The Spatial Association of Gene Expression Evolves from Synchrony to Asynchrony and Stochasticity with Age
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{"title"=>"The spatial association of gene expression evolves from synchrony to asynchrony and stochasticity with age", "type"=>"journal", "authors"=>[{"first_name"=>"Qi", "last_name"=>"Wang", "scopus_author_id"=>"57199479350"}, {"first_name"=>"Jianhua", "last_name"=>"Huang", "scopus_author_id"=>"56505759800"}, {"first_name"=>"Xinmin", "last_name"=>"Zhang", "scopus_author_id"=>"23394243200"}, {"first_name"=>"Bin", "last_name"=>"Wu", "scopus_author_id"=>"56718894800"}, {"first_name"=>"Xiaoyu", "last_name"=>"Liu", "scopus_author_id"=>"55865420100"}, {"first_name"=>"Ziyin", "last_name"=>"Shen", "scopus_author_id"=>"7403324091"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"362489473", "doi"=>"10.1371/journal.pone.0024076", "sgr"=>"80052413197", "scopus"=>"2-s2.0-80052413197", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "pmid"=>"21912663"}, "id"=>"d4ee64a8-fb1f-3e8a-b3a6-4ee0e4fd5566", "abstract"=>"For multicellular organisms, different tissues coordinate to integrate physiological functions, although this systematically and gradually declines in the aging process. Therefore, an association exists between tissue coordination and aging, and investigating the evolution of tissue coordination with age is of interest. In the past decade, both common and heterogeneous aging processes among tissues were extensively investigated. The results on spatial association of gene changes that determine lifespan appear complex and paradoxical. To reconcile observed commonality and heterogeneity of gene changes among tissues and to address evolution feature of tissue coordination with age, we introduced a new analytical strategy to systematically analyze genome-wide spatio-temporal gene expression profiles. We first applied the approach to natural aging process in three species (Rat, Mouse and Drosophila) and then to anti-aging process in Mouse. The results demonstrated that temporal gene expression alteration in different tissues experiences a progressive association evolution from spatial synchrony to asynchrony and stochasticity with age. This implies that tissue coordination gradually declines with age. Male mice showed earlier spatial asynchrony in gene expression than females, suggesting that male animals are more prone to aging than females. The confirmed anti-aging interventions (resveratrol and caloric restriction) enhanced tissue coordination, indicating their underlying anti-aging mechanism on multiple tissue levels. Further, functional analysis suggested asynchronous DNA/protein damage accumulation as well as asynchronous repair, modification and degradation of DNA/protein in tissues possibly contributes to asynchronous and stochastic changes of tissue microenvironment. This increased risk for a variety of age-related diseases such as neurodegeneration and cancer that eventually accelerate organismal aging and death. Our study suggests a novel molecular event occurring in aging process of multicellular species that may represent an intrinsic molecular mechanism of aging.", "link"=>"http://www.mendeley.com/research/spatial-association-gene-expression-evolves-synchrony-asynchrony-stochasticity-age", "reader_count"=>26, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>9, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>3, "Student > Master"=>3, "Lecturer"=>3, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>9, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>3, "Student > Master"=>3, "Lecturer"=>3, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Engineering"=>2, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>14, "Medicine and Dentistry"=>3, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>14}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>4}}, "reader_count_by_country"=>{"Japan"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/372961", "https://ndownloader.figshare.com/files/372979", "https://ndownloader.figshare.com/files/372997", "https://ndownloader.figshare.com/files/373018", "https://ndownloader.figshare.com/files/373033", "https://ndownloader.figshare.com/files/373045", "https://ndownloader.figshare.com/files/373061"], "description"=>"<div><p>For multicellular organisms, different tissues coordinate to integrate physiological functions, although this systematically and gradually declines in the aging process. Therefore, an association exists between tissue coordination and aging, and investigating the evolution of tissue coordination with age is of interest. In the past decade, both common and heterogeneous aging processes among tissues were extensively investigated. The results on spatial association of gene changes that determine lifespan appear complex and paradoxical. To reconcile observed commonality and heterogeneity of gene changes among tissues and to address evolution feature of tissue coordination with age, we introduced a new analytical strategy to systematically analyze genome-wide spatio-temporal gene expression profiles. We first applied the approach to natural aging process in three species (Rat, Mouse and <em>Drosophila</em>) and then to anti-aging process in Mouse. The results demonstrated that temporal gene expression alteration in different tissues experiences a progressive association evolution from spatial synchrony to asynchrony and stochasticity with age. This implies that tissue coordination gradually declines with age. Male mice showed earlier spatial asynchrony in gene expression than females, suggesting that male animals are more prone to aging than females. The confirmed anti-aging interventions (resveratrol and caloric restriction) enhanced tissue coordination, indicating their underlying anti-aging mechanism on multiple tissue levels. Further, functional analysis suggested asynchronous DNA/protein damage accumulation as well as asynchronous repair, modification and degradation of DNA/protein in tissues possibly contributes to asynchronous and stochastic changes of tissue microenvironment. This increased risk for a variety of age-related diseases such as neurodegeneration and cancer that eventually accelerate organismal aging and death. Our study suggests a novel molecular event occurring in aging process of multicellular species that may represent an intrinsic molecular mechanism of aging.