InParanoid 6: eukaryotic ortholog clusters with inparalogs

Berglund, Ann-Charlotte; Sjölund, Erik; Östlund, Gabriel; Sonnhammer, Erik L. L.

doi:10.1093/nar/gkm1020

Cited by 193 publications

(189 citation statements)

References 12 publications

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“…This resulted in 11,430 yeast/fly, 17,534 yeast/human, and 75,415 fly/human orthologous pairs. To test the robustness of our findings with respect to the orthology assignments, we repeated all of the analyses using Inparanoid assignments (53,54), both many-to-many and one-to-one relationships (supplemental Table 1), obtaining identical trends (supplemental Fig. 2).…”

Section: Methodsmentioning

confidence: 99%

The Role of Structural Disorder in the Rewiring of Protein Interactions through Evolution

Mosca

Pache

Aloy

2012

Molecular & Cellular Proteomics

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Structurally disordered regions play a key role in proteinprotein interaction networks and the evolution of highly connected proteins, enabling the molecular mechanisms for multiple binding. However, the role of protein disorder in the evolution of interaction networks has only been investigated through the analysis of individual proteins, making it impossible to distinguish its specific impact in the (re)shaping of their interaction environments. Now, the availability of large interactomes for several model organisms permits exploration of the role of disorder in protein interaction networks not only at the level of the interacting proteins but of the interactions themselves. By comparing the interactomes of human, fly, and yeast, we discovered that, despite being much more abundant, disordered interactions are significantly less conserved than their ordered counterparts. Furthermore, our analyses provide evidence that this happens not only because disordered proteins are less conserved but also because they display a higher capacity to rewire their interaction neighborhood through evolution. Overall, our results support the hypothesis that conservation of disorder gives a clear evolutionary advantage, facilitating the change of interaction partners during evolution. Moreover, this mechanism is not exclusive of a few anecdotal cases but a global feature present in the interactome networks of entire organisms.

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Section: Methodsmentioning

confidence: 99%

The Role of Structural Disorder in the Rewiring of Protein Interactions through Evolution

Mosca

Pache

Aloy

2012

Molecular & Cellular Proteomics

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“…Following site-specific mutation of all HREs, we could show that HRE1 may be needed for general exon definition. The mutation of this sequence motif leads to increased exon skipping of both exon 3 and exon 4, suggesting a crucial role for HRE1 in general splicing, possibly affecting the branch point of this intron (Arning et al, 1996;Berglund et al, 2008;Kramer and Utans, 1991). The HRE2, HRE3 and HRE4 elements influence mutually exclusive splicing.…”

Section: Fig 7 Subcellular Localization Of How(s) and How(l)mentioning

confidence: 99%

The regulation of glial-specific splicing ofNeurexin IVrequires HOW and Cdk12 activity

2012

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SUMMARYThe differentiation of the blood-brain barrier (BBB) is an essential process in the development of a complex nervous system and depends on alternative splicing. In the fly BBB, glial cells establish intensive septate junctions that require the cell-adhesion molecule Neurexin IV. Alternative splicing generates two different Neurexin IV isoforms: Neurexin IV exon3 , which is found in cells that form septate junctions, and Neurexin IV exon4 , which is found in neurons that form no septate junctions. Here, we show that the formation of the BBB depends on the RNA-binding protein HOW (Held out wings), which triggers glial specific splicing of Neurexin IV exon3 . Using a set of splice reporters, we show that one HOW-binding site is needed to include one of the two mutually exclusive exons 3 and 4, whereas binding at the three further motifs is needed to exclude exon 4. The differential splicing is controlled by nuclear access of HOW and can be induced in neurons following expression of nuclear HOW. Using a novel in vivo two-color splicing detector, we then screened for genes required for full HOW activity. This approach identified Cyclin-dependent kinase 12 (Cdk12) and the splicesosomal component Prp40 as major determinants in regulating HOWdependent splicing of Neurexin IV. Thus, in addition to the control of nuclear localization of HOW, the phosphorylation of the Cterminal domain of the RNA polymerase II by Cdk12 provides an elegant mechanism in regulating timed splicing of newly synthesized mRNA molecules.

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“…Examining the administrative changes possibly intervening articulation disparity in paralogous Gene families under particular conditions. Frias-Lopez.et.al [13] they report here worldwide examination of communicated qualities in a normally happening microbial group. We initially adjusted RNA enhancement innovations to create a lot of cDNA from little amounts of aggregate microbial group RNA.…”

Section: Litrature Surveymentioning

confidence: 95%

Evolutionary clustering annotation of ortho-paralogous gene in a multi species using Venn diagram visualization

Nair¹,

Sarath²

2018

IJET

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The evolutionary analysis of the genome of the immediate cluster is an important part of comparative genomics research. Identifying the overlap between immediate homologous clusters allows us to elucidate the function and evolution of proteins between species. Here, we report a network platform called Ortho-paralogous Venn-diagram representation that can be used to compare and visualize a wide range of ortho-paralogous clustering of genomes. In our work Ortho-paralogous Venn-diagram results show a functional summary of interactive Venn diagrams, summary counts, and interspecies shared cluster separations and intersections. Ortho-paralogous Venn-diagram also uses a variety of sequence analysis tools to gain an in-depth understanding of the cluster. In addition, Ortho-paralogous Venn identifies direct homologous clusters of single copy genes and allows custom search of specific gene clusters. It enables us in wide analysis of the genes and protein by comparing the genes using Venn diagram .Here the user can upload our own gene sequences into the application ,using three clustering approach to check the best clustering approches like SOM,K-means and advanced clustering after that we are using the Venn diagram repersentator to evolutionary cluster the genes having similar functionality and structural similarity from the uploaded data.Here we are using a venn diagram representation as an application which used to cluster the orthologous and paralogous gene on basics of their evolution and functional aspects.it enables us in wide analysis of the genes and protein by comparing the genes using venn diagram representation.here the user can upload our own gene sequences into the application where the venn diagram representator clusters.the genes having similar functionality and structural similarity from the uploaded data.

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InParanoid 6: eukaryotic ortholog clusters with inparalogs

Cited by 193 publications

References 12 publications

The Role of Structural Disorder in the Rewiring of Protein Interactions through Evolution

The Role of Structural Disorder in the Rewiring of Protein Interactions through Evolution

The regulation of glial-specific splicing ofNeurexin IVrequires HOW and Cdk12 activity

Evolutionary clustering annotation of ortho-paralogous gene in a multi species using Venn diagram visualization

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