Abstract:
BACKGROUND:Chlamydomonas reinhardtii is the model organism that serves as a reference for studies in algal genomics and physiology. It is of special interest in the study of the evolution of regulatory pathways from algae to higher plants. Additionally, it has recently gained attention as a potential source for bio-fuel and bio-hydrogen production. The genome of Chlamydomonas is available, facilitating the analysis of its transcriptome by RNA-seq data. This has produced a massive amount of data that remains fragmented making necessary the application of integrative approaches based on molecular systems biology. RESULTS:We constructed a gene co-expression network based on RNA-seq data and developed a web-based tool, ChlamyNET, for the exploration of the Chlamydomonas transcriptome. ChlamyNET exhibits a scale-free and small world topology. Applying clustering techniques, we identified nine gene clusters that capture the structure of the transcriptome under the analyzed conditions. One of the most central clusters was shown to be involved in carbon/nitrogen metabolism and signalling, whereas one of the most peripheral clusters was involved in DNA replication and cell cycle regulation. The transcription factors and regulators in the Chlamydomonas genome have been identified in ChlamyNET. The biological processes potentially regulated by them as well as their putative transcription factor binding sites were determined. The putative light regulated transcription factors and regulators in the Chlamydomonas genome were analyzed in order to provide a case study on the use of ChlamyNET. Finally, we used an independent data set to cross-validate the predictive power of ChlamyNET. CONCLUSIONS:The topological properties of ChlamyNET suggest that the Chlamydomonas transcriptome posseses important characteristics related to error tolerance, vulnerability and information propagation. The central part of ChlamyNET constitutes the core of the transcriptome where most authoritative hub genes are located interconnecting key biological processes such as light response with carbon and nitrogen metabolism. Our study reveals that key elements in the regulation of carbon and nitrogen metabolism, light response and cell cycle identified in higher plants were already established in Chlamydomonas. These conserved elements are not only limited to transcription factors, regulators and their targets, but also include the cis-regulatory elements recognized by them.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Romero-Campero FJ,Perez-Hurtado I,Lucas-Reina E,Romero JM,Valverde Fdoi
10.1186/s12864-016-2564-ysubject
Has Abstractpub_date
2016-03-12 00:00:00pages
227issn
1471-2164pii
10.1186/s12864-016-2564-yjournal_volume
17pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Adaptations to a new environment, such as a polluted one, often involve large modifications of the existing phenotypes. Changes in gene expression and regulation during critical developmental stages may explain these phenotypic changes. Embryos from a population of the teleost fish, Fundulus heteroclitus, in...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-779
更新日期:2013-11-11 00:00:00
abstract:BACKGROUND:The desiccation-tolerant moss Bryum argenteum is an important component of the Biological Soil Crusts (BSCs) found in the Gurbantunggut desert. Desiccation tolerance is defined as the ability to revive from the air dried state. To elucidate the molecular mechanisms related to desiccation tolerance, we employ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1633-y
更新日期:2015-05-28 00:00:00
abstract:BACKGROUND:Environmental heterogeneity continuously produces a selective pressure that results in genomic variation among organisms; understanding this relationship remains a challenge in evolutionary biology. Here, we evaluated the degree of genome-environmental association of seven stonefly species across a wide geog...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5453-3
更新日期:2019-01-24 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs), short approximately 21-nucleotide RNA molecules, play an important role in post-transcriptional regulation of gene expression. The number of known miRNA hairpins registered in the miRBase database is rapidly increasing, but recent reports suggest that many miRNAs with restricted temporal ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-204
更新日期:2009-04-30 00:00:00
abstract:BACKGROUND:Ancestry informative markers (AIMs) are a type of genetic marker that is informative for tracing the ancestral ethnicity of individuals. Application of AIMs has gained substantial attention in population genetics, forensic sciences, and medical genetics. Single nucleotide polymorphisms (SNPs), the materials ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-346
更新日期:2012-07-28 00:00:00
abstract:BACKGROUND:The sequence of the pathogen Mycobacterium tuberculosis (Mtb) strain H37Rv has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other Mtb strains and closely related bacteria present an opportunity to apply the power of comparative genomics to...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-120
更新日期:2012-03-28 00:00:00
