Statistical Analysis of the Processes Controlling Choline and Ethanolamine Glycerophospholipid Molecular Species Composition
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{"title"=>"Statistical analysis of the processes controlling choline and ethanolamine glycerophospholipid molecular species composition", "type"=>"journal", "authors"=>[{"first_name"=>"Kourosh", "last_name"=>"Zarringhalam", "scopus_author_id"=>"23669720300"}, {"first_name"=>"Lu", "last_name"=>"Zhang", "scopus_author_id"=>"54391955700"}, {"first_name"=>"Michael A.", "last_name"=>"Kiebish", "scopus_author_id"=>"8935383200"}, {"first_name"=>"Kui", "last_name"=>"Yang", "scopus_author_id"=>"7404291455"}, {"first_name"=>"Xianlin", "last_name"=>"Han", "scopus_author_id"=>"7402401137"}, {"first_name"=>"Richard W.", "last_name"=>"Gross", "scopus_author_id"=>"7403106500"}, {"first_name"=>"Jeffrey", "last_name"=>"Chuang", "scopus_author_id"=>"7201692555"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"364882949", "sgr"=>"84861465241", "pmid"=>"22662143", "scopus"=>"2-s2.0-84861465241", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "doi"=>"10.1371/journal.pone.0037293", "issn"=>"19326203"}, "id"=>"723c77e4-b48f-3b07-b273-5693269410b9", "abstract"=>"The regulation and maintenance of the cellular lipidome through biosynthetic, remodeling, and catabolic mechanisms are critical for biological homeostasis during development, health and disease. These complex mechanisms control the architectures of lipid molecular species, which have diverse yet highly regulated fatty acid chains at both the sn1 and sn2 positions. Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) serve as the predominant biophysical scaffolds in membranes, acting as reservoirs for potent lipid signals and regulating numerous enzymatic processes. Here we report the first rigorous computational dissection of the mechanisms influencing PC and PE molecular architectures from high-throughput shotgun lipidomic data. Using novel statistical approaches, we have analyzed multidimensional mass spectrometry-based shotgun lipidomic data from developmental mouse heart and mature mouse heart, lung, brain, and liver tissues. We show that in PC and PE, sn1 and sn2 positions are largely independent, though for low abundance species regulatory processes may interact with both the sn1 and sn2 chain simultaneously, leading to cooperative effects. Chains with similar biochemical properties appear to be remodeled similarly. We also see that sn2 positions are more regulated than sn1, and that PC exhibits stronger cooperative effects than PE. A key aspect of our work is a novel statistically rigorous approach to determine cooperativity based on a modified Fisher's exact test using Markov Chain Monte Carlo sampling. This computational approach provides a novel tool for developing mechanistic insight into lipidomic regulation.", "link"=>"http://www.mendeley.com/research/statistical-analysis-processes-controlling-choline-ethanolamine-glycerophospholipid-molecular-specie-1", "reader_count"=>20, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>10, "Student > Master"=>2, "Other"=>2, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>10, "Student > Master"=>2, "Other"=>2, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Mathematics"=>1, "Agricultural and Biological Sciences"=>10, "Neuroscience"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>10}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"United States"=>2, "United Kingdom"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/327090", "https://ndownloader.figshare.com/files/327266"], "description"=>"<div><p>The regulation and maintenance of the cellular lipidome through biosynthetic, remodeling, and catabolic mechanisms are critical for biological homeostasis during development, health and disease. These complex mechanisms control the architectures of lipid molecular species, which have diverse yet highly regulated fatty acid chains at both the sn1 and sn2 positions. Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) serve as the predominant biophysical scaffolds in membranes, acting as reservoirs for potent lipid signals and regulating numerous enzymatic processes. Here we report the first rigorous computational dissection of the mechanisms influencing PC and PE molecular architectures from high-throughput shotgun lipidomic data. Using novel statistical approaches, we have analyzed multidimensional mass spectrometry-based shotgun lipidomic data from developmental mouse heart and mature mouse heart, lung, brain, and liver tissues. We show that in PC and PE, sn1 and sn2 positions are largely independent, though for low abundance species regulatory processes may interact with both the sn1 and sn2 chain simultaneously, leading to cooperative effects. Chains with similar biochemical properties appear to be remodeled similarly. We also see that sn2 positions are more regulated than sn1, and that PC exhibits stronger cooperative effects than PE. A key aspect of our work is a novel statistically rigorous approach to determine cooperativity based on a modified Fisher's exact test using Markov Chain Monte Carlo sampling. This computational approach provides a novel tool for developing mechanistic insight into lipidomic regulation.