</p> </div>", "links"=>[], "tags"=>["spatial", "evolves", "synchrony", "asynchrony", "stochasticity"], "article_id"=>133662, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Qi Wang", "Jianhua Huang", "Xinmin Zhang", "Bin Wu", "Xiaoyu Liu", "Ziyin Shen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0024076.s001", "https://dx.doi.org/10.1371/journal.pone.0024076.s002", "https://dx.doi.org/10.1371/journal.pone.0024076.s003", "https://dx.doi.org/10.1371/journal.pone.0024076.s004", "https://dx.doi.org/10.1371/journal.pone.0024076.s005", "https://dx.doi.org/10.1371/journal.pone.0024076.s006", "https://dx.doi.org/10.1371/journal.pone.0024076.s007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Spatial_Association_of_Gene_Expression_Evolves_from_Synchrony_to_Asynchrony_and_Stochasticity_with_Age/133662", "title"=>"The Spatial Association of Gene Expression Evolves from Synchrony to Asynchrony and Stochasticity with Age", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-09-02 01:01:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/739110"], "description"=>"<p>The dynamic tissues association network of gene expression with age were illustrated respectively for (A) rat, p<0.001; (B) Drosophila melanogaster, p<0.005; (C) female mice, p<0.005; and (D) male mice, p<0.005. Red, gene set with increased expression at a certain age phase in a tissue; green, decreased expression. Node names incorporate tissue name,age phase, and expression direction. For example, the red node named A_10Mv4M_up (A) denotes an upregulated gene set from 4 to 10 months in adrenal gland (A). The connection between red (or green) nodes illustrates a significant number of genes synchronously increased (or decreased) in expression in the two connected tissues; red and green describe asynchronous behavior. For nodes not connected into networks, genes in the tissue lacked significant association with the others, reflecting a stochastic space relationship.</p>", "links"=>[], "tags"=>["spatial"], "article_id"=>409482, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Qi Wang", "Jianhua Huang", "Xinmin Zhang", "Bin Wu", "Xiaoyu Liu", "Ziyin Shen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0024076.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Temporal_evolution_of_spatial_association_of_gene_expression_during_natural_aging_/409482", "title"=>"Temporal evolution of spatial association of gene expression during natural aging.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-02 02:38:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/739179"], "description"=>"<p>The gene with expression alterations from 18 to 27 months in liver (L), muscle (M), adipose (A) and heart (H) from mice fed a standard diet with a low dose of resveratrol (SDLR) or a standard diet with high resveratrol (SDHR) showed significant restoration of spatial association compared to two reference groups of mice without anti-aging interventions fed a standard diet (SD) ad libitum or a high-calorie diet (HC) ad libitum, losing spatial association at 27 months. Similar restoration occurred in calorie-restricted mouse groups subjected to every-other-day feeding (EOD), every-other-day feeding with low resveratrol (EODLR), or every-other-day feeding with high resveratrol (EODHR).</p>", "links"=>[], "tags"=>["spatial", "aging", "anti-aging", "caloric", "resveratrol"], "article_id"=>409550, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Qi Wang", "Jianhua Huang", "Xinmin Zhang", "Bin Wu", "Xiaoyu Liu", "Ziyin Shen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0024076.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reversion_of_spatial_association_of_gene_expression_in_aging_tissue_under_the_anti_aging_intervention_of_caloric_restriction_or_resveratrol_treatment_p_lt_0_01_/409550", "title"=>"Reversion of spatial association of gene expression in aging tissue under the anti-aging intervention of caloric restriction or resveratrol treatment (p<0.01).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-02 02:39:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/739242"], "description"=>"<p>The overall network of gene association through time and space were depicted for natural aging process of (A) male rats (p<0.0001), and (B) female mice (p<0.0005), showing age-related genes in particular age phases of tissues significantly occurring in another phase of the same or different tissues.</p>", "links"=>[], "tags"=>["genes", "reveals", "commonality"], "article_id"=>409611, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Qi Wang", "Jianhua Huang", "Xinmin Zhang", "Bin Wu", "Xiaoyu Liu", "Ziyin Shen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0024076.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Four_dimensional_genes_association_reveals_commonality_and_diversity_in_time_and_space_/409611", "title"=>"Four-dimensional genes association reveals commonality and diversity in time and space.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-02 02:40:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/739317"], "description"=>"<p>Note: refer to <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0024076#pone-0024076-t001\" target=\"_blank\">table 1</a>.</p>", "links"=>[], "tags"=>["genes", "synchronous", "occurring", "anti-aging", "processes", "treated", "dietary", "resveratrol"], "article_id"=>409682, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Qi Wang", "Jianhua Huang", "Xinmin Zhang", "Bin Wu", "Xiaoyu Liu", "Ziyin Shen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0024076.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enriched_functional_terms_for_genes_with_synchronous_expression_commonly_occurring_in_mouse_anti_aging_processes_treated_by_dietary_restriction_EOD_and_resveratrol_intervention_SDLR_SDHR_/409682", "title"=>"Enriched functional terms for genes with synchronous expression commonly occurring in mouse anti-aging processes treated by dietary restriction (EOD) and resveratrol intervention (SDLR, SDHR).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-09-02 02:41:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/739357"], "description"=>"<p>Note: ES (count) here designates Ease Score and gene count of the term in DAVID system; ‘NA’ means the term is not significant annotation for this genes set; GO_BP designates the Gene Ontology Biological Process annotations; SP designates the set of keywords annotations drawn from the Swiss-Prot and Protein Information Resource databases; BioCarta and KEGG respectively denotes gene pathway annotations from the KEGG and BioCarta database.</p>", "links"=>[], "tags"=>["genes", "synchronous", "asynchronous", "occurring", "aging"], "article_id"=>409725, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Qi Wang", "Jianhua Huang", "Xinmin Zhang", "Bin Wu", "Xiaoyu Liu", "Ziyin Shen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0024076.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enriched_functional_terms_for_genes_with_synchronous_and_asynchronous_expression_commonly_occurring_in_Rat_and_Mouse_natural_aging_process_/409725", "title"=>"Enriched functional terms for genes with synchronous and asynchronous expression commonly occurring in Rat and Mouse natural aging process.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-09-02 02:42:05"}

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Relative Metric

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