Functional enrichment analysis is pivotal for interpreting highthroughput omics data in life science.It is crucial for this type of tool to use the latest annotation databases for as many organisms as possible.To meet...Functional enrichment analysis is pivotal for interpreting highthroughput omics data in life science.It is crucial for this type of tool to use the latest annotation databases for as many organisms as possible.To meet these requirements,we present here an updated version of our popular Bioconductor package,clusterProfiler 4.0.This package has been enhanced considerably compared with its original version published 9 years ago.The new version provides a universal interface for functional enrichment analysis in thousands of organisms based on internally supported ontologies and pathways as well as annotation data provided by users or derived from online databases.It also extends the dplyr and ggplot2 packages to offer tidy interfaces for data operation and visualization.Other new features include gene set enrichment analysis and comparison of enrichment results from multiple gene lists.We anticipate that clusterProfiler 4.0 will be applied to a wide range of scenarios across diverse organisms.展开更多
Size distributions of 29 elements in aerosols collected at urban,rural and curbside sites in Beijing were studied.High levels of Mn,Ni,As,Cd and Pb indicate the pollution of toxic heavy metals cannot be neglected in B...Size distributions of 29 elements in aerosols collected at urban,rural and curbside sites in Beijing were studied.High levels of Mn,Ni,As,Cd and Pb indicate the pollution of toxic heavy metals cannot be neglected in Beijing.Principal component analysis （PCA） indicates 4 sources of combustion emission,crust related sources,traffic related sources and volatile species from coal combustion.The elements can be roughly divided into 3 groups by size distribution and enrichment factors method （EFs）.Group 1 elements are crust related and mainly found within coarse mode including Al,Mg,Ca,Sc,Ti,Fe,Sr,Zr and Ba;Group 2 elements are fossil fuel related and mostly concentrated in accumulation mode including S,As,Se,Ag,Cd,Tl and Pb;Group 3 elements are multi-source related and show multi-mode distribution including Be,Na,K,Cr,Mn,Co,Ni,Cu,Zn,Ga,Mo,Sn and Sb.The EFs of Be,S,Cr,Co,Ni,Cu,Ga,Se,Mo,Ag,Cd,Sb,Tl and Pb show higher values in winter than in summer indicating sources of coal combustion for heating in winter.The abundance of Cu and Sb in coarse mode is about 2–6 times higher at curbside site than at urban site indicating their traffic sources.Coal burning may be the major source of Pb in Beijing since the phase out of leaded gasoline,as the EFs of Pb are comparable at both urban and curbside sites,and about two times higher in winter than that in summer.展开更多
人类活动导致的大气和气候变化将极大地改变作物的生长环境,其中最大的一个变化就是大气二氧化碳(CO2)浓度的迅速上升:从工业革命前的平均270μmol/mol上升到目前的381μmol/mol,到2050年至少超过550μmol/mol。FACE(Free-air CO2 enric...人类活动导致的大气和气候变化将极大地改变作物的生长环境,其中最大的一个变化就是大气二氧化碳(CO2)浓度的迅速上升:从工业革命前的平均270μmol/mol上升到目前的381μmol/mol,到2050年至少超过550μmol/mol。FACE(Free-air CO2 enrichment,开放式空气中CO2浓度增高)试验是目前评估未来高浓度CO2对作物生长和产量实际影响的最佳方法。水稻无疑是人类最重要的食物来源,迄今为止人类利用FACE技术开展水稻响应和适应的研究已有10a(19982008年)的历史。以生长发育为主线,首次系统综述了10a水稻FACE试验在该领域的研究成果,总结了FACE情形下高浓度CO2(模拟本世纪中叶大气CO2浓度)对主要供试水稻品种(小区面积大于4m2)光合作用、生育进程、地上部生长、地下部生长、物质分配、籽粒灌浆、产量构成以及倒伏性状等影响的研究进展,比较了FACE与非FACE研究之间以及中国和日本FACE研究(世界上唯一的两个大型水稻FACE研究)之间的异同点。根据研究进展以及当前的技术水平,文章最后提出了该领域的3个优先课题:(1)FACE情形下杂交稻生产力响应高于预期的生物学机制;(2)FACE情形下CO2与主要栽培措施的互作效应;(3)FACE情形下CO2与主要空气污染物臭氧的互作效应。这些响应的机理性解析将有助于从根本上减少人类预测未来粮食安全的不确定性,进而更加有效地制订出应对全球变化的适应策略。展开更多
基金This work was supported by a startup fund from Southern Medical University.
