basis of most comparative genomic and metagenomic studies and are essential for proper phylogenetic and func-tional analyses. The third version of the eggNOG database ..."
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Cited by 53 (7 self)
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Orthologous relationships form the basis of most comparative genomic and metagenomic studies and are essential for proper phylogenetic and func-tional analyses. The third version of the eggNOG database
ApiDB: integrated resources for the apicomplexan bioinformatics resource center
- NUCLEIC ACIDS RESEARCH
, 2007
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evolutionary distances
, 2006
"... SUMMARY: We have created a tool for ortholog and phylogenetic profile retrieval called Roundup. Roundup is backed by a massive repository of orthologs and associated evolutionary distances that was built using the reciprocal smallest distance algorithm, an approach that hasbeenshown to improveuponal ..."
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Cited by 33 (5 self)
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SUMMARY: We have created a tool for ortholog and phylogenetic profile retrieval called Roundup. Roundup is backed by a massive repository of orthologs and associated evolutionary distances that was built using the reciprocal smallest distance algorithm, an approach that hasbeenshown to improveuponalternativeapproaches of ortholog detection, such as reciprocal blast. Presently, the Roundup repository contains all possible pair-wise comparisons for over 250 genomes, including 32 Eukaryotes, more than doubling the coverage of any similar resource. The orthologs are accessible through an intuitive web interface that allows searches by genome or gene identifier, presenting results as phylogenetic profiles together with gene and molecular function annotations. Results may be downloaded as phylogenetic matrices for subsequent analysis, including the construction of whole-genome phylogenies based on gene-content data.
MetaPhOrs: orthology and paralogy predictions from multiple phylogennetic evidence using a consistency-based confidence score. Nucleic Acids Res
, 2010
"... from multiple phylogenetic evidence using a consistency-based confidence score ..."
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Cited by 27 (4 self)
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from multiple phylogenetic evidence using a consistency-based confidence score
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs,”Nucleic
- Acids Research
, 2013
"... The concept of orthology provides a foundation for formulating hypotheses on gene and genome evolu-tion, and thus forms the cornerstone of comparative genomics, phylogenomics and metagenomics. We present the update of OrthoDB—the hierarchical catalog of orthologs ..."
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Cited by 19 (0 self)
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The concept of orthology provides a foundation for formulating hypotheses on gene and genome evolu-tion, and thus forms the cornerstone of comparative genomics, phylogenomics and metagenomics. We present the update of OrthoDB—the hierarchical catalog of orthologs
T1DBase: integration and presentation of complex data for type 1 diabetes research
- Nucleic Acids Res
, 2007
"... website and database that supports the type 1 diabetes (T1D) research community. T1DBase provides a consolidated T1D-oriented view of the complex data world that now confronts medical researchers and enables scientists to navigate from information they know to information that is new to them. Overvi ..."
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Cited by 15 (0 self)
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website and database that supports the type 1 diabetes (T1D) research community. T1DBase provides a consolidated T1D-oriented view of the complex data world that now confronts medical researchers and enables scientists to navigate from information they know to information that is new to them. Overview pages for genes and markers summarize information for these elements. The Gene Dossier summarizes information for a list of genes. GBrowse [Stein et al. (2002) Genome Res., 10, 1599–1610] displays genes and other features in their genomic context, and Cytoscape [Shannon et al. (2003) Genome Res., 13, 2498–2504] shows genes in the context of interacting proteins and genes. The Beta Cell Gene Atlas shows gene expression in b cells, islets, and related cell types and lines, and the Tissue Expression Viewer shows expression across other tissues. The Microarray Viewer shows expression from more than 20 array experiments. The Beta Cell Gene Expression Bank contains manually curated gene and pathway anno-tations for genes expressed in b cells. T1DMart is a query tool for markers and genotypes. PosterPages are ‘home pages ’ about specific topics or datasets. The key challenge, now and in the future, is to provide powerful informatics capabilities to T1D scientists in a form they can use to enhance their research.
Kriventseva E: OrthoDB: The hierarchical catalog of eukaryotic orthologs
- in 2011. Nucleic Acids Research 2011
"... The concept of homology drives speculation on a gene’s function in any given species when its biological roles in other species are characterized. With reference to a specific species radiation homologous relations define orthologs, i.e. descendants from a single gene of the ancestor. The large-scal ..."
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Cited by 13 (1 self)
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The concept of homology drives speculation on a gene’s function in any given species when its biological roles in other species are characterized. With reference to a specific species radiation homologous relations define orthologs, i.e. descendants from a single gene of the ancestor. The large-scale delineation of gene genealogies is a challenging task, and the numerous approaches to the problem reflect the importance of the concept of orthology as a cornerstone for comparative studies. Here, we present the updated OrthoDB catalog of eukaryotic orthologs delineated at each radiation of the species phylogeny in an explicitly hierarchical manner of over 100 species of vertebrates, arthropods and fungi (including the metazoa level). New database features include functional annotations, and quantification of evolutionary divergence and relations among orthologous groups. The interface features extended phyletic profile querying and enhanced text-based searches. The ever-increasing sampling of sequenced eukaryotic genomes brings a clearer account of the majority of gene genealogies that will facilitate informed hypotheses of gene function in newly sequenced genomes. Furthermore, uniform analysis across lineages as different as vertebrates, arthropods and fungi with divergence levels varying from several to hundreds of millions of years will provide essential data for uncovering and quantifying long-term trends of gene evolution. OrthoDB is freely accessible from
EuPathDB: the eukaryotic pathogen database
- Nucleic Acids Res
, 2013
"... ABSTRACT EuPathDB (http://eupathdb.org) resources include 11 databases supporting eukaryotic pathogen genomic and functional genomic data, isolate data and phylogenomics. EuPathDB resources are built using the same infrastructure and provide a sophisticated search strategy system enabling complex i ..."
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Cited by 13 (2 self)
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ABSTRACT EuPathDB (http://eupathdb.org) resources include 11 databases supporting eukaryotic pathogen genomic and functional genomic data, isolate data and phylogenomics. EuPathDB resources are built using the same infrastructure and provide a sophisticated search strategy system enabling complex interrogations of underlying data. Recent advances in EuPathDB resources include the design and implementation of a new data loading workflow, a new database supporting Piroplasmida (i.e. Babesia and Theileria), the addition of large amounts of new data and data types and the incorporation of new analysis tools. New data include genome sequences and annotation, strand-specific RNA-seq data, splice junction predictions (based on RNAseq), phosphoproteomic data, high-throughput phenotyping data, single nucleotide polymorphism data based on high-throughput sequencing (HTS) and expression quantitative trait loci data. New analysis tools enable users to search for DNA motifs and define genes based on their genomic colocation, view results from searches graphically (i.e. genes mapped to chromosomes or isolates displayed on a map) and analyze data from columns in result tables (word cloud and histogram summaries of column content). The manuscript herein describes updates to EuPathDB since the previous report published in NAR in 2010.
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains
- Nucleic Acid Res
, 2009
"... superfamilies of predicted protein structural domains ..."
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Cited by 12 (9 self)
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superfamilies of predicted protein structural domains
