Thousands of Rab GTPases for the Cell Biologist
Publication Date
October 13, 2011
Journal
PLOS Computational Biology
Authors
Yoan Diekmann, Elsa Seixas, Marc Gouw, Filipe Tavares Cadete, et al
Volume
7
Issue
10
Pages
e1002217
DOI
http://doi.org/10.1371/journal.pcbi.1002217
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1002217
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22022256
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192815
Europe PMC
http://europepmc.org/abstract/MED/22022256
Web of Science
000297262700040
Scopus
80055078598
Mendeley
http://www.mendeley.com/research/thousands-rab-gtpases-cell-biologist
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Mendeley | Further Information

{"title"=>"Thousands of Rab GTPases for the cell biologist", "type"=>"journal", "authors"=>[{"first_name"=>"Yoan", "last_name"=>"Diekmann", "scopus_author_id"=>"16307081300"}, {"first_name"=>"Elsa", "last_name"=>"Seixas", "scopus_author_id"=>"6602979460"}, {"first_name"=>"Marc", "last_name"=>"Gouw", "scopus_author_id"=>"54404619600"}, {"first_name"=>"Filipe", "last_name"=>"Tavares-Cadete", "scopus_author_id"=>"36006578100"}, {"first_name"=>"Miguel C.", "last_name"=>"Seabra", "scopus_author_id"=>"7004369652"}, {"first_name"=>"José B.", "last_name"=>"Pereira-Leal", "scopus_author_id"=>"55940842900"}], "year"=>2011, "source"=>"PLoS Computational Biology", "identifiers"=>{"isbn"=>"1553-7358 (Electronic)\\r1553-734X (Linking)", "scopus"=>"2-s2.0-80055078598", "pmid"=>"22022256", "issn"=>"1553734X", "pui"=>"362834464", "doi"=>"10.1371/journal.pcbi.1002217", "sgr"=>"80055078598"}, "id"=>"45cfd883-2d63-3853-84dd-d2e27f69e1cd", "abstract"=>"Rab proteins are small GTPases that act as essential regulators of vesicular trafficking. 44 subfamilies are known in humans, performing specific sets of functions at distinct subcellular localisations and tissues. Rab function is conserved even amongst distant orthologs. Hence, the annotation of Rabs yields functional predictions about the cell biology of trafficking. So far, annotating Rabs has been a laborious manual task not feasible for current and future genomic output of deep sequencing technologies. We developed, validated and benchmarked the Rabifier, an automated bioinformatic pipeline for the identification and classification of Rabs, which achieves up to 90% classification accuracy. We cataloged roughly 8.000 Rabs from 247 genomes covering the entire eukaryotic tree. The full Rab database and a web tool implementing the pipeline are publicly available at www.RabDB.org. For the first time, we describe and analyse the evolution of Rabs in a dataset covering the whole eukaryotic phylogeny. We found a highly dynamic family undergoing frequent taxon-specific expansions and losses. We dated the origin of human subfamilies using phylogenetic profiling, which enlarged the Rab repertoire of the Last Eukaryotic Common Ancestor with Rab14, 32 and RabL4. Furthermore, a detailed analysis of the Choanoflagellate Monosiga brevicollis Rab family pinpointed the changes that accompanied the emergence of Metazoan multicellularity, mainly an important expansion and specialisation of the secretory pathway. Lastly, we experimentally establish tissue specificity in expression of mouse Rabs and show that neo-functionalisation best explains the emergence of new human Rab subfamilies. With the Rabifier and RabDB, we provide tools that easily allows non-bioinformaticians to integrate thousands of Rabs in their analyses. RabDB is designed to enable the cell biology community to keep pace with the increasing number of fully-sequenced genomes and change the scale at which we perform comparative analysis in cell biology.", "link"=>"http://www.mendeley.com/research/thousands-rab-gtpases-cell-biologist", "reader_count"=>105, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>5, "Librarian"=>2, "Researcher"=>29, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>37, "Student > Postgraduate"=>2, "Student > Master"=>11, "Student > Bachelor"=>9, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>5, "Librarian"=>2, "Researcher"=>29, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>37, "Student > Postgraduate"=>2, "Student > Master"=>11, "Student > Bachelor"=>9, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>80, "Medicine and Dentistry"=>3, "Neuroscience"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>2, "Sports and Recreations"=>1, "Chemistry"=>3, "Social Sciences"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>6}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>3}, "Social Sciences"=>{"Social Sciences"=>1}, "Sports and Recreations"=>{"Sports and Recreations"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>6}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>80}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Environmental Science"=>{"Environmental Science"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>2}}, "reader_count_by_country"=>{"Canada"=>1, "Netherlands"=>1, "Brazil"=>1, "United Kingdom"=>2, "France"=>1, "Portugal"=>2, "Germany"=>1, "Spain"=>1}, "group_count"=>0}

