Gene co-expression networks provide an important tool for systems biology studies. Using microarray data from the Array Express database, we constructed an Arabidopsis gene co-expression network, termed At GGM2014, ba...Gene co-expression networks provide an important tool for systems biology studies. Using microarray data from the Array Express database, we constructed an Arabidopsis gene co-expression network, termed At GGM2014, based on the graphical Gaussian model, which contains 102,644 co-expression gene pairs among 18,068 genes. The network was grouped into 622 gene co-expression modules. These modules function in diverse house-keeping, cell cycle, development, hormone response, metabolism, and stress response pathways. We developed a tool to facilitate easy visualization of the expression patterns of these modules either in a tissue context or their regulation under different treatment conditions. The results indicate that at least six modules with tissue-specific expression pattern failed to record modular regulation under various stress conditions. This discrepancy could be best explained by the fact that experiments to study plant stress responses focused mainly on leaves and less on roots, and thus failed to recover specific regulation pattern in other tissues. Overall, the modular structures revealed by our network provide extensive information to generate testable hypotheses about diverse plant signaling pathways. At GGM2014 offers a constructive tool for plant systems biology studies.展开更多
Aims Harsh environmental conditions in alpine ecosystems shape vegetation structure into patches,where many different plant species cluster and grow together.Yet,which factors are important for the structure and dynam...Aims Harsh environmental conditions in alpine ecosystems shape vegetation structure into patches,where many different plant species cluster and grow together.Yet,which factors are important for the structure and dynamics of such plant–patch networks remains poorly understood.We aim to assess which and how environmental and biotic factors predict the assembly of plant–patch networks along a mountain range.Methods We examined the distribution of plant species in more than 5500 vegetation patches in 37 Mediterranean alpine grasslands distributed along a 500 m altitudinal gradient(National Park of Sierra Guadarrama,Spain).We established a plant–patch network for each grassland community and analyzed how nestedness and modularity vary with environmental(altitude,insolation and soil conditions)and biotic factors(number of species per plot,mean patch area and total pasture area).Important Findings Plant–patch networks showed consistent,non-random patterns characterized by a nested,but not modular,structure,which suggests that positive associations among co-occurring specialists promote their growth within patches as subsets of a pool with more generalist species.Both nestedness and modularity of plant–patch networks varied among grasslands.Specifically,nestedness decreased with increasing species per plot and increased with mean patch area,while it was independent of environmental variables;modularity increased with increasing pasture area and species per plot.The negative relationship between species per plot and nested patterns may be linked to the restricted number of species that can coexist within the same patch at a given size.Moreover,the positive relationship between patch size and nestedness indicates that the growth of rare plant species within vegetation patches occupied by more abundant species is facilitated in bigger rather than smaller patches.Furthermore,these results indicate that the nested assembly of vegetation patches may be independent of abiotic conditions.These findings suggest that large and unfragmented vegetation patches are fundamental for the maintenance of plant diversity in alpine grasslands.Looking at species distribution at fine spatial scales may shed new light on the biotic processes underlying plant network assembly and provide novel ways for conserving biodiversity.展开更多
This paper discusses a popular community definition in complex network research in terms of the conditions under which a community is minimal, that is, the community cannot be split into several smaller communities or...This paper discusses a popular community definition in complex network research in terms of the conditions under which a community is minimal, that is, the community cannot be split into several smaller communities or split and reorganized with other network elements into new communities. The result provides a base on which further optimization computation of the quantitative measure for community identification can be realized.展开更多
基金supported by US National Science Foundation grants DBI-0723722 and DBI-1042344 to SPDKUC Davis funds to SPDK
文摘Gene co-expression networks provide an important tool for systems biology studies. Using microarray data from the Array Express database, we constructed an Arabidopsis gene co-expression network, termed At GGM2014, based on the graphical Gaussian model, which contains 102,644 co-expression gene pairs among 18,068 genes. The network was grouped into 622 gene co-expression modules. These modules function in diverse house-keeping, cell cycle, development, hormone response, metabolism, and stress response pathways. We developed a tool to facilitate easy visualization of the expression patterns of these modules either in a tissue context or their regulation under different treatment conditions. The results indicate that at least six modules with tissue-specific expression pattern failed to record modular regulation under various stress conditions. This discrepancy could be best explained by the fact that experiments to study plant stress responses focused mainly on leaves and less on roots, and thus failed to recover specific regulation pattern in other tissues. Overall, the modular structures revealed by our network provide extensive information to generate testable hypotheses about diverse plant signaling pathways. At GGM2014 offers a constructive tool for plant systems biology studies.
基金supported by the Madrid Regional Government(grant REMEDINAL TE-CM-S2018/EMT-4338)the Ministry of Economy and Competitiveness of Spain,(grants ROOTs-CGL2015-66809-P-)and AdAptA-CGL2012-33528)partially by the Swiss National Science Foundation to GL(grants IZSEZ0_180195 and P2ZHP3_187938).
文摘Aims Harsh environmental conditions in alpine ecosystems shape vegetation structure into patches,where many different plant species cluster and grow together.Yet,which factors are important for the structure and dynamics of such plant–patch networks remains poorly understood.We aim to assess which and how environmental and biotic factors predict the assembly of plant–patch networks along a mountain range.Methods We examined the distribution of plant species in more than 5500 vegetation patches in 37 Mediterranean alpine grasslands distributed along a 500 m altitudinal gradient(National Park of Sierra Guadarrama,Spain).We established a plant–patch network for each grassland community and analyzed how nestedness and modularity vary with environmental(altitude,insolation and soil conditions)and biotic factors(number of species per plot,mean patch area and total pasture area).Important Findings Plant–patch networks showed consistent,non-random patterns characterized by a nested,but not modular,structure,which suggests that positive associations among co-occurring specialists promote their growth within patches as subsets of a pool with more generalist species.Both nestedness and modularity of plant–patch networks varied among grasslands.Specifically,nestedness decreased with increasing species per plot and increased with mean patch area,while it was independent of environmental variables;modularity increased with increasing pasture area and species per plot.The negative relationship between species per plot and nested patterns may be linked to the restricted number of species that can coexist within the same patch at a given size.Moreover,the positive relationship between patch size and nestedness indicates that the growth of rare plant species within vegetation patches occupied by more abundant species is facilitated in bigger rather than smaller patches.Furthermore,these results indicate that the nested assembly of vegetation patches may be independent of abiotic conditions.These findings suggest that large and unfragmented vegetation patches are fundamental for the maintenance of plant diversity in alpine grasslands.Looking at species distribution at fine spatial scales may shed new light on the biotic processes underlying plant network assembly and provide novel ways for conserving biodiversity.
基金The research is supported by the Ministry of Science and Technology of China under Grant No.2006CB503905Some authors are also supported by the National Natural Science Foundation of China under Grant Nos.10631070 and 10701080the JSPS(Japan Society for the Promotion of Science)-NSFC(National Natural Science Foundation of China) collaboration project under Grant No.10711140116
文摘This paper discusses a popular community definition in complex network research in terms of the conditions under which a community is minimal, that is, the community cannot be split into several smaller communities or split and reorganized with other network elements into new communities. The result provides a base on which further optimization computation of the quantitative measure for community identification can be realized.
