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  1. AU=Alhuzimi Eman
  2. AU="Wuerzberger-Davis, Shelly M"
  3. AU="Clippinger, Amy J"
  4. AU="M. S. Islam"
  5. AU="Borrego-Jiménez, Jaime"
  6. AU="Kaoru Dohi"
  7. AU="Tornai, Gábor J"
  8. AU="D'Avella, Christopher"
  9. AU="Lim, Boon L."
  10. AU="Heselden, Marie"
  11. AU=Dias?Polak David
  12. AU="Shahid Umar"
  13. AU="Abu-Shmais, Alexandria A"
  14. AU="Takenaka, Haruka"
  15. AU="Bramley, Andrea"
  16. AU="Sang Hong Lee"

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  1. Artikel ; Online: Can Predicted Protein 3D Structures Provide Reliable Insights into whether Missense Variants Are Disease Associated?

    Ittisoponpisan, Sirawit / Islam, Suhail A / Khanna, Tarun / Alhuzimi, Eman / David, Alessia / Sternberg, Michael J E

    Journal of molecular biology

    2019  Band 431, Heft 11, Seite(n) 2197–2212

    Abstract: Knowledge of protein structure can be used to predict the phenotypic consequence of a missense variant. Since structural coverage of the human proteome can be roughly tripled to over 50% of the residues if homology-predicted structures are included in ... ...

    Abstract Knowledge of protein structure can be used to predict the phenotypic consequence of a missense variant. Since structural coverage of the human proteome can be roughly tripled to over 50% of the residues if homology-predicted structures are included in addition to experimentally determined coordinates, it is important to assess the reliability of using predicted models when analyzing missense variants. Accordingly, we assess whether a missense variant is structurally damaging by using experimental and predicted structures. We considered 606 experimental structures and show that 40% of the 1965 disease-associated missense variants analyzed have a structurally damaging change in the mutant structure. Only 11% of the 2134 neutral variants are structurally damaging. Importantly, similar results are obtained when 1052 structures predicted using Phyre2 algorithm were used, even when the model shares low (<40%) sequence identity to the template. Thus, structure-based analysis of the effects of missense variants can be effectively applied to homology models. Our in-house pipeline, Missense3D, for structurally assessing missense variants was made available at http://www.sbg.bio.ic.ac.uk/~missense3d.
    Mesh-Begriff(e) Algorithms ; Gene Frequency ; Genetic Predisposition to Disease ; Humans ; Models, Molecular ; Mutation, Missense ; Protein Conformation ; Proteins/chemistry ; Proteins/genetics
    Chemische Substanzen Proteins
    Sprache Englisch
    Erscheinungsdatum 2019-04-14
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2019.04.009
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Properties of human genes guided by their enrichment in rare and common variants.

    Alhuzimi, Eman / Leal, Luis G / Sternberg, Michael J E / David, Alessia

    Human mutation

    2017  Band 39, Heft 3, Seite(n) 365–370

    Abstract: We analyzed 563,099 common (minor allele frequency, MAF≥0.01) and rare (MAF < 0.01) genetic variants annotated in ExAC and UniProt and 26,884 disease-causing variants from ClinVar and UniProt occurring in the coding region of 17,975 human protein-coding ... ...

    Abstract We analyzed 563,099 common (minor allele frequency, MAF≥0.01) and rare (MAF < 0.01) genetic variants annotated in ExAC and UniProt and 26,884 disease-causing variants from ClinVar and UniProt occurring in the coding region of 17,975 human protein-coding genes. Three novel sets of genes were identified: those enriched in rare variants (n = 32 genes), in common variants (n = 282 genes), and in disease-causing variants (n = 800 genes). Genes enriched in rare variants have far greater similarities in terms of biological and network properties to genes enriched in disease-causing variants, than to genes enriched in common variants. However, in half of the genes enriched in rare variants (AOC2, MAMDC4, ANKHD1, CDC42BPB, SPAG5, TRRAP, TANC2, IQCH, USP54, SRRM2, DOPEY2, and PITPNM1), no disease-causing variants have been identified in major, publicly available databases. Thus, genetic variants in these genes are strong candidates for disease and their identification, as part of sequencing studies, should prompt further in vitro analyses.
    Mesh-Begriff(e) Disease/genetics ; Genes ; Genes, Essential ; Genetic Variation ; Humans ; Mutation/genetics
    Sprache Englisch
    Erscheinungsdatum 2017-12-21
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1126646-6
    ISSN 1098-1004 ; 1059-7794
    ISSN (online) 1098-1004
    ISSN 1059-7794
    DOI 10.1002/humu.23377
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: Landscape of Pleiotropic Proteins Causing Human Disease: Structural and System Biology Insights.

