Abstract:
BACKGROUND:The mosquito species Aedes aegypti is the primary vector of many arboviral diseases, including dengue and yellow fevers, that are responsible for a large worldwide health burden. The biological rhythms of mosquitoes regulate many of the physiological processes and behaviors that influence the transmission of these diseases. For insight into the molecular basis of biological rhythms, diel and circadian gene expression profiling has been carried out for many species. To bring these resources to Aedes aegypti researchers, we used microarray technology to carry out a genome wide assessment of gene expression during the 24 hour light/dark (LD) cycle and during constant darkness (DD). The purpose of this report is to describe the methods, the validation of the results, and the organization of this database resource. DESCRIPTION:The Aedes aegypti Circadian Database is a publicly accessible database that can be searched via a text-based query to visualize 44 hour temporal expression patterns of a given gene in Ae. aegypti heads under diel (observed under a 12 hour/12 hour LD cycle) and circadian (observed under DD) conditions. Profiles of gene expression under these conditions were assayed by Nimblegen 12-plex microarrays and rhythmicity was objectively assessed by the JTK_CYCLE algorithm. The output of the search is a graphical representation of the expression data along with computed period length, the time-of-day of gene expression peaks, and statistical determination for rhythmicity. CONCLUSION:Our results show that at least 7.9% of the gene set present in the Aedes aegypti head are rhythmic under LD conditions and 6.7% can be considered circadian, oscillating under constant dark conditions. We present these results in the Aedes aegypti Circadian Database through Bioclock, a public website hosted by the University of Notre Dame at http://www.nd.edu/~bioclock/. This website allows searchable browsing of this quantitative gene expression information. The visualization allows for gene-by-gene comparison of transcript expression under both diel and circadian conditions, and the results are presented graphically in a plot profile of gene expression. The Ae. aegypti Circadian Database provides a community resource for observing diel and circadian fluctuations in gene expression across the Ae. aegypti genome.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Leming MT,Rund SS,Behura SK,Duffield GE,O'Tousa JEdoi
10.1186/1471-2164-15-1128subject
Has Abstractpub_date
2014-12-17 00:00:00pages
1128issn
1471-2164pii
1471-2164-15-1128journal_volume
15pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Fusion genes are known to be drivers of many common cancers, so they are potential markers for diagnosis, prognosis or therapy response. The advent of paired-end RNA sequencing enhances our ability to discover fusion genes. While there are available methods, routine analyses of large number of samples are st...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5156-1
更新日期:2018-11-01 00:00:00
abstract:BACKGROUND:RNA amplification is necessary for profiling gene expression from small tissue samples. Previous studies have shown that the T7 based amplification techniques are reproducible but may distort the true abundance of targets. However, the consequences of such distortions on the ability to detect biological vari...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-252
更新日期:2006-10-09 00:00:00
abstract:BACKGROUND:Tubulin isotypes and expression patterns are highly regulated in diverse organisms. The genome sequence of the protozoan parasite Leishmania major contains three distinct beta-tubulin loci. To investigate the diversity of beta-tubulin genes, we have compared the published genome sequence to draft genome sequ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-137
更新日期:2006-06-06 00:00:00
abstract:BACKGROUND:The identification of genetic markers associated with complex traits that are expensive to record such as feed intake or feed efficiency would allow these traits to be included in selection programs. To identify large-effect QTL, we performed a series of genome-wide association studies and functional analyse...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1004
更新日期:2014-11-20 00:00:00
abstract:BACKGROUND:BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specif...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-379
更新日期:2011-07-27 00:00:00
abstract:BACKGROUND:Theileria parva is an intracellular parasite that causes a lymphoproliferative disease in cattle. It does so by inducing cancer-like phenotypes in the host cells it infects, although the molecular and regulatory mechanisms involved remain poorly understood. RNAseq data, and the resulting updated genome annot...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2444-5
