ライフサイエンスコーパス: orthology

1 based only on bacterial phenotypes and gene orthology.

2 sophila persimilis, provided nucleotide site orthology.

3 nships between the species, supporting CenH3 orthology.

4 ogenetic context to determine copy number or orthology.

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

6 e two species reveals an unexpected level of orthology.

7 arallel evolution) rather than of functional orthology.

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

9 n in-house OrthoMCL algorithm for predicting orthology.

10 on knowledge between organisms based on gene orthology.

11 stimating species trees without knowledge of orthology.

12 at different levels, including domain-level orthology.

13 facilitates cross-species analyses based on orthology.

14 mplex has been inferred based on homology or orthology.

15 m the Hepacivirus genus of flaviviruses with orthology across murine rodents.

16 sis of the integrations and determined their orthology across placental mammals (Eutheria) via the sy

17 Subsequently, we assessed patterns of orthology among these loci and those controlling the tra

18 Orthology analyses based on the markers revealed that Hy

19 Gene orthology analyses reveal that CAM-related gene families

20 Orthology analysis is a fundamental tool in comparative

21 nome Kyoto Encyclopedia of Genes and Genomes Orthology analysis was performed to investigate the diff

22 Third, orthology analysis with other infectious bacteria to ass

23 Based on our classification and orthology analysis, a direct ortholog APETALA1 (AP1), an

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

25 Through intron orthology analysis, we discovered that minor-like intron

26 enes than any of the other 41 animals in our orthology analysis.

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

28 s that pangenes recapitulate phylogeny-based orthologies and produce complete soft-core gene sets.

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

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

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

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

33 Receptor orthology and intermediate sequences also revealed the h

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

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

36 Low gene orthology and little chromosomal synteny paradoxically c

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

38 Extensive orthology and nucleotide colinearity between the genomes

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

40 Concepts of orthology and paralogy are become increasingly important

41 Orthology and paralogy are key concepts of evolutionary

42 Orthology and paralogy assignments were shown to be self

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

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

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

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

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

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

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

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

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

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

53 y implements a formulation that encodes gene orthology as a bipartite network and gene expression dat

54 have added a new benchmark based on curated orthology assertion from the Vertebrate Gene Nomenclatur

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

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

57 red duplicated genes due to complications in orthology assignment.

58 ubling the amount of genomes, the quality of orthology assignments and functional annotations (80% co

59 Though orthology assignments between vertebrate and tunicate pl

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

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

62 Orthology assignments were used to construct a synteny m

63 lity (DC) effectively identifies error-prone orthology assignments without relying on arbitrary param

64 er to make more informed decisions regarding orthology assignments, leading to a more accurate final

65 We examine orthology at bidirectional promoters, use discriminatory

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

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

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

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

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

71 e and BLAST baseline methods, as well as two orthology-based methods.

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

73 achieves competitive performance with using orthology-based pairing.

74 e pathways from rice (Oryza sativa) and gene-orthology-based pathway projections to 129 additional sp

75 of the metabolic network by considering both orthology-based pathways and species-specific reactions.

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

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

78 uration in rice (320 reference pathways) and orthology-based projections to 106 species.

79 The Orthology Benchmark Service is the gold standard for ort

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

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

82 assembly's utility by resolving genome-wide orthologies between the axolotl and other vertebrates, i

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

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

85 f 12 conserved palindromes showing no spacer orthology between human and rhesus macaque.

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

87 challenges associated with determination of orthology between neuropeptides in different taxa.

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

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

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

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

92 Orthology between these proteins and S. cerevisiae Slx4

93 ROADIES also eliminates the need to infer orthology by leveraging existing discordance-aware metho

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

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

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

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

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

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

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

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

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

103 paralog information, disease models based on orthology, customizable tables within reports and overvi

104 The new GO annotation and orthology data are available for searching in Hymenopter

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

106 genomes to create the Intron Annotation and Orthology Database (IAOD).

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

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

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

110 e) gene frequency, identified using the KEGG Orthology database, was significantly increased in the h

111 the Kyoto Encyclopedia of Genes and Genomes Orthology database.

112 As provided by several orthology databases, hierarchical orthologous groups (HO

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

114 We have also generated orthology datasets that encompass all HGD species and pr

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

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

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

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

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

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

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

122 ne models and the development of an improved orthology detection pipeline.

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

124 recently reported algorithm for large-scale orthology detection.

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

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

127 Since our orthology determination procedure does not employ a spec

128 Following orthology determination through a series of BLAST search

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

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

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

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

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

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

135 arge-scale comparative genomics and advanced orthology evaluation techniques, we identified 157 bilat

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

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

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

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

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

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

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

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

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

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

146 We identified 72 orthology groups containing ISGs in both zebrafish and h

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

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

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

150 y sequences from other genomes into specific orthology groups.

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

152 nematodes can have Hox genes from up to six orthology groups.