    Ittisoponpisan, Sirawit / Alhuzimi, Eman / Sternberg, Michael J E / David, Alessia

    Human mutation

    2017  Band 38, Heft 3, Seite(n) 289–296

    Abstract: Pleiotropy is the phenomenon by which the same gene can result in multiple phenotypes. Pleiotropic proteins are emerging as important contributors to rare and common disorders. Nevertheless, little is known on the mechanisms underlying pleiotropy and the ...

    Abstract Pleiotropy is the phenomenon by which the same gene can result in multiple phenotypes. Pleiotropic proteins are emerging as important contributors to rare and common disorders. Nevertheless, little is known on the mechanisms underlying pleiotropy and the characteristic of pleiotropic proteins. We analyzed disease-causing proteins reported in UniProt and observed that 12% are pleiotropic (variants in the same protein cause more than one disease). Pleiotropic proteins were enriched in deleterious and rare variants, but not in common variants. Pleiotropic proteins were more likely to be involved in the pathogenesis of neoplasms, neurological, and circulatory diseases and congenital malformations, whereas non-pleiotropic proteins in endocrine and metabolic disorders. Pleiotropic proteins were more essential and had a higher number of interacting partners compared with non-pleiotropic proteins. Significantly more pleiotropic than non-pleiotropic proteins contained at least one intrinsically long disordered region (P < 0.001). Deleterious variants occurring in structurally disordered regions were more commonly found in pleiotropic, rather than non-pleiotropic proteins. In conclusion, pleiotropic proteins are an important contributor to human disease. They represent a biologically different class of proteins compared with non-pleiotropic proteins and a better understanding of their characteristics and genetic variants can greatly aid in the interpretation of genetic studies and drug design.
    Mesh-Begriff(e) Computational Biology ; Databases, Genetic ; Genetic Association Studies ; Genetic Pleiotropy ; Genetic Predisposition to Disease ; Homeodomain Proteins/chemistry ; Homeodomain Proteins/genetics ; Homeodomain Proteins/metabolism ; Humans ; Intrinsically Disordered Proteins/chemistry ; Intrinsically Disordered Proteins/genetics ; Intrinsically Disordered Proteins/metabolism ; Models, Molecular ; Odds Ratio ; Protein Binding ; Protein Conformation ; Proteins/chemistry ; Proteins/genetics ; Proteins/metabolism ; Signal Transduction ; Structure-Activity Relationship ; Systems Biology/methods ; Vinculin/chemistry ; Vinculin/genetics ; Vinculin/metabolism
    Chemische Substanzen Homeodomain Proteins ; Intrinsically Disordered Proteins ; Proteins ; Vinculin (125361-02-6)
    Sprache Englisch
    Erscheinungsdatum 2017-01-11
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1126646-6
    ISSN 1098-1004 ; 1059-7794
    ISSN (online) 1098-1004
    ISSN 1059-7794
    DOI 10.1002/humu.23155
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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    Verfügbar in ZB MED Köln/Königswinter

    Zs.A 3586: Hefte anzeigen Standort:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
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  4. Artikel: Can Predicted Protein 3D Structures Provide Reliable Insights into whether Missense Variants Are Disease Associated?

    Ittisoponpisan, Sirawit / Islam, Suhail A / Khanna, Tarun / Alhuzimi, Eman / David, Alessia / Sternberg, Michael J.E

    Journal of molecular biology. 2019 May 17, v. 431, no. 11

    2019  

    Abstract: Knowledge of protein structure can be used to predict the phenotypic consequence of a missense variant. Since structural coverage of the human proteome can be roughly tripled to over 50% of the residues if homology-predicted structures are included in ... ...