更新日期:2016-02-20 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:The technological evolution of platforms for detecting genome-wide copy number imbalances has allowed the discovery of an unexpected amount of human sequence that is variable in copy number among individuals. This type of human variation can make an important contribution to human diversity and disease susce...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-573
更新日期:2008-11-28 00:00:00
abstract:BACKGROUND:Intramuscular fat (IMF) is one of the most important factors positively associated with meat quality. Triglycerides (TGs), as the main component of IMF, play an essential role in muscle lipid metabolism. This transcriptome analysis of pectoralis muscle tissue aimed to identify functional genes and biological...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6221-0
更新日期:2019-11-15 00:00:00
abstract:BACKGROUND:The obligate intracellular parasite Toxoplasma gondii establishes a life-long chronic infection within any warm-blooded host. After ingestion of an encysted parasite, T. gondii disseminates throughout the body as a rapidly replicating form during acute infection. Over time and after stimulation of the host i...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-806
更新日期:2014-09-20 00:00:00
abstract:BACKGROUND:Aging is affected by genetic and environmental factors, and cigarette smoking is strongly associated with accumulation of senescent cells. In this study, we wanted to identify genes that may potentially be beneficial for cell survival in response to cigarette smoke and thereby may contribute to development o...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5409-z
更新日期:2019-01-09 00:00:00
abstract:BACKGROUND:The identification of cell type-specific genes (markers) is an essential step for the deconvolution of the cellular fractions, primarily, from the gene expression data of a bulk sample. However, the genes with significant changes identified by pair-wise comparisons cannot indeed represent the specificity of ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06888-1
更新日期:2020-09-23 00:00:00
abstract:BACKGROUND:The recent advances in next generation sequencing technology have made the sequencing of RNA (i.e., RNA-Seq) an extemely popular approach for gene expression analysis. Identification of significant differential expression represents a crucial initial step in these analyses, on which most subsequent inference...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2848-2
更新日期:2016-08-04 00:00:00
abstract:BACKGROUND:Floral transition is a critical event in the life cycle of a flowering plant as it determines its reproductive success. Despite extensive studies of specific genes that regulate this process, the global changes in transcript expression profiles at the point when a vegetative meristem transitions into an infl...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1688-9
更新日期:2015-06-18 00:00:00
abstract:BACKGROUND:The increasing numbers of 3D compounds and protein complexes stored in databases contribute greatly to current advances in biotechnology, being employed in several pharmaceutical and industrial applications. However, screening and retrieving appropriate candidates as well as handling false positives presents...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-S4-S26
更新日期:2010-12-02 00:00:00
abstract:BACKGROUND:Hard ticks (family Ixodidae) are obligatory hematophagous ectoparasites of worldwide medical and veterinary importance. The haploid genomes of multiple species of ixodid ticks exceed 1 Gbp, prompting questions regarding gene, segmental and whole genome duplication in this phyletic group. The availability of ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2350-2
更新日期:2016-03-16 00:00:00
abstract:BACKGROUND:Hemolymph plays key roles in honey bee molecule transport, immune defense, and in monitoring the physiological condition. There is a lack of knowledge regarding how the proteome achieves these biological missions for both the western and eastern honey bees (Apis mellifera and Apis cerana). A time-resolved pr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-563
更新日期:2014-07-05 00:00:00
abstract:BACKGROUND:Plant nucleotide-binding site (NBS)-leucine-rich repeat (LRR) proteins encoded by resistance genes play an important role in the responses of plants to various pathogens, including viruses, bacteria, fungi, and nematodes. In this study, a comprehensive analysis of NBS-encoding genes within the whole cucumber...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-109
更新日期:2013-02-19 00:00:00
