ライフサイエンスコーパス: orthology

1 sophila persimilis, provided nucleotide site orthology.

2 nships between the species, supporting CenH3 orthology.

3 ogenetic context to determine copy number or orthology.

4 , RBH, RSD and INPARANOID, to determine gene orthology.

5 e two species reveals an unexpected level of orthology.

6 arallel evolution) rather than of functional orthology.

7 L1 can partially replace DAF-16, proving the orthology.

8 on knowledge between organisms based on gene orthology.

9 at different levels, including domain-level orthology.

10 facilitates cross-species analyses based on orthology.

11 mplex has been inferred based on homology or orthology.

12 based only on bacterial phenotypes and gene orthology.

13 Orthology analysis is a fundamental tool in comparative

14 Third, orthology analysis with other infectious bacteria to ass

15 t join efforts to enhance various aspects of orthology analysis, such as defining standard formats an

16 ory of gene families is the determination of orthologies and paralogies.

17 asing need for clear information about their orthologies and/or functional equivalents in model organ

18 re rapidly evolving, raising questions about orthology and conservation of function across species.

19 information that can be transferred based on orthology and for rapidly identifying the relevant GO te

20 ations of this perspective for inferences of orthology and functional evolution.

21 Receptor orthology and intermediate sequences also revealed the h

22 nd statistical features of RNA structure and orthology and large scale chromosomal recombination even

23 ls describe 'equivalog' families, where both orthology and lateral gene transfer may be part of the e

24 Low gene orthology and little chromosomal synteny paradoxically c

25 Pathogenicity-related factor prediction, orthology and multigene family classification, transcrip

26 Extensive orthology and nucleotide colinearity between the genomes

27 gy, providing definitive information on gene orthology and paralogy across broad evolutionary distanc

28 Concepts of orthology and paralogy are become increasingly important

29 Orthology and paralogy are key concepts of evolutionary

30 Orthology and paralogy assignments were shown to be self

31 assess and improve the underlying quality of orthology and paralogy assignments.

32 gene families, where the distinction between orthology and paralogy is key.

33 talogue of gene trees that determine precise orthology and paralogy relations across these species.

34 phylogenetic trees, allowing mapping of the orthology and paralogy relationships of sequenced plant

35 For each gene family, orthology and paralogy relationships were uncertain.

36 al approaches employed for identification of orthology and paralogy, and considers evolutionary and f

37 they contain, obscuring the relationships of orthology and paralogy.

38 ake functional predictions of genes based on orthology and set theory, but our approach to predicting

39 and Kyoto Encyclopedia of Genes and Genomes' Orthology annotation databases.

40 tend to be dysfunctional or pseudogenic, and orthologies are restricted to close taxa.

41 e, we analyze 121 cases for which functional orthology assignment is ambiguous when sequence similari

42 ability of various 'omics data, high-quality orthology assignment is crucial for evolutionary and fun

43 red duplicated genes due to complications in orthology assignment.

44 Though orthology assignments between vertebrate and tunicate pl

45 In this report we utilize orthology assignments for pairs of genes co-regulated by

46 rently provides sets of gene predictions and orthology assignments for three clades: (i) amniotes, in

47 Orthology assignments were used to construct a synteny m

48 We examine orthology at bidirectional promoters, use discriminatory

49 To date, most analyses have inferred orthology based either on pure sequence similarity or us

50 tion of genes beyond that provided by simple orthology-based annotation endeavors.

51 in the group of singleton TFs, the standard orthology-based approach was inefficient, and thus, we d

52 orthologs and paralogs for most genes; (ii) orthology-based approach, which used the function(s) of

53 alysis in other species, we continue to make orthology-based inferences of pathways in non-human spec

54 An orthology-based nomenclature for this gene family has pr

55 y, MORPHIN investigates human diseases by an orthology-based projection of a set of model organism ge

56 liana and 27 nonmodel plant species using an orthology-based projection of nonmodel plant genes on th

57 Using the Quest for Orthologs consortium orthology benchmark service, we show that these changes

58 an automated web-based service to facilitate orthology benchmarking.

