Evola : Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees

スポンサーリンク

概要

• 論文の詳細を見る

• Orthologs are genes in different species that evolved from a common ancestral gene by speciation.Currently, with the rapid growth of transcriptomedata of various species, more reliable orthology information is prerequisite for further studies. However, detection of orthologs could be erroneous if pairwise distance-based methods, such as reciprocal BLAST searches, are utilized. Thus, as a sub-database of H-InvDB, an integrated database of annotated human genes (http://h-invitational.jp/), we constructed a fully curated database of evolutionary features of human genes, called ‘Evola’. In the process of the ortholog detection, computational analysis based on conserved genome synteny and transcript sequencesimilarity was followed by manual curation byresearchers examining phylogenetic trees. In total,18 968 human genes have orthologs among 11 vertebrates (chimpanzee, mouse, cow, chicken, zebrafish, etc.), either computationally detected or manually curated orthologs. Evola provides amino acid sequence alignments and phylogenetic trees of orthologs and homologs. In ‘dN/dS view’, natural selection on genes can be analyzed between human and other species. In ‘Locus maps’, all transcript variants and their exon/intron structures can be compared among orthologous gene loci. We expect the Evola to serve as a comprehensive and reliable database to be utilized in comparative analyses for obtaining new knowledge about human genes. Evola is available at http://www.h-invitational.jp/ evola/.

• Oxford University Pressの論文

著者

• Suzuki Yoichi

  Department Of Medical Genetics Tohoku University School Of Medicine

• Sakata Yoshiyuki

  Department Of Medical Genetics Tohoku University School Of Medicine

• Suzuki Y

  Department Of Medical Genetics Tohoku University School Of Medicine

• SUZUKI Yasuyo

  Department of Clinical Genetics, Medical Institute of Bioregulation, Kyushu University

• Hanada Kouichi

  Departoment Of Neurology And Geriatrics Kagoshima University Graduate School Of Medical And Dental S

• Hashimoto Katsuyuki

  Division Of Genetic Resources National Institute Of Infectious Diseases

関連論文

• A novel KCNQ4 one-base deletion in a large pedigree with hearing loss : implication for the genotype-phenotype correlation
• Functional analysis of PTPN11/SHP-2 mutants identified in Noonan syndrome and childhood leukemia
• Novel IRF6 mutations in Japanese patients with Van der Woude Syndrome : two missense mutations (R45Q and P396S) and a 17-kb deletion
• Lack of evidence for a significant association between nonsyndromic cleft lip with or without cleft palate and the retinoic acid receptor alpha gene in the Japanese population
• Chromosomal localization, structure, single-nucleotide polymorphisms, and expression of the human H-protein gene of the glycine cleavage system (GCSH), a candidate gene for nonketotic hyperglycinemia
• Haplotype analysis suggests that the two predominant mutations in Japanese patients with holocarboxylase synthetase deficiency are founder mutations
• A one-base deletion (183delC) and a missense mutation (D276H) in the T-protein gene from a Japanese family with nonketotic hyperglycinemia
• Mutation and polymorphic marker analyses of 65K- and 67K-glutamate decarboxylase genes in two families with pyridoxine-dependent epilepsy
• DINUCLEOTIDE REPEAT POLYMORPHISM IN 65k-GLUTAMATE DECARBOXYLASE GENE
• No Association of Polymorphisms in the 5' Region of the CD14 Gene and Food Allergy in a Japanese Population
• CIPRO 2.5 : Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality
• Sequence analysis, gene expression, and chromosomal assignment of mouse Borg4 gene and its human orthologue
• Adult onset limb-girdle type mitochondrial myopathy with a mitochondrial DNA np8291 A-to-G substitution
• Phenotypes of X-linked Charcot-Marie-Tooth disease and altered trafficking of mutant Connexin 32 (GJB1)
• Neonatal-Onset Brainstem Reticular Reflex Myoclonus Following a Prenatal Brain Insult : Generalized Myoclonic Jerk and a Brainstem Lesion
• Cloning, expression analysis, and chromosomal localization of a novel butyrophilin-like receptor
• Isolation and chromosomal mapping of a novel human gene showing homology to Na^+/PO4 cotransporter
• A novel human gene whose product shares significant homology with the bovine brain-specific protein p25 on chromosome 5p15.3
• Isolation, tissue expression, and chromosomal assignment of a novel human gene which encodes a protein with RING finger motif
• Cloning, expression analysis, and chromosomal localization of HIP1R, an isolog of huntingtin interacting protein (HIP1)
• Isolation, tissue expression, and chromosomal assignment of human RGS5, a novel G-protein signaling regulator gene
• Ehlers-Danlos Syndrome and Congenital Heart Anomalies
• Primary Hypoparathyroidism in Turner's Syndrome
• A novel therapeutic trial of homogentisic aciduria in a murine model of alkaptonuria
• Pheophorbide a Content and Chlorophyllase Activity in Green Tea
• II-C-12 The reduced expression of capillary tight junction comprised proteins in a patient with myopathy(THE 45TH ANNUAL MEETING OF THE JAPAN SOCIETY OF HISTOCHEMISTRY AND CYTOCHEMISTRY)
• Detection of Chlorophyll Breakdown Products in the Senescent Leaves of Higher Plants
• Evola : Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees
• Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
• Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis : new insight into intron and operon populations
• The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts
• A genome-wide association study identifies RNF213 as the first Moyamoya disease gene
• Association of the MMP9 gene with childhood cedar pollen sensitization and pollinosis

もっと見る 閉じる

スポンサーリンク