Transcriptomic Analysis of the Rice White Tip Nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae)
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{"title"=>"Transcriptomic analysis of the rice white tip nematode, phelenchoides besseyi (Nematoda: Aphelenchoididae)", "type"=>"journal", "authors"=>[{"first_name"=>"Feng", "last_name"=>"Wang", "scopus_author_id"=>"56739463700"}, {"first_name"=>"Danlei", "last_name"=>"Li", "scopus_author_id"=>"55792826900"}, {"first_name"=>"Zhiying", "last_name"=>"Wang", "scopus_author_id"=>"36951937700"}, {"first_name"=>"Airong", "last_name"=>"Dong", "scopus_author_id"=>"56115390400"}, {"first_name"=>"Lihong", "last_name"=>"Liu", "scopus_author_id"=>"55715369800"}, {"first_name"=>"Buyong", "last_name"=>"Wang", "scopus_author_id"=>"52464792800"}, {"first_name"=>"Qiaoli", "last_name"=>"Chen", "scopus_author_id"=>"55322320200"}, {"first_name"=>"Xiaohan", "last_name"=>"Liu", "scopus_author_id"=>"56114730300"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84898638368", "doi"=>"10.1371/journal.pone.0091591", "sgr"=>"84898638368", "pmid"=>"24637831", "issn"=>"19326203", "pui"=>"372838514"}, "id"=>"152052d5-e816-399d-a318-e4e8c7624bf9", "abstract"=>"BACKGROUND: The rice white tip nematode Aphelenchoides besseyi, a devastating nematode whose genome has not been sequenced, is distributed widely throughout almost all the rice-growing regions of the world. The aims of the present study were to define the transcriptome of A. besseyi and to identify parasite-related, mortality-related or host resistance-overcoming genes in this nematode.\\n\\nMETHODOLOGY AND PRINCIPAL FINDINGS: Using Solexa/Illumina sequencing, we profiled the transcriptome of mixed-stage populations of A. besseyi. A total of 51,270 transcripts without gaps were produced based on high-quality clean reads. Of all the A. besseyi transcripts, 9,132 KEGG Orthology assignments were annotated. Carbohydrate-active enzymes of glycoside hydrolases (GHs), glycosyltransferases (GTs), carbohydrate esterases (CEs) and carbohydrate-binding modules (CBMs) were identified. The presence of the A. besseyi GH45 cellulase gene was verified by in situ hybridization. Given that 13 unique A. besseyi potential effector genes were identified from 41 candidate effector homologs, further studies of these homologs are merited. Finally, comparative analyses were conducted between A. besseyi contigs and Caenorhabditis elegans genes to look for orthologs of RNAi phenotypes, neuropeptides and peptidases.\\n\\nCONCLUSIONS AND SIGNIFICANCE: The present results provide comprehensive insight into the genetic makeup of A. besseyi. Many of this species' genes are parasite related, nematode mortality-related or necessary to overcome host resistance. The generated transcriptome dataset of A. besseyi reported here lays the foundation for further studies of the molecular mechanisms related to parasitism and facilitates the development of new control strategies for this species.", "link"=>"http://www.mendeley.com/research/transcriptomic-analysis-rice-white-tip-nematode-phelenchoides-besseyi-nematoda-aphelenchoididae", "reader_count"=>27, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>6, "Researcher"=>6, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>1, "Student > Master"=>1, "Other"=>1, "Student > Bachelor"=>2, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>6, "Researcher"=>6, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>1, "Student > Master"=>1, "Other"=>1, "Student > Bachelor"=>2, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Materials Science"=>1, "Agricultural and Biological Sciences"=>17, "Medicine and Dentistry"=>1, "Computer Science"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>17}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"United States"=>1, "Taiwan"=>1, "United Kingdom"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1423739"], "description"=>"<p>A and B: Antisense probe in a male nematode. C and D: Antisense probe in a female nematode. E: Control sense probe in a female nematode. The scale bars represent 20 µm. G: esophageal glands; S: stylet; M: metacarpus.</p>", "links"=>[], "tags"=>["agriculture", "Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "microbiology", "Parasitology", "Parasite physiology", "Plant science", "Plant pathology", "Plant pests", "Zoology", "Nematology", "Infectious diseases", "Parasitic diseases", "gh45", "cellulase", "mrna", "hybridization", "digoxigenin-labeled", "antisense"], "article_id"=>964717, "categories"=>["Biological Sciences"], "users"=>["Feng Wang", "Danlei Li", "Zhiying Wang", "Airong Dong", "Lihong Liu", "Buyong Wang", "Qiaoli Chen", "Xiaohan Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091591.g005", "stats"=>{"downloads"=>3, "page_views"=>32, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Localization_of_A_besseyi_GH45_cellulase_mRNA_by_in_situ_hybridization_using_digoxigenin_labeled_antisense_or_sense_probes_/964717", "title"=>"Localization