</p> </div>", "links"=>[], "tags"=>["processes", "controlling", "choline", "ethanolamine", "glycerophospholipid", "molecular"], "article_id"=>124551, "categories"=>["Biological Sciences", "Biochemistry"], "users"=>["Kourosh Zarringhalam", "Lu Zhang", "Michael A. Kiebish", "Kui Yang", "Xianlin Han", "Richard W. Gross", "Jeffrey Chuang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0037293.s001", "https://dx.doi.org/10.1371/journal.pone.0037293.s002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Statistical_Analysis_of_the_Processes_Controlling_Choline_and_Ethanolamine_Glycerophospholipid_Molecular_Species_Composition/124551", "title"=>"Statistical Analysis of the Processes Controlling Choline and Ethanolamine Glycerophospholipid Molecular Species Composition", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-05-25 01:15:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/631872"], "description"=>"<p>For each of sn1 (A) and sn2 (B) positions, the dissimilarity between PC and PE marginal acyl distributions was measured by Jensen-Shannon Divergence (JSD). The highest similarity was observed for mature heart sn2 (), while the lowest similarity was observed for mature lung sn2 (). A trend of decreasing JSD was observed during heart development from day 7 to day 35, for both sn1 (, ) and sn2 (, ).</p>", "links"=>[], "tags"=>["divergence", "pc", "pe", "marginal", "acyl"], "article_id"=>302359, "categories"=>["Biological Sciences", "Biochemistry"], "users"=>["Kourosh Zarringhalam", "Lu Zhang", "Michael A. Kiebish", "Kui Yang", "Xianlin Han", "Richard W. Gross", "Jeffrey Chuang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0037293.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Jensen_Shannon_divergence_of_PC_and_PE_marginal_acyl_distributions_/302359", "title"=>"Jensen-Shannon divergence of PC and PE marginal acyl distributions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-25 00:39:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/631943"], "description"=>"<p>Trajectories of marginal probabilities of PC (red circles) and PE (blue triangles) for sn1 16∶0 (A), sn1 18∶0 (B), sn2 20∶4 (C), and sn2 22∶6 (D). PC and PE marginal probabilities closely follow each other in B, C, and D, suggesting these chain types are substrates of these two phospholipids' shared processes controlling species composition. The two curves in A are divergent, indicating that acyl chain regulation of sn1 16∶0 in PC and PE differs.</p>", "links"=>[], "tags"=>["pe", "acyl", "marginal", "probabilities"], "article_id"=>302429, "categories"=>["Biological Sciences", "Biochemistry"], "users"=>["Kourosh Zarringhalam", "Lu Zhang", "Michael A. Kiebish", "Kui Yang", "Xianlin Han", "Richard W. Gross", "Jeffrey Chuang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0037293.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PC_and_PE_acyl_chain_marginal_probabilities_during_heart_development_/302429", "title"=>"PC and PE acyl chain marginal probabilities during heart development.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-25 00:40:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/632020"], "description"=>"<p>For PC mature heart, a set of sn1 chain types (C) and a set of sn2 chain types 16∶0, 18∶1, 18∶2, 20∶3, 20∶4, 22∶5, 22∶6 (D) were each clustered. Within each of these clusters, conditional acyl distributions were highly homogeneous. It is interesting to note that at each of the sn1 and sn2 positions, the most abundant chains (panels A and B) tend to be clustered together (panels C and D), indicating similar conditional effects.</p>", "links"=>[], "tags"=>["distributions", "clustering", "acyl"], "article_id"=>302513, "categories"=>["Biological Sciences", "Biochemistry"], "users"=>["Kourosh Zarringhalam", "Lu Zhang", "Michael A. Kiebish", "Kui Yang", "Xianlin Han", "Richard W. Gross", "Jeffrey Chuang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0037293.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Conditional_distributions_and_clustering_of_acyl_chains_/302513", "title"=>"Conditional distributions and clustering of acyl chains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-25 00:41:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/632110"], "description"=>"<p>The sn2 conditional probabilities given sn1 chain types, closely follow each other. Shown are conditional probabilities for the four major sn2 chain types 18∶1 (A), 18∶2 (B), 20∶4 (C), and 22∶6 (D).</p>", "links"=>[], "tags"=>["acyl", "conditional", "probabilities"], "article_id"=>302599, "categories"=>["Biological Sciences", "Biochemistry"], "users"=>["Kourosh Zarringhalam", "Lu Zhang", "Michael A. Kiebish", "Kui Yang", "Xianlin Han", "Richard W. Gross", "Jeffrey Chuang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0037293.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PC_acyl_chain_conditional_probabilities_during_heart_development_/302599", "title"=>"PC acyl chain conditional probabilities during heart development.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-25 00:43:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/632180"], "description"=>"<p>Heatmaps of the joint distribution (<i>l</i>eft), the independent product distribution (<i>m</i>iddle), and their standardized residual (<i>r</i>ight) for mature heart PC (<i>t</i>op) and PE (<i>b</i>ottom). The joint and the product distributions are similar, suggesting that the acyl chains at the sn1 and the sn2 positions are largely independent.</p>", "links"=>[], "tags"=>["distributions", "mature"], "article_id"=>302673, "categories"=>["Biological Sciences", "Biochemistry"], "users"=>["Kourosh Zarringhalam", "Lu Zhang", "Michael A. Kiebish", "Kui Yang", "Xianlin Han", "Richard W. Gross", "Jeffrey Chuang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0037293.