Abstract:
BACKGROUND:The completed sequence of the Anopheles gambiae genome has enabled genome-wide analyses of gene expression and regulation in this principal vector of human malaria. These investigations have created a demand for efficient methods of cataloguing and analyzing the large quantities of data that have been produced. The organization of genome-wide data into one unified database makes possible the efficient identification of spatial and temporal patterns of gene expression, and by pairing these findings with comparative algorithms, may offer a tool to gain insight into the molecular mechanisms that regulate these expression patterns. DESCRIPTION:We provide a publicly-accessible database and integrated data-mining tool, angaGEDUCI, that unifies 1) stage- and tissue-specific microarray analyses of gene expression in An. gambiae at different developmental stages and temporal separations following a bloodmeal, 2) functional gene annotation, 3) genomic sequence data, and 4) promoter sequence comparison algorithms. The database can be used to study genes expressed in particular stages, tissues, and patterns of interest, and to identify conserved promoter sequence motifs that may play a role in the regulation of such expression. The database is accessible from the address http://www.angaged.bio.uci.edu. CONCLUSION:By combining gene expression, function, and sequence data with integrated sequence comparison algorithms, angaGEDUCI streamlines spatial and temporal pattern-finding and produces a straightforward means of developing predictions and designing experiments to assess how gene expression may be controlled at the molecular level.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Dissanayake SN,Marinotti O,Ribeiro JM,James AAdoi
10.1186/1471-2164-7-116subject
Has Abstractpub_date
2006-05-17 00:00:00pages
116issn
1471-2164pii
1471-2164-7-116journal_volume
7pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Wild sugarcane Saccharum spontaneum plants vary in ploidy, which complicates the utilization of its germplasm in sugarcane breeding. Investigations on cold tolerance in relation to different ploidies in S. spontaneum may promote the exploitation of its germplasm and accelerate the improvement of sugarcane va...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06917-z
更新日期:2020-07-22 00:00:00
abstract:BACKGROUND:Pre-harvest sprouting frequently occurs in Triticum aestivum (wheat) and Hordeum vulgare (barley) at the end of the maturity period due to high rainfall, particularly in Asian monsoon areas. Seed dormancy is a major mechanism preventing pre-harvest sprouting in these crops. RESULTS:We identified orthologous...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3880-6
更新日期:2017-06-29 00:00:00
abstract:BACKGROUND:Pseudogenes are ubiquitous genetic elements that derive from functional genes after mutational inactivation. Characterization of pseudogenes is important to understand genome dynamics and evolution, and its significance increases when several genomes of related organisms can be compared. Among yeasts, only t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-260
更新