59 evolutionary analysis shows a lack of direct orthology between any of the four human members and the

60 The likely orthology between Cdc45 and RecJ reveals new lines of en

61 litrichinae cDNAs indicates that there is no orthology between MHC class I loci in genera of this phy

62 hallenge, that do not rely on sequence-based orthology between rat and human genes to translate pathw

63 duplicated in tetrapods, making for a direct orthology between the Ciona intestinalis gene CiPax6 and

64 y relies on the existence of one-to-one gene orthology between the human and mouse.

65 served than protein sequences, the extent of orthology between the lincRNomes is unexpectedly high, w

66 Orthology between these proteins and S. cerevisiae Slx4

67 s of and legitimacy of disagreements between orthology calls, the context dependency of orthology def

68 The observation that functional orthology cannot be identified through analysis of expre

69 Zebrafish have two genes in the Otx5/crx orthology class, and we previously showed that crx can t

70 relationships between gene sets, termed the orthology coefficient (OC), was developed.

71 Starting from tree-free estimates of orthology, cograph editing can sufficiently reduce the n

72 A comparison with databases of gene orthology, conservation, and essentiality identified pro

73 ood, and they are already beneficial to both orthology consumers and providers.

74 onarch genome shares prominent similarity in orthology content, microsynteny, and protein family size

75 e genomes; the much lower extent of sequence orthology covering less than half of the genomes; the pr

76 s that address this goal, including enhanced orthology data, Human Disease Model Reports, protein dom

77 QuartetS-DB is a new orthology database constructed using the QuartetS algori

78 dataset from the TreeFam-A manually curated orthology database show that PHOG provides a combination

79 oto Encyclopedia of Genes and Genomes (KEGG) orthology database, distributed across categories expect

80 the Kyoto Encyclopedia of Genes and Genomes Orthology database.

81 rain Resource, IMSR, the update of mammalian orthology datasets and the electronic publication of cla

82 n orthology calls, the context dependency of orthology definitions, special challenges encountered wh

83 us genes, QuartetS has been shown to improve orthology detection accuracy while maintaining computati

84 Nearly all existing algorithms for orthology detection are based on sequence comparison.

85 igh throughput and an opportunity to improve orthology detection by leveraging evolutionary evidence

86 The use of conserved genome synteny in orthology detection has been relatively under-employed i

87 Here, we report a novel orthology detection method, termed QuartetS, that exploi

88 omic data offers both a challenge to develop orthology detection methods that are simultaneously accu

89 Many different methods exist for orthology detection, which makes it difficult to decide

90 recently reported algorithm for large-scale orthology detection.

91 e both the potential and the difficulties of orthology determination in variable gene families, on wh

92 netic framework, thus making character-based orthology determination on a genomic scale possible.

93 Since our orthology determination procedure does not employ a spec

94 mates the labor-intensive procedures of gene orthology determination within a character-based phyloge

95 In contrast, orthology determination within a character-based phyloge

96 se previous findings in which we analyze, by orthology determination, the extent to which genes that

97 al graph displays of GO annotations, and new orthology displays including sequence information and gr

98 Previous phylogenetic comparisons based on orthology, diversity, and expression patterns identified

99 d that combines information from expression, orthology, domain co-occurrence, post-translational modi

100 g sequence, structural, transcriptional, and orthology features.

101 ew the latest developments and issues in the orthology field, and summarize the most recent results r

102 e resources, and the opportunity to leverage orthology for searches across genera.

103 n of conserved non-coding sequences, predict orthology for specific rice and maize rops.

104 have to rely heavily on the establishment of orthologies from model species.

105 roaches are used to enable querying based on orthology, functional assignment, and taxonomic or user-

106 and expression data with external sources of orthology, gene ontology, gene interaction and pathway i

107 We present the Orthology Group Cleaner (the OGCleaner), a tool designed

108 ing of neuropeptide GPCRs identified several orthology groups and allowed the reconstruction of the p

109 ner), a tool designed for filtering putative orthology groups as homology or non-homology clusters by

110 acement of protein sequences to phylogenomic orthology groups in the PhyloFacts database.