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/724407"], "description"=>"<p>(<b>A</b>) Snapshots of the database <a href=\"http://www.RabDB.org\" target=\"_blank\">www.RabDB.org</a> which provides public access to the results of the Rabifier applied to the Superfamily database <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#pcbi.1002217-Wilson1\" target=\"_blank\">[41]</a> and the online version of the Rabifier. (<b>B</b>) Statistics of the current content of <a href=\"http://www.RabDB.org\" target=\"_blank\">www.RabDB.org</a> in terms of number of genomes (left), absolute number of Rabs either belonging to a subfamily also present in humans or not (middle), and the relative fraction of the two types of Rabs for a given branch (right). The cladogram (<i>i.e.</i> the branch length are arbitrary, see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#pcbi.1002217-Baldauf1\" target=\"_blank\">[114]</a>) of the eukaryotic taxa is derived from <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#pcbi.1002217-Burki1\" target=\"_blank\">[115]</a>.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "cell biology", "computer science", "Evolutionary biology"], "article_id"=>394752, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Yoan Diekmann", "Elsa Seixas", "Marc Gouw", "Filipe Tavares-Cadete", "Miguel C. Seabra", "José B. Pereira-Leal"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002217.g003", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Resources_we_make_available_/394752", "title"=>"Resources we make available.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-10-13 01:19:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/724572"], "description"=>"<p>For each of the eukaryotic taxa (as derived from <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#pcbi.1002217-Burki1\" target=\"_blank\">[115]</a>), (<b>A</b>) displays the relative size compared to Metazoa of each human Rab subfamily on average per genome. The dashed line represents the average in Metazoan genomes, <i>i.e.</i> any circle lying on that line represents a human subfamily that has the same amount of members on average per genome than on average in Metazoa. Similarly, any circle to the left represents a subfamily that is smaller compared to Metazoa, finally, all on the right are expanded compared to the Metazoan average. Note that the axis are in logarithmic scale. In addition to the numbers indicating the human Rab subfamily, a colour code to distinguish subfamilies is shown below, where similar colours indicate proximity in the phylogenetic tree of human Rabs. The same plot for all other Rabs is shown in (B), again on a logarithmic scale. All sequences used are accessible at <a href=\"http://www.RabDB.org\" target=\"_blank\">www.RabDB.org</a>. Abbreviations: subfamily (sf.).</p>", "links"=>[], "tags"=>["subfamily", "expansions", "metazoa", "dataset", "247"], "article_id"=>394925, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Yoan Diekmann", "Elsa Seixas", "Marc Gouw", "Filipe Tavares-Cadete", "Miguel C. Seabra", "José B. Pereira-Leal"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002217.g005", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Rab_subfamily_expansions_relative_to_Metazoa_in_a_dataset_of_247_genomes_/394925", "title"=>"Rab subfamily expansions relative to Metazoa in a dataset of 247 genomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-10-13 01:22:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/724215"], "description"=>"<p>(<b>A</b>) Identification- and (<b>B</b>) classification-procedure implemented by the Rabifier, see <b><a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#s2\" target=\"_blank\">Results and Discussion</a></b> for details on the two phases. Panel (<b>C</b>) shows descriptive statistics from the application of the Rabifier to 247 genomes in the Superfamily database, and details about <i>Monosiga brevicollis</i>. Abbreviations: best BLAST hit (BH) <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#pcbi.1002217-Altschul1\" target=\"_blank\">[37]</a>, Rab family motif (RabF) <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#pcbi.1002217-PereiraLeal1\" target=\"_blank\">[24]</a>, reverse Ψ-BLAST (RPS-BLAST) <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#pcbi.1002217-Altschul2\" target=\"_blank\">[38]</a>, subfamily (sf.), Rab not classified to any subfamily within our internal reference set (RabX).