abstract:BACKGROUND:The Spemann/Mangold organizer is a transient tissue critical for patterning the gastrula stage vertebrate embryo and formation of the three germ layers. Despite its important role during development, there are still relatively few genes with specific expression in the organizer and its derivatives. Foxa2 is ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-511
更新日期:2008-10-30 00:00:00
abstract:BACKGROUND:Fusarium graminearum virus 1 strain-DK21 (FgV1-DK21) is a mycovirus that confers hypovirulence to F. graminearum, which is the primary phytopathogenic fungus that causes Fusarium head blight (FHB) disease in many cereals. Understanding the interaction between mycoviruses and plant pathogenic fungi is necessa...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-173
更新日期:2012-05-06 00:00:00
abstract:BACKGROUND:Parkinson's disease (PD) is a chronic progressive neurodegenerative disorder that is clinically defined in terms of motor symptoms. These are preceded by prodromal non-motor manifestations that prove the systemic nature of the disease. Identifying genes and pathways altered in living patients provide new inf...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2058-3
更新日期:2015-10-28 00:00:00
abstract:BACKGROUND:Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups and an allotetraploid genomic group, AD. The mitochondrial genomes supply new information to understand both the evolution process and the mechanism of cytoplasmic male sterility. Based on previously released mitochondrial genomes ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4282-5
更新日期:2017-11-13 00:00:00
abstract:BACKGROUND:Pectobacterium spp. are necrotrophic bacterial plant pathogens of the family Pectobacteriaceae, responsible for a wide spectrum of diseases of important crops and ornamental plants including soft rot, blackleg, and stem wilt. P. carotovorum is a genetically heterogeneous species consisting of three valid sub...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5269-6
更新日期:2018-12-07 00:00:00
abstract:BACKGROUND:The steroid hormone environment in healthy horses seems to have a significant impact on the efficiency of their uterine immune response. The objective of this study was to characterize the changes in gene expression in the equine endometrium in response to the introduction of bacterial pathogens and the infl...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2139-3
更新日期:2015-11-14 00:00:00
abstract:BACKGROUND:Identification of acute or recent hepatitis C virus (HCV) infections is important for detecting outbreaks and devising timely public health interventions for interruption of transmission. Epidemiological investigations and chemistry-based laboratory tests are 2 main approaches that are available for identifi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4269-2
更新日期:2017-12-06 00:00:00
abstract:BACKGROUND:The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also unc...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6123-1
更新日期:2019-10-23 00:00:00
abstract:BACKGROUND:Progress in the fields of protein separation and identification technologies has accelerated research into biofluids proteomics for protein biomarker discovery. Urine has become an ideal and rich source of biomarkers in clinical proteomics. Here we performed a proteomic analysis of urine samples from pregnan...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-777
更新日期:2013-11-11 00:00:00
abstract:BACKGROUND:The tuberous root of sweet potato is an important agricultural and biological organ. There are not sufficient transcriptomic and genomic data in public databases for understanding of the molecular mechanism underlying the tuberous root formation and development. Thus, high throughput transcriptome sequencing...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-726
更新日期:2010-12-24 00:00:00
abstract:BACKGROUND:The phytoflagellated protozoan, Euglena gracilis, has been proposed as an attractive feedstock for the accumulation of valuable compounds such as β-1,3-glucan, also known as paramylon, and wax esters. The production of wax esters proceeds under anaerobic conditions, designated as wax ester fermentation. In s...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2540-6
更新日期:2016-03-03 00:00:00
abstract:BACKGROUND:Obtaining reliable and reproducible two-color microarray gene expression data is critically important for understanding the biological significance of perturbations made on a cellular system. Microarray design, RNA preparation and labeling, hybridization conditions and data acquisition and analysis are varia...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-5-20
更新日期:2004-03-09 00:00:00
abstract:BACKGROUND:Molecular mechanisms underlying coral larval competence, the ability of larvae to respond to settlement cues, determine their dispersal potential and are potential targets of natural selection. Here, we profiled competence, fluorescence and genome-wide gene expression in embryos and larvae of the reef-buildi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4392-0
更新日期:2018-01-04 00:00:00
abstract:BACKGROUND:DNA microarray technology has had a great impact on muscle research and microarray gene expression data has been widely used to identify gene signatures characteristic of the studied conditions. With the rapid accumulation of muscle microarray data, it is of great interest to understand how to compare and co...