of <i>A. besseyi</i> GH45 cellulase mRNA by <i>in situ</i> hybridization using digoxigenin-labeled antisense or sense probes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-17 03:54:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1423735"], "description"=>"<p>A: The alignment shows the comparison between <i>A. besseyi</i> GH45 cellulase and its homologs. Active site residues are marked with red asterisks. The GH45 cellulase consensus sequences are boxed with a red line and highlighted with a magnifying lens. Asterisks, double dots and single dots denote fully conserved, strongly conserved and weakly conserved amino acid residues, respectively. B: The maximum likelihood tree shows the relationship between <i>A. besseyi</i> GH45 cellulase and homologs. One thousand bootstrap replicates were performed, and the node labels represent the percentage of bootstrap support.</p>", "links"=>[], "tags"=>["agriculture", "Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "microbiology", "Parasitology", "Parasite physiology", "Plant science", "Plant pathology", "Plant pests", "Zoology", "Nematology", "Infectious diseases", "Parasitic diseases", "polygenetic", "gh45", "cellulase", "amino", "homologs", "ncbi"], "article_id"=>964713, "categories"=>["Biological Sciences"], "users"=>["Feng Wang", "Danlei Li", "Zhiying Wang", "Airong Dong", "Lihong Liu", "Buyong Wang", "Qiaoli Chen", "Xiaohan Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091591.g004", "stats"=>{"downloads"=>3, "page_views"=>36, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignment_and_polygenetic_tree_of_the_A_besseyi_GH45_cellulase_amino_acid_sequence_with_its_homologs_identified_from_the_NCBI_database_/964713", "title"=>"Alignment and polygenetic tree of the <i>A. besseyi</i> GH45 cellulase amino acid sequence with its homologs identified from the NCBI database.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-17 03:54:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1423747"], "description"=>"<p>Potential effectors identified in <i>A. besseyi</i>.</p>", "links"=>[], "tags"=>["agriculture", "Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "microbiology", "Parasitology", "Parasite physiology", "Plant science", "Plant pathology", "Plant pests", "Zoology", "Nematology", "Infectious diseases", "Parasitic diseases", "effectors"], "article_id"=>964725, "categories"=>["Biological Sciences"], "users"=>["Feng Wang", "Danlei Li", "Zhiying Wang", "Airong Dong", "Lihong Liu", "Buyong Wang", "Qiaoli Chen", "Xiaohan Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091591.t004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Potential_effectors_identified_in_A_besseyi_/964725", "title"=>"Potential effectors identified in <i>A. besseyi</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-17 03:54:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1423729"], "description"=>"<p>A: Assignment of <i>C. elegans</i>, <i>A. besseyi</i> and other plant-parasitic nematodes. B: Assignment of <i>C. elegans</i>, <i>A. besseyi</i> and the animal-parasitic nematode <i>A. suum</i>. Ab: <i>A. besseyi</i>, Bx: <i>B. xylophilus</i>, Mi: <i>M. incognita</i>, Ce: <i>C. elegans</i>, Bm: <i>B. malayi</i>, As: <i>A. suum</i>.</p>", "links"=>[], "tags"=>["agriculture", "Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "microbiology", "Parasitology", "Parasite physiology", "Plant science", "Plant pathology", "Plant pests", "Zoology", "Nematology", "Infectious diseases", "Parasitic diseases", "intersections", "lists", "nematode", "kegg", "orthology"], "article_id"=>964707, "categories"=>["Biological Sciences"], "users"=>["Feng Wang", "Danlei Li", "Zhiying Wang", "Airong Dong", "Lihong Liu", "Buyong Wang", "Qiaoli Chen", "Xiaohan Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091591.g003", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_intersections_of_lists_of_nematode_KEGG_Orthology_KO_assignments_/964707", "title"=>"The intersections of lists of nematode KEGG Orthology (KO) assignments.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-17 03:54:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1423746"], "description"=>"<p>*(bitscore>40 and E-value</p>", "links"=>[], "tags"=>["agriculture", "Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "microbiology", "Parasitology", "Parasite physiology", "Plant science", "Plant pathology", "Plant pests", "Zoology", "Nematology", "Infectious diseases", "Parasitic diseases", "genes", "rnai"], "article_id"=>964724, "categories"=>["Biological Sciences"], "users"=>["Feng Wang", "Danlei Li", "Zhiying Wang", "Airong Dong", "Lihong Liu", "Buyong Wang", "Qiaoli Chen", "Xiaohan Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091591.t005", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Presence_of_genes_involved_in_the_RNAi_pathway_/964724", "title"=>"Presence of genes involved in the RNAi pathway.