文摘Functional enrichment analysis is pivotal for interpreting highthroughput omics data in life science.It is crucial for this type of tool to use the latest annotation databases for as many organisms as possible.To meet these requirements,we present here an updated version of our popular Bioconductor package,clusterProfiler 4.0.This package has been enhanced considerably compared with its original version published 9 years ago.The new version provides a universal interface for functional enrichment analysis in thousands of organisms based on internally supported ontologies and pathways as well as annotation data provided by users or derived from online databases.It also extends the dplyr and ggplot2 packages to offer tidy interfaces for data operation and visualization.Other new features include gene set enrichment analysis and comparison of enrichment results from multiple gene lists.We anticipate that clusterProfiler 4.0 will be applied to a wide range of scenarios across diverse organisms.
基金supported by the special fund of the State Key Joint Laboratory of Environment Simulation and Pollution Control (No. 11K03ESPCT)the National Department Public Benefit Research Foundation (Ministry of Environmental Protection of the People’s Republic of China) (No. 201009001,201109002)
文摘Size distributions of 29 elements in aerosols collected at urban,rural and curbside sites in Beijing were studied.High levels of Mn,Ni,As,Cd and Pb indicate the pollution of toxic heavy metals cannot be neglected in Beijing.Principal component analysis （PCA） indicates 4 sources of combustion emission,crust related sources,traffic related sources and volatile species from coal combustion.The elements can be roughly divided into 3 groups by size distribution and enrichment factors method （EFs）.Group 1 elements are crust related and mainly found within coarse mode including Al,Mg,Ca,Sc,Ti,Fe,Sr,Zr and Ba;Group 2 elements are fossil fuel related and mostly concentrated in accumulation mode including S,As,Se,Ag,Cd,Tl and Pb;Group 3 elements are multi-source related and show multi-mode distribution including Be,Na,K,Cr,Mn,Co,Ni,Cu,Zn,Ga,Mo,Sn and Sb.The EFs of Be,S,Cr,Co,Ni,Cu,Ga,Se,Mo,Ag,Cd,Sb,Tl and Pb show higher values in winter than in summer indicating sources of coal combustion for heating in winter.The abundance of Cu and Sb in coarse mode is about 2–6 times higher at curbside site than at urban site indicating their traffic sources.Coal burning may be the major source of Pb in Beijing since the phase out of leaded gasoline,as the EFs of Pb are comparable at both urban and curbside sites,and about two times higher in winter than that in summer.
文摘人类活动导致的大气和气候变化将极大地改变作物的生长环境,其中最大的一个变化就是大气二氧化碳(CO2)浓度的迅速上升:从工业革命前的平均270μmol/mol上升到目前的381μmol/mol,到2050年至少超过550μmol/mol。FACE(Free-air CO2 enrichment,开放式空气中CO2浓度增高)试验是目前评估未来高浓度CO2对作物生长和产量实际影响的最佳方法。水稻无疑是人类最重要的食物来源,迄今为止人类利用FACE技术开展水稻响应和适应的研究已有10a(19982008年)的历史。以生长发育为主线,首次系统综述了10a水稻FACE试验在该领域的研究成果,总结了FACE情形下高浓度CO2(模拟本世纪中叶大气CO2浓度)对主要供试水稻品种(小区面积大于4m2)光合作用、生育进程、地上部生长、地下部生长、物质分配、籽粒灌浆、产量构成以及倒伏性状等影响的研究进展,比较了FACE与非FACE研究之间以及中国和日本FACE研究(世界上唯一的两个大型水稻FACE研究)之间的异同点。根据研究进展以及当前的技术水平,文章最后提出了该领域的3个优先课题:(1)FACE情形下杂交稻生产力响应高于预期的生物学机制;(2)FACE情形下CO2与主要栽培措施的互作效应;(3)FACE情形下CO2与主要空气污染物臭氧的互作效应。这些响应的机理性解析将有助于从根本上减少人类预测未来粮食安全的不确定性,进而更加有效地制订出应对全球变化的适应策略。