    Abstract Knowledge of protein structure can be used to predict the phenotypic consequence of a missense variant. Since structural coverage of the human proteome can be roughly tripled to over 50% of the residues if homology-predicted structures are included in addition to experimentally determined coordinates, it is important to assess the reliability of using predicted models when analyzing missense variants. Accordingly, we assess whether a missense variant is structurally damaging by using experimental and predicted structures. We considered 606 experimental structures and show that 40% of the 1965 disease-associated missense variants analyzed have a structurally damaging change in the mutant structure. Only 11% of the 2134 neutral variants are structurally damaging. Importantly, similar results are obtained when 1052 structures predicted using Phyre2 algorithm were used, even when the model shares low (<40%) sequence identity to the template. Thus, structure-based analysis of the effects of missense variants can be effectively applied to homology models. Our in-house pipeline, Missense3D, for structurally assessing missense variants was made available at http://www.sbg.bio.ic.ac.uk/~missense3d
    Schlagwörter algorithms ; humans ; models ; mutants ; phenotype ; protein structure ; proteome ; sequence analysis
    Sprache Englisch
    Erscheinungsverlauf 2019-0517
    Umfang p. 2197-2212.
    Erscheinungsort Elsevier Ltd
    Dokumenttyp Artikel
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2019.04.009
    Datenquelle NAL Katalog (AGRICOLA)

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  5. Artikel ; Online: Genome sequence of the date palm Phoenix dactylifera L.

    Al-Mssallem, Ibrahim S / Hu, Songnian / Zhang, Xiaowei / Lin, Qiang / Liu, Wanfei / Tan, Jun / Yu, Xiaoguang / Liu, Jiucheng / Pan, Linlin / Zhang, Tongwu / Yin, Yuxin / Xin, Chengqi / Wu, Hao / Zhang, Guangyu / Ba Abdullah, Mohammed M / Huang, Dawei / Fang, Yongjun / Alnakhli, Yasser O / Jia, Shangang /
    Yin, An / Alhuzimi, Eman M / Alsaihati, Burair A / Al-Owayyed, Saad A / Zhao, Duojun / Zhang, Sun / Al-Otaibi, Noha A / Sun, Gaoyuan / Majrashi, Majed A / Li, Fusen / Tala / Wang, Jixiang / Yun, Quanzheng / Alnassar, Nafla A / Wang, Lei / Yang, Meng / Al-Jelaify, Rasha F / Liu, Kan / Gao, Shenghan / Chen, Kaifu / Alkhaldi, Samiyah R / Liu, Guiming / Zhang, Meng / Guo, Haiyan / Yu, Jun

    Nature communications

    2013  Band 4, Seite(n) 2274

    Abstract: Date palm (Phoenix dactylifera L.) is a cultivated woody plant species with agricultural and economic importance. Here we report a genome assembly for an elite variety (Khalas), which is 605.4 Mb in size and covers >90% of the genome (~671 Mb) and >96% ... ...

    Abstract Date palm (Phoenix dactylifera L.) is a cultivated woody plant species with agricultural and economic importance. Here we report a genome assembly for an elite variety (Khalas), which is 605.4 Mb in size and covers >90% of the genome (~671 Mb) and >96% of its genes (~41,660 genes). Genomic sequence analysis demonstrates that P. dactylifera experienced a clear genome-wide duplication after either ancient whole genome duplications or massive segmental duplications. Genetic diversity analysis indicates that its stress resistance and sugar metabolism-related genes tend to be enriched in the chromosomal regions where the density of single-nucleotide polymorphisms is relatively low. Using transcriptomic data, we also illustrate the date palm's unique sugar metabolism that underlies fruit development and ripening. Our large-scale genomic and transcriptomic data pave the way for further genomic studies not only on P. dactylifera but also other Arecaceae plants.
    Mesh-Begriff(e) Arecaceae/genetics ; Base Sequence ; Carbohydrate Metabolism/genetics ; Chromosomes, Plant/genetics ; Gene Duplication/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Genome, Plant/genetics ; Molecular Sequence Annotation ; Multigene Family/genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results ; Synteny/genetics
    Sprache Englisch
    Erscheinungsdatum 2013-08-02
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/ncomms3274
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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