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-17 03:54:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1423743"], "description"=>"<p>The classification of <i>A. besseyi</i> pathways.</p>", "links"=>[], "tags"=>["agriculture", "Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "microbiology", "Parasitology", "Parasite physiology", "Plant science", "Plant pathology", "Plant pests", "Zoology", "Nematology", "Infectious diseases", "Parasitic diseases", "classification"], "article_id"=>964721, "categories"=>["Biological Sciences"], "users"=>["Feng Wang", "Danlei Li", "Zhiying Wang", "Airong Dong", "Lihong Liu", "Buyong Wang", "Qiaoli Chen", "Xiaohan Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091591.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_classification_of_A_besseyi_pathways_/964721", "title"=>"The classification of <i>A. besseyi</i> pathways.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-17 03:54:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1423742"], "description"=>"<p>The most common 5 <i>A. besseyi</i> pathways consistent with <i>C. elegans</i>.</p>", "links"=>[], "tags"=>["agriculture", "Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "microbiology", "Parasitology", "Parasite physiology", "Plant science", "Plant pathology", "Plant pests", "Zoology", "Nematology", "Infectious diseases", "Parasitic diseases", "pathways"], "article_id"=>964720, "categories"=>["Biological Sciences"], "users"=>["Feng Wang", "Danlei Li", "Zhiying Wang", "Airong Dong", "Lihong Liu", "Buyong Wang", "Qiaoli Chen", "Xiaohan Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091591.t002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_most_common_5_A_besseyi_pathways_consistent_with_C_elegans_/964720", "title"=>"The most common 5 <i>A. besseyi</i> pathways consistent with <i>C. elegans</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-17 03:54:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1423740"], "description"=>"<p>Carbohydrate-active enzymes identified in <i>A. besseyi</i>.</p>", "links"=>[], "tags"=>["agriculture", "Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "microbiology", "Parasitology", "Parasite physiology", "Plant science", "Plant pathology", "Plant pests", "Zoology", "Nematology", "Infectious diseases", "Parasitic diseases", "enzymes"], "article_id"=>964718, "categories"=>["Biological Sciences"], "users"=>["Feng Wang", "Danlei Li", "Zhiying Wang", "Airong Dong", "Lihong Liu", "Buyong Wang", "Qiaoli Chen", "Xiaohan Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091591.t003", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Carbohydrate_active_enzymes_identified_in_A_besseyi_/964718", "title"=>"Carbohydrate-active enzymes identified in <i>A. besseyi</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-17 03:54:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1423719"], "description"=>"<p>The ten most common NR hierarchies identified in the <i>A. besseyi</i> sequences.</p>", "links"=>[], "tags"=>["agriculture", "Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "microbiology", "Parasitology", "Parasite physiology", "Plant science", "Plant pathology", "Plant pests", "Zoology", "Nematology", "Infectious diseases", "Parasitic diseases", "nr", "hierarchies"], "article_id"=>964697, "categories"=>["Biological Sciences"], "users"=>["Feng Wang", "Danlei Li", "Zhiying Wang", "Airong Dong", "Lihong Liu", "Buyong Wang", "Qiaoli Chen", "Xiaohan Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091591.g001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_ten_most_common_NR_hierarchies_identified_in_the_A_besseyi_sequences_/964697", "title"=>"The ten most common NR hierarchies identified in the <i>A. besseyi</i> sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-17 03:54:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1423748", "https://ndownloader.figshare.com/files/1423749"], "description"=>"<div><p>Background</p><p>The rice white tip nematode <i>Aphelenchoides besseyi</i>, a devastating nematode whose genome has not been sequenced, is distributed widely throughout almost all the rice-growing regions of the world. The aims of the present study were to define the transcriptome of <i>A. besseyi</i> and to identify parasite-related, mortality-related or host resistance-overcoming genes in this nematode.</p><p>Methodology and Principal Findings</p><p>Using Solexa/Illumina sequencing, we profiled the transcriptome of mixed-stage populations of <i>A. besseyi</i>. A total of 51,270 transcripts without gaps were produced based on high-quality clean reads. Of all the <i>A. besseyi</i> transcripts, 9,132 KEGG Orthology assignments were annotated. Carbohydrate-active enzymes of glycoside hydrolases (GHs), glycosyltransferases (GTs), carbohydrate esterases (CEs) and carbohydrate-binding modules (CBMs) were identified. The presence of the <i>A. besseyi</i> GH45 cellulase gene was verified by <i>in situ</i> hybridization. Given that 13 unique <i>A. besseyi</i> potential effector genes were identified from 41 candidate effector homologs, further studies of these homologs are merited. Finally, comparative analyses were conducted between <i>A. besseyi</i> contigs and <i>Caenorhabditis elegans</i> genes to look for orthologs of RNAi phenotypes, neuropeptides and peptidases.