abstract:BACKGROUND:Mitochondrial genomes (mtDNA) of multicellular animals (Metazoa) with bilateral symmetry (Bilateria) are compact and usually carry 13 protein-coding genes for subunits of three respiratory complexes and ATP synthase. However, occasionally reported exceptions to this typical mtDNA organization prompted specul...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3626-5
更新日期:2017-03-31 00:00:00
abstract:BACKGROUND:Rainbow trout is a significant fish farming species under temperate climates. Female reproduction traits play an important role in the economy of breeding companies with the sale of fertilized eggs. The objectives of this study are threefold: to estimate the genetic parameters of female reproduction traits, ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06955-7
更新日期:2020-08-14 00:00:00
abstract:BACKGROUND:The increased multi-omics information on carefully phenotyped patients in studies of complex diseases requires novel methods for data integration. Unlike continuous intensity measurements from most omics data sets, phenome data contain clinical variables that are binary, ordinal and categorical. RESULTS:In ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2170-4
更新日期:2015-11-11 00:00:00
abstract:BACKGROUND:Little is known about the genome sequences of Euphausiacea (krill) although these crustaceans are abundant components of the pelagic ecosystems in all oceans and used for aquaculture and pharmaceutical industry. This study reports the results of an expressed sequence tag (EST) sequencing project from differe...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-45
更新日期:2008-01-28 00:00:00
abstract:BACKGROUND:Invasive aspergillosis is started after germination of Aspergillus fumigatus conidia that are inhaled by susceptible individuals. Fungal hyphae can grow in the lung through the epithelial tissue and disseminate hematogenously to invade into other organs. Low fungaemia indicates that fungal elements do not re...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1853-1
更新日期:2015-08-27 00:00:00
abstract:BACKGROUND:Arsenic is a carcinogen that is known to induce cell transformation and tumor formation. Although studies have been performed to examine the modulation of signaling molecules caused by arsenic exposure, the molecular mechanisms by which arsenic causes cancer are still unclear. We hypothesized that arsenic al...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-115
更新日期:2008-03-03 00:00:00
abstract:BACKGROUND:Gene expression profiling is a promising approach to better estimate patient prognosis; however, there are still unresolved problems, including little overlap among similarly developed gene sets and poor performance of a developed gene set in other datasets. RESULTS:We applied a gene sets approach to develo...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-177
更新日期:2008-04-16 00:00:00
abstract:BACKGROUND:Plants contain significant quantities of small RNAs (sRNAs) derived from various sRNA biogenesis pathways. Many of these sRNAs play regulatory roles in plants. Previous analysis revealed that numerous sRNAs in corn, rice and soybean seeds have high sequence similarity to animal genes. However, exogenous RNA ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-381
更新日期:2012-08-08 00:00:00
abstract:BACKGROUND:Following the association of Cronobacter spp. to several publicized fatal outbreaks in neonatal intensive care units of meningitis and necrotising enterocolitis, the World Health Organization (WHO) in 2004 requested the establishment of a molecular typing scheme to enable the international control of the org...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1121
更新日期:2014-12-16 00:00:00
abstract:BACKGROUND:Sugarcane (Saccharum L. plant) is an important crop for sugar and bio-energy production around the world. Among sugarcane diseases, smut caused by Sporisorium scitamineum is one of the major fungal diseases causing severe losses to the sugarcane industry. The use of PCR reference genes is essential to the no...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4854-z
更新日期:2018-06-19 00:00:00
abstract:BACKGROUND:Phlebotomine sand flies (Diptera, Nematocera) are important vectors of several pathogens, including Leishmania parasites, causing serious diseases of humans and dogs. Despite their importance as disease vectors, most aspects of sand fly biology remain unknown including the molecular basis of their reproducti...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5898-4
更新日期:2019-06-25 00:00:00
abstract:BACKGROUND:Next-generation sequencing is providing researchers with a relatively fast and affordable option for developing genomic resources for organisms that are not among the traditional genetic models. Here we present a de novo assembly of the guppy (Poecilia reticulata) transcriptome using 454 sequence reads, and ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-202
更新日期:2011-04-20 00:00:00