</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "cell biology", "computer science", "Evolutionary biology"], "article_id"=>394567, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Yoan Diekmann", "Elsa Seixas", "Marc Gouw", "Filipe Tavares-Cadete", "Miguel C. Seabra", "José B. Pereira-Leal"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002217.g001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flowchart_of_the_Rabifier_/394567", "title"=>"Flowchart of the Rabifier.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-10-13 01:16:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/724662"], "description"=>"<p>A black dot reads as presence of the corresponding subfamily in the respective species. Rab subfamilies are ordered according to the top phylogenetic tree generated as explained in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#s3\" target=\"_blank\"><b>Materials and Methods</b></a>. Branches with bootstrap support above 58 are coloured in red. The tree on the left represents the species' branching order and is derived from <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#pcbi.1002217-Burki1\" target=\"_blank\">[115]</a>–<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#pcbi.1002217-Elias1\" target=\"_blank\">[118]</a> together with the naming of the partially nested monophyletic groups on the right.</p>", "links"=>[], "tags"=>["profiles", "rab", "subfamilies"], "article_id"=>395014, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Yoan Diekmann", "Elsa Seixas", "Marc Gouw", "Filipe Tavares-Cadete", "Miguel C. Seabra", "José B. Pereira-Leal"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002217.g006", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_profiles_of_human_Rab_subfamilies_in_selected_organisms_/395014", "title"=>"Phylogenetic profiles of human Rab subfamilies in selected organisms.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-10-13 01:23:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/724310"], "description"=>"<p>(<b>A</b>) summarises the validation in normal mode, <i>i.e.</i> without taking the subfamily score produced by Rabifier into account, against the Rab families of <i>Trypanosoma brucei </i><a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#pcbi.1002217-Ackers1\" target=\"_blank\">[32]</a>, <i>Entamoeba histolytica </i><a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#pcbi.1002217-SaitoNakano2\" target=\"_blank\">[30]</a> and <i>Monosiga brevicollis</i>, which we annotated in (<b>E</b>). Three quantities needed to judge the performance of the Rabifier are shown for Rabs belonging to human and other subfamilies separately: sequences erroneously classified as not being a Rab by the Rabifier (red), sequences correctly identified as Rabs, however, wrongly classified at subfamily level (light green), and those which were entirely correct (dark green). (<b>B</b>) displays the distribution of confidence scores associated to each subfamily call, respecting the same colour code as above. The blue line indicates the threshold which we propose on default, and below which subfamily classification may be rejected and treated as a undefined RabX. That choice is based on the ROC-curve <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#pcbi.1002217-Fawcett1\" target=\"_blank\">[113]</a> analysis shown in (<b>C</b>), which plots the true positive rate against the false positive rate for each possible confidence threshold <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#pcbi.1002217-Fawcett1\" target=\"_blank\">[113]</a> and provides a combined measure of the accuracy of a classifier (Area under the curve, AUC <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#pcbi.1002217-Hanley1\" target=\"_blank\">[39]</a>). The effect of choosing an 0.4 confidence threshold (blue circle) on the classification accuracy, <i>i.e.</i> running the Rabifier in high confidence mode, is shown in the inlay. (<b>D</b>) plots the improvement in terms of the three quantities discussed above the Rabifier achieves compared to an alternative strategy (see <b><a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#s2\" target=\"_blank\">Results and Discussion</a></b> for details on its implementation). (<b>E</b>) Phylogenetic tree of the human and <i>M. brevicollis</i> Rab family on which the manual classification of the latter Rab family was based (bootstrap support above 70% shown). Colours indicate the results of the corresponding automated annotation for that specific sequence. Abbreviations: subfamily (sf.), annotation (annot.).