</p><p>Conclusions and Significance</p><p>The present results provide comprehensive insight into the genetic makeup of <i>A. besseyi</i>. Many of this species' genes are parasite related, nematode mortality-related or necessary to overcome host resistance. The generated transcriptome dataset of <i>A. besseyi</i> reported here lays the foundation for further studies of the molecular mechanisms related to parasitism and facilitates the development of new control strategies for this species.</p></div>", "links"=>[], "tags"=>["agriculture", "Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "microbiology", "Parasitology", "Parasite physiology", "Plant science", "Plant pathology", "Plant pests", "Zoology", "Nematology", "Infectious diseases", "Parasitic diseases", "transcriptomic"], "article_id"=>964726, "categories"=>["Biological Sciences"], "users"=>["Feng Wang", "Danlei Li", "Zhiying Wang", "Airong Dong", "Lihong Liu", "Buyong Wang", "Qiaoli Chen", "Xiaohan Liu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0091591.s001", "https://dx.doi.org/10.1371/journal.pone.0091591.s002"], "stats"=>{"downloads"=>13, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Transcriptomic_Analysis_of_the_Rice_White_Tip_Nematode_Aphelenchoides_besseyi_Nematoda_Aphelenchoididae_/964726", "title"=>"Transcriptomic Analysis of the Rice White Tip Nematode, <i>Aphelenchoides besseyi</i> (Nematoda: Aphelenchoididae)", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-03-17 03:54:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1423745"], "description"=>"<p>Neuropeptide genes in <i>A. besseyi</i>.</p>", "links"=>[], "tags"=>["agriculture", "Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "microbiology", "Parasitology", "Parasite physiology", "Plant science", "Plant pathology", "Plant pests", "Zoology", "Nematology", "Infectious diseases", "Parasitic diseases", "genes"], "article_id"=>964723, "categories"=>["Biological Sciences"], "users"=>["Feng Wang", "Danlei Li", "Zhiying Wang", "Airong Dong", "Lihong Liu", "Buyong Wang", "Qiaoli Chen", "Xiaohan Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091591.t006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Neuropeptide_genes_in_A_besseyi_/964723", "title"=>"Neuropeptide genes in <i>A. besseyi</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-17 03:54:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1423744"], "description"=>"<p>Summary of peptidases in <i>A. besseyi</i>.</p>", "links"=>[], "tags"=>["agriculture", "Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "microbiology", "Parasitology", "Parasite physiology", "Plant science", "Plant pathology", "Plant pests", "Zoology", "Nematology", "Infectious diseases", "Parasitic diseases", "peptidases"], "article_id"=>964722, "categories"=>["Biological Sciences"], "users"=>["Feng Wang", "Danlei Li", "Zhiying Wang", "Airong Dong", "Lihong Liu", "Buyong Wang", "Qiaoli Chen", "Xiaohan Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091591.t007", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_peptidases_in_A_besseyi_/964722", "title"=>"Summary of peptidases in <i>A. besseyi</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-03-17 03:54:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1423725"], "description"=>"<p>The most abundant Gene Ontology terms present in the dataset for the cellular component, molecular function and biological process categories.</p>", "links"=>[], "tags"=>["agriculture", "Computational biology", "genome analysis", "Transcriptome analysis", "genetics", "genomics", "microbiology", "Parasitology", "Parasite physiology", "Plant science", "Plant pathology", "Plant pests", "Zoology", "Nematology", "Infectious diseases", "Parasitic diseases", "abundant", "ontology", "dataset", "cellular", "molecular"], "article_id"=>964703, "categories"=>["Biological Sciences"], "users"=>["Feng Wang", "Danlei Li", "Zhiying Wang", "Airong Dong", "Lihong Liu", "Buyong Wang", "Qiaoli Chen", "Xiaohan Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0091591.g002", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_most_abundant_Gene_Ontology_terms_present_in_the_dataset_for_the_cellular_component_molecular_function_and_biological_process_categories_/964703", "title"=>"The most abundant Gene Ontology terms present in the dataset for the cellular component, molecular function and biological process categories.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-03-17 03:54:45"}

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Relative Metric

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