111 es express additional Hox genes belonging to orthology groups that are absent from C. elegans but pre

112 PhyloFacts resource, and contains over 366 K orthology groups with a minimum of three species.

113 y sequences from other genomes into specific orthology groups.

114 n plants that can be further divided into 19 orthology groups.

115 For some C1qDC-encoding genes, strict orthology has been retained throughout vertebrate evolut

116 ups (COGs) framework that is widely used for orthology identification in prokaryotes.

117 While it is usually the case that orthology implies functional equivalence, this is not al

118 ewer Kyoto Encyclopedia of Genes and Genomes Orthologies in almost all metabolic categories were dete

119 positive selection appear to underlie hidden orthology in Platyhelminthes.

120 analyzing very anciently rooted orthologies, orthology in the light of whole-genome duplications, and

121 Eukaryotic Orthologous Groups) and KO (KEGG Orthology) in addition to Pfam domains; (iii) informatio

122 rs based on known gene relationships such as orthology incorporated using fused regression.

123 of the ortholog database providers, as most orthology inference algorithms scale at least quadratica

124 ght novel transcriptomes, strictly enforcing orthology inference criteria, and progressively examinin

125 Accurate orthology inference is a fundamental step in many phylog

126 As in any phylogenetics experiment, accurate orthology inference is critical to phylo-transcriptomics

127 Achieving high accuracy in orthology inference is essential for many comparative, e

128 to improve the scalability and robustness of orthology inference methods.

129 and guides the development of more accurate orthology inference methods.

130 it is difficult to assess the performance of orthology inference methods.

131 cs", is compared to other recently published orthology inference pipelines, and benchmarked using a s

132 the OMA algorithm: (i) refining the pairwise orthology inference step to account for same-species par

133 nd others) and the infrastructure for making orthology inferences available (e.g. interfaces with mod

134 e, and offers a useful platform to integrate orthology information into functional inference and evol

135 work alignment), which integrates functional orthology information that can be obtained from differen

136 pecies requires further considerations (e.g. orthology information, expression data and networks from

137 The determination of gene orthology is a prerequisite for mining and utilizing the

138 The concept of orthology is key to decoding evolutionary relationships

139 Here, we test the hypothesis that orthology is predictive of R-gene genomic location in th

140 ct consequence of our approach based on gene orthology is the lack of selectivity of the compounds ov

141 igher abundance of functional genes and KEGG orthology (KO) groups involved in nitrogen cycling in th

142 lusters of Orthologous Groups (COG) and KEGG Orthology (KO) groups.

143 oves network inference performance even when orthology mapping and conservation are incomplete.

144 d by sequence similarity-based methods, when orthology mapping involves gene fusions and horizontal g

145 s by three popular sequence similarity-based orthology mapping programs.

146 ks, such as protein structure prediction and orthology mapping, which rely heavily on homology search

147 ovides the foundation for detailed conserved-orthology maps showing the correspondence between conser

148 ein-coupled receptor PSs, this work presents orthology markers to study ancestral neuron types that w

149 Orthology of the other genomic sequence with the porcine

150 cannabinoid receptor, CB1, highlighting the orthology of the receptors.

151 Here, we investigated the phylogeny and orthology of these proteins to understand better their o

152 phenotypes in other species by means of the orthology of underlying genes.

153 n additional tool to substantiate functional orthology only partially overlapped with expressolog cla

154 untered when analyzing very anciently rooted orthologies, orthology in the light of whole-genome dupl

155 etting a quick-but-approximate result (using orthology over pre-computed results) or having a full-bl

156 n variation data and the introduction of new orthology/paralog annotations based on gene trees.

157 to deduce both obvious and otherwise-cryptic orthology, paralogy and other relationships among genes.

158 s a semi-independent method to delineate the orthology/paralogy relation for a refined set of homolog

159 t which associates taxa abundances with KEGG orthology pathways.

160 oMCL-DB provides a centralized warehouse for orthology prediction among multiple species, and will be

161 a basis to support developments for improved orthology prediction and to explore new approaches.