journal_title:BMC genomics
pub_type: 杂志文章,meta分析
doi:10.1186/1471-2164-12-113
更新日期:2011-02-16 00:00:00
abstract:BACKGROUND:Clostridium sticklandii belongs to a cluster of non-pathogenic proteolytic clostridia which utilize amino acids as carbon and energy sources. Isolated by T.C. Stadtman in 1954, it has been generally regarded as a "gold mine" for novel biochemical reactions and is used as a model organism for studying metabol...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-555
更新日期:2010-10-11 00:00:00
abstract:BACKGROUND:Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and thre...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6619-8
更新日期:2020-03-04 00:00:00
abstract:BACKGROUND:Acinetobacter baumannii is a major health problem. The most common infection caused by A. baumannii is hospital acquired pneumonia, and the associated mortality rate is approximately 50%. Neither in vivo nor ex vivo expression profiling has been performed at the proteomic or transcriptomic level for pneumoni...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1608-z
更新日期:2015-05-30 00:00:00
abstract:BACKGROUND:Caixin and Zicaitai (Brassica rapa) belong to Southern and Central China respectively. Zicaitai contains high amount of anthocyanin in leaf and stalk resulting to the purple color. Stalk is the major edible part and stalk color is an economically important trait for the two vegetables. The aim of this study ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5693-2
更新日期:2019-05-07 00:00:00
abstract:BACKGROUND:Biocontrol of bacterial pathogens by bacteriophages (phages) represents a promising strategy. Vibrio alginolyticus, a gram-negative bacterium, is a notorious pathogen responsible for the loss of economically important farmed marine animals. To date, few V. alginolyticus phages have been successfully isolated...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5131-x
更新日期:2018-10-11 00:00:00
abstract:BACKGROUND:Adenosine to inosine (A-to-I) RNA-editing is an essential post-transcriptional mechanism that occurs in numerous sites in the human transcriptome, mainly within Alu repeats. It has been shown to have consistent levels of editing across individuals in a few targets in the human brain and altered in several hu...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-608
更新日期:2010-10-28 00:00:00
abstract:BACKGROUND:Respiratory syncytial virus (RSV) is an important cause of lower respiratory tract infection in young children. The degree of disease severity is determined by the host response to infection. Lung macrophages play an important early role in the host response to infection and we have used a systems-based appr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-190
更新日期:2013-03-18 00:00:00
abstract:BACKGROUND:The Pregnancy-associated glycoproteins (PAGs) belong to a large family of aspartic peptidases expressed exclusively in the placenta of species in the Artiodactyla order. In cattle, the PAG gene family is comprised of at least 22 transcribed genes, as well as some variants. Phylogenetic analyses have shown th...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-185
更新日期:2009-04-24 00:00:00
abstract:BACKGROUND:Cytoplasmic male sterility (CMS) is not only important for exploiting heterosis in crop plants, but also as a model for investigating nuclear-cytoplasmic interaction. CMS may be caused by mutations, rearrangement or recombination in the mitochondrial genome. Understanding the mitochondrial genome is often th...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-322
更新日期:2014-04-30 00:00:00
abstract:BACKGROUND:Rhesus macaques serve a critical role in the study of human biomedical research. While both Indian and Chinese rhesus macaques are commonly used, genetic differences between these two subspecies affect aspects of their behavior and physiology, including response to simian immunodeficiency virus (SIV) infecti...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-43
更新日期:2007-02-07 00:00:00