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

154 xpression, gene function, mutant phenotypes, orthology, human disease models, nomenclature and reagen

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

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

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

158 positive selection appear to underlie hidden orthology in Platyhelminthes.

159 The methods to build and visualize syntenic orthology in the GENESPACE R package offer a significant

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

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

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

163 a scalable and robust approach, based on the Orthology Index (OI), to effectively identify orthologou

164 ource to compare existing and new methods of orthology inference (the bedrock for many comparative ge

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

166 rther highlighting the value of domain-based orthology inference approaches.

167 bottleneck to reliably perform comprehensive orthology inference at large scale across broad taxonomi

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

169 y Benchmark Service is the gold standard for orthology inference evaluation, supported and maintained

170 Accurate orthology inference is a fundamental step in many phylog

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

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

173 introduce KinOrtho, a query- and graph-based orthology inference method that combines full-length and

174 using sets of genes inferred with different orthology inference methods and established the geologic

175 Notably, the use of different orthology inference methods was a substantial contributo

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

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

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

179 e the importance of investigating effects of orthology inference on phylogenetic analyses to resolve

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

181 Orthology inference revealed strong conservation of TE s

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

183 gene loss after the WGT using the Polyploidy Orthology Inference Tool (POInT).

184 polyploid genomes with POInT, the Polyploidy Orthology Inference Tool.

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

186 owse), a web portal that gives access to the orthology inferences made for polyploid genomes with POI

187 It also gives confidence estimates for those orthology inferences.

188 ene co-clusters in two species based on gene orthology information and gene expression data.

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

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

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

192 Orthology-informed transcriptomic comparisons and co-exp

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

194 Between human and mouse, gene-level orthology is currently present for nearly 16k protein-co

195 The concept of orthology is key to decoding evolutionary relationships

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

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

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

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

200 rence proteins from multiple databases [KEGG Orthology (KO), Enzyme Commission (E.C.), Gene Ontology

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

202 air of organisms and identifies a fine-scale orthology mapping at the exon and then transcript level.

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

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

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

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

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

208 is; (vi) annotation of orthogroups with KEGG Orthology numbers; and (vii) a map of pairwise average n

209 The shared orthology of conserved sex-determining region genes betw

210 Orthology of the other genomic sequence with the porcine

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

212 Our results show the orthology of the symbiotic transfer of lipids across lan

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

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

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

216 rison of related complexes in the context of orthology or paralogy.

217 em which pits network features against known orthology, or more recently, as a joint embedding proble

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

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

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

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

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

223 t which associates taxa abundances with KEGG orthology pathways.

224 s a function of evolutionary time, 2) across orthology prediction algorithms, and 3) with reference t

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

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

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

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

229 services for fast functional annotation and orthology prediction of custom genomics or metagenomics

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

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

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

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

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

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

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

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

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

239 The HGNC Comparison of Orthology Predictions (HCOP) search tool integrates and

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

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

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

243 Because its orthology predictions are underpinned by evolutionary ev

244 HCOP was originally designed to show orthology predictions between human and mouse but has be

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

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

247 temporary bioinformatic workflows, including orthology predictions via OrthoMCL, and integrated the a

248 e primary contributors to inconsistencies in orthology predictions.

249 ied formal gene nomenclature, and consistent orthology predictions.

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

251 owledge to another 82 plant species via gene-orthology projection using the Reactome data model and f

252 Orthology properties suggest that the Lepidoptera are th

253 otation pertaining to protein family scores, orthology, protein interaction/association studies, bidi

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

255 Unfortunately, determining orthology relation through computational methods is not

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

257 Determining orthology relations among genes across multiple genomes

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

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

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

261 t information for accurate identification of orthology relationship.

262 The established orthology relationships also provide a useful reference

263 These orthology relationships are also used to predict GO anno

264 Predicting orthology relationships between species is a vital compo

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

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

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

268 ly-annotated gene and transcript models with orthology relationships within tunicates, and with echin

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

270 eggNOG is a public database of orthology relationships, gene evolutionary histories and

271 developed to efficiently investigate complex orthology relationships.

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

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

274 microbial functional features (based on KEGG orthology) relevant to known gut biochemical activities.

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

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

277 e processing, database knowledge extraction, orthology search and powerful graph algorithms to create

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

279 LNT1 orthologs are functionally similar, and orthology searches coupled with homology modeling reveal

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

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

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

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

284 Phylogenetic analysis identified no direct orthology to bilaterian peptidergic systems and supports

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

286 nges by integrating conserved gene order and orthology to define the expected physical position of al

287 canonical cannabinoid receptor, NPR-19, with orthology to human CB(1)/CB(2) (Oakes et al., 2017).

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

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

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

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

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

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

294 Hierarchical contig orthology was rapidly assessed by constructing detailed

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

296 ardizing gene nomenclature, and basing it on orthology where possible, facilitates discussion and gen

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

298 from Kyoto Encyclopedia of Genes and Genomes orthologies with linear regression models.

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

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