162 Viewer, combining information from different orthology prediction methodologies, was developed to eff

163 the model organism communities with improved orthology prediction methods allowing pathway inference

164 A relatively new class of orthology prediction strategies combines aspects of mult

165 Although these have been successful in orthology prediction to some extent, we seek to go beyon

166 Here we present OrthoReD, an open-source orthology prediction tool with accuracy comparable to pu

167 OrthoReD is not only fast and accurate as an orthology prediction tool, but also gives researchers fl

168 At the same time, in silico orthology prediction tools often require large computati

169 imilar to the outputs of two other published orthology prediction tools, OrthologID and/or OrthoDB, f

170 , including genome-wide association studies, orthology prediction, and motif scanning.

171 bine them with custom data for 'client-side' orthology prediction.

172 into a TreeFam gene tree and provides quick orthology prediction.

173 The database provides orthology predictions among 1621 complete genomes (1365

174 It has orthology predictions and gene trees for 109 species in

175 reas who have an interest in highly accurate orthology predictions and their applications.

176 Because its orthology predictions are underpinned by evolutionary ev

177 a large-scale, systematic comparison of the orthology predictions of QuartetS with those of four oth

178 ontained in these networks will yield better orthology predictions than sequence similarity alone.

179 e same workflows, including creation of gene orthology profiles, so data are easily compared across d

180 Orthology properties suggest that the Lepidoptera are th

181 nalysis pipeline and the ability to leverage orthology provides a powerful resource for in silico exp

182 Unfortunately, determining orthology relation through computational methods is not

183 on-transitivity and hierarchic nature of the orthology relation.

184 Determining orthology relations among genes across multiple genomes

185 y events such as expansion of gene families, orthology relations and protein evolution.

186 ant shark and human, implying a many-to-many orthology relationship between lamprey and gnathostome H

187 rs across maps, or through the gene homology/orthology relationship data stored in the Ensembl Compar

188 t information for accurate identification of orthology relationship.

189 The established orthology relationships also provide a useful reference

190 These orthology relationships are also used to predict GO anno

191 Predicting orthology relationships between species is a vital compo

192 f individual genomes, and of the synteny and orthology relationships between them.

193 ference sequence for C. glabrata, as well as orthology relationships that interconnect Locus Summary

194 Moreover, eggNOG now provides pairwise orthology relationships within OGs based on analysis of

195 ary data types extended the scope of complex orthology relationships, especially between more distant

196 developed to efficiently investigate complex orthology relationships.

197 trace algorithm and a method that depends on orthology relationships.

198 y a hCDK13 chimera, suggesting the following orthology relationships: Bur1 <--> CDK9 and Ctk1 <--> CD

199 rk-based transfer methods, but that relaxing orthology requirements does not improve results.

200 QuartetS-DB is one of the largest orthology resources available to date.

201 ting a reduced dataset to limit the scope of orthology search for each gene of interest.

202 related database resources, such as the HCOP orthology search tool and manually curated gene family w

203 irement of OrthoReD is achieved by repeating orthology searches on one gene of interest at a time, th

204 re achievable, complements classification by orthology, superfamily, domain or motif.

205 Aside from orthology, the lineage-specific order and orientation of

206 genes have been evolving rapidly, such that orthology throughout the primate lineage is unclear.

207 AG subfamily strongly supports evolutionary orthology to C-class organ identity genes.

208 With BovineMine, bovine researchers can use orthology to leverage the curated gene pathways of model

209 his elaborate signaling network shows little orthology to metazoan counterparts yet displays many inn

210 ever, two small regions from distal 1q (with orthology to mouse chromosome 11) appear to have a diffe

211 It is the largest human autosome with orthology to only a single mouse chromosome, mapping ent

212 , and (ii) minimizing errors in the pairwise orthology verification step by testing the consistency o

213 A new Integrative Orthology Viewer, combining information from different o

214 Hierarchical contig orthology was rapidly assessed by constructing detailed

215 This lack of functional orthology was supported as functional assays in vitro ha

216 es are based on the concepts of homology and orthology, which were originally introduced to study gen

217 entified four Dlx genes in P. marinus, whose orthology with gnathostome Dlx genes provides a model fo

218 d divergence, revealing large blocks of gene orthology with rodents, scattered regions with more rece