</p>", "links"=>[], "tags"=>["benchmarking"], "article_id"=>394673, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Yoan Diekmann", "Elsa Seixas", "Marc Gouw", "Filipe Tavares-Cadete", "Miguel C. Seabra", "José B. Pereira-Leal"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002217.g002", "stats"=>{"downloads"=>1, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Validation_and_benchmarking_of_the_Rabifier_/394673", "title"=>"Validation and benchmarking of the Rabifier.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-10-13 01:17:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/724509"], "description"=>"<p>Number of different Rab subfamilies found in our dataset. Human sf. are shown in blue, and other known sf. in orange. The last four categories are hypothetical subfamilies we propose in the context of this paper (see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#s3\" target=\"_blank\"><b>Materials and Methods</b></a> for details on the procedure): subfamilies whose members span more than one taxon (red), those spanning more than on genome (green), subfamilies with several members yet only present in one organism (brown) and finally singletons (grey) which are not similar to any other known Rab. All members and subfamilies can be browsed in our website at <a href=\"http://www.RabDB.org\" target=\"_blank\">www.RabDB.org</a>. Abbreviations: hypothetical (hypo.), subfamily (sf.).</p>", "links"=>[], "tags"=>["subfamilies"], "article_id"=>394864, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Yoan Diekmann", "Elsa Seixas", "Marc Gouw", "Filipe Tavares-Cadete", "Miguel C. Seabra", "José B. Pereira-Leal"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002217.g004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Rab_subfamilies_in_or_dataset_/394864", "title"=>"Rab subfamilies in or dataset.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-10-13 01:21:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/366534", "https://ndownloader.figshare.com/files/366548", "https://ndownloader.figshare.com/files/366603", "https://ndownloader.figshare.com/files/366647", "https://ndownloader.figshare.com/files/366714", "https://ndownloader.figshare.com/files/366789", "https://ndownloader.figshare.com/files/373686", "https://ndownloader.figshare.com/files/373793", "https://ndownloader.figshare.com/files/373844", "https://ndownloader.figshare.com/files/373987", "https://ndownloader.figshare.com/files/374112", "https://ndownloader.figshare.com/files/374155"], "description"=>"<div><p>Rab proteins are small GTPases that act as essential regulators of vesicular trafficking. 44 subfamilies are known in humans, performing specific sets of functions at distinct subcellular localisations and tissues. Rab function is conserved even amongst distant orthologs. Hence, the annotation of Rabs yields functional predictions about the cell biology of trafficking. So far, annotating Rabs has been a laborious manual task not feasible for current and future genomic output of deep sequencing technologies. We developed, validated and benchmarked the Rabifier, an automated bioinformatic pipeline for the identification and classification of Rabs, which achieves up to 90% classification accuracy. We cataloged roughly 8.000 Rabs from 247 genomes covering the entire eukaryotic tree. The full Rab database and a web tool implementing the pipeline are publicly available at <a href=\"http://www.RabDB.org\">www.RabDB.org</a>. For the first time, we describe and analyse the evolution of Rabs in a dataset covering the whole eukaryotic phylogeny. We found a highly dynamic family undergoing frequent taxon-specific expansions and losses. We dated the origin of human subfamilies using phylogenetic profiling, which enlarged the Rab repertoire of the Last Eukaryotic Common Ancestor with Rab14, 32 and RabL4. Furthermore, a detailed analysis of the Choanoflagellate <em>Monosiga brevicollis</em> Rab family pinpointed the changes that accompanied the emergence of Metazoan multicellularity, mainly an important expansion and specialisation of the secretory pathway. Lastly, we experimentally establish tissue specificity in expression of mouse Rabs and show that neo-functionalisation best explains the emergence of new human Rab subfamilies. With the Rabifier and RabDB, we provide tools that easily allows non-bioinformaticians to integrate thousands of Rabs in their analyses. RabDB is designed to enable the cell biology community to keep pace with the increasing number of fully-sequenced genomes and change the scale at which we perform comparative analysis in cell biology.