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_joint_and_product_distributions_for_mature_heart_/302673", "title"=>"Comparison of joint and product distributions for mature heart.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-25 00:44:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/632258"], "description"=>"<p>The overall deviation of the joint distribution from the expected independent distribution was scored using JSD for PC (A) and PE (B). The lowest JSD was observed in lung PE (), while the highest was observed in liver PE (). During heart development from day to day , a trend of decreasing JSD was observed in PC (, ), while PE displayed stable JSD during the time period, (, ).</p>", "links"=>[], "tags"=>["Computational biology", "Biochemistry"], "article_id"=>302749, "categories"=>["Biological Sciences", "Biochemistry"], "users"=>["Kourosh Zarringhalam", "Lu Zhang", "Michael A. Kiebish", "Kui Yang", "Xianlin Han", "Richard W. Gross", "Jeffrey Chuang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0037293.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Deviation_from_independence_as_a_function_of_tissue_type_/302749", "title"=>"Deviation from independence, as a function of tissue type.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-25 00:45:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/632313"], "description"=>"<p>For each of PC sn1, PE sn1, PC sn2, PE sn2, the variation of their marginal distributions across conditions was quantified using a multi-distribution JSD. The sample conditions in (A) are heart development time points: day 1, 7, 14, 17, 21, 28, 35. The sample conditions in (B) are four different anatomies: mature heart, brain, lung, and liver. We found that the sn2 position varies more than sn1, suggesting sn2 positions are more subject to regulation than sn1. This conclusion is consistent for each of PC and PE for both temporal variation and anatomical variation.</p>", "links"=>[], "tags"=>["sn1", "sn2", "acyl"], "article_id"=>302808, "categories"=>["Biological Sciences", "Biochemistry"], "users"=>["Kourosh Zarringhalam", "Lu Zhang", "Michael A. Kiebish", "Kui Yang", "Xianlin Han", "Richard W. Gross", "Jeffrey Chuang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0037293.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparing_complexity_of_sn1_and_sn2_acyl_chain_remodeling_/302808", "title"=>"Comparing complexity of sn1 and sn2 acyl chain remodeling.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-25 00:46:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/632379"], "description"=>"<p>Two-way Contingency table for mature heart PC sample. The structural zeros are denoted by . The variance effective sample size is .</p>", "links"=>[], "tags"=>["mature"], "article_id"=>302872, "categories"=>["Biological Sciences", "Biochemistry"], "users"=>["Kourosh Zarringhalam", "Lu Zhang", "Michael A. Kiebish", "Kui Yang", "Xianlin Han", "Richard W. Gross", "Jeffrey Chuang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0037293.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PC_mature_heart_/302872", "title"=>"PC mature heart.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-25 00:47:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/632407"], "description"=>"<p>For each sample, we identified subsets of sn1 and sn2 fatty acids (FA) for which the subsets passed the independence test (p0.05). The of Total Species indicates the total fraction of PC made up by species in the independent set for the tissue type.</p>", "links"=>[], "tags"=>["quasi-independence", "pc", "molecular"], "article_id"=>302897, "categories"=>["Biological Sciences", "Biochemistry"], "users"=>["Kourosh Zarringhalam", "Lu Zhang", "Michael A. Kiebish", "Kui Yang", "Xianlin Han", "Richard W. Gross", "Jeffrey Chuang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0037293.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Test_of_quasi_independence_on_PC_molecular_species_distributions_/302897", "title"=>"Test of quasi-independence on PC molecular species distributions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-25 00:48:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/632447"], "description"=>"<p>For each sample, we identified subsets of sn1 and sn2 fatty acids (FA) for which the subsets passed the independence test (p0.05). The of Total Species indicates the total fraction of PE made up by species in the independent set for the tissue type.</p>", "links"=>[], "tags"=>["quasi-independence", "pe", "molecular"], "article_id"=>302937, "categories"=>["Biological Sciences", "Biochemistry"], "users"=>["Kourosh Zarringhalam", "Lu Zhang", "Michael A. Kiebish", "Kui Yang", "Xianlin Han", "Richard W. Gross", "Jeffrey Chuang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0037293.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Test_of_quasi_independence_on_PE_molecular_species_distributions_/302937", "title"=>"Test of quasi-independence on PE molecular species distributions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-25 00:48:57"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"1"}
  • {"unique-ip"=>"8", "full-text"=>"4", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2015", "month"=>"11"}
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Relative Metric

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