</p> </div>", "links"=>[], "tags"=>["thousands", "rab", "gtpases", "biologist"], "article_id"=>132430, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Yoan Diekmann", "Elsa Seixas", "Marc Gouw", "Filipe Tavares-Cadete", "Miguel C. Seabra", "José B. Pereira-Leal"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1002217.s001", "https://dx.doi.org/10.1371/journal.pcbi.1002217.s002", "https://dx.doi.org/10.1371/journal.pcbi.1002217.s003", "https://dx.doi.org/10.1371/journal.pcbi.1002217.s004", "https://dx.doi.org/10.1371/journal.pcbi.1002217.s005", "https://dx.doi.org/10.1371/journal.pcbi.1002217.s006", "https://dx.doi.org/10.1371/journal.pcbi.1002217.s007", "https://dx.doi.org/10.1371/journal.pcbi.1002217.s008", "https://dx.doi.org/10.1371/journal.pcbi.1002217.s009", "https://dx.doi.org/10.1371/journal.pcbi.1002217.s010", "https://dx.doi.org/10.1371/journal.pcbi.1002217.s011", "https://dx.doi.org/10.1371/journal.pcbi.1002217.s012"], "stats"=>{"downloads"=>6, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Thousands_of_Rab_GTPases_for_the_Cell_Biologist/132430", "title"=>"Thousands of Rab GTPases for the Cell Biologist", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-10-13 00:40:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/724824"], "description"=>"<p>Summary of PCR experiments establishing expression (black squares) or lack thereof (white squares) of mouse Rabs in six tissues and five mouse cell lines. Stars on the bottom indicate subfamilies which we found already present in LECA, and that predate the evolution of multicellularity (see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#pcbi-1002217-g007\" target=\"_blank\"><b>Figure 7</b></a>). Branches coloured in blue in the phylogenetic tree of mouse Rabs on the left are those for which we test the hypothesis that derived subfamilies are expressed in the same or in a subset of tissues of the Rab they were derived from (see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#pcbi-1002217-g007\" target=\"_blank\"><b>Figure 7</b></a> for a summary of which Rabs have a clear origin). Abbreviations: subfamily (sf.), primary Hepatocytes (Prim. Hepatoc.), multicellularity (multic.), last eukaryotic common ancestor (LECA).</p>", "links"=>[], "tags"=>["specificity", "derived", "rabs"], "article_id"=>395179, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Yoan Diekmann", "Elsa Seixas", "Marc Gouw", "Filipe Tavares-Cadete", "Miguel C. Seabra", "José B. Pereira-Leal"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002217.g008", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Increasing_tissue_specificity_in_expression_of_derived_Rabs_in_mice_/395179", "title"=>"Increasing tissue specificity in expression of derived Rabs in mice.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-10-13 01:26:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/724761"], "description"=>"<p>Each level represents a nested evolutionary stage from the LECA to humans (derived from <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#pcbi.1002217-Burki1\" target=\"_blank\">[115]</a>, <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002217#pcbi.1002217-ShalchianTabrizi1\" target=\"_blank\">[119]</a>) with one circle per human subfamily. Those subfamilies for which we could establish a clear origin, that is which subfamily it was derived from by duplication, are right from the dotted line with the subfamily it was derived from attached at the bottom right.</p>", "links"=>[], "tags"=>["evolutionary", "duplication"], "article_id"=>395114, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Yoan Diekmann", "Elsa Seixas", "Marc Gouw", "Filipe Tavares-Cadete", "Miguel C. Seabra", "José B. Pereira-Leal"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002217.g007", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_evolutionary_age_and_duplication_origin_of_human_subfamilies_/395114", "title"=>"Summary of evolutionary age and duplication origin of human subfamilies.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-10-13 01:25:14"}

PMC Usage Stats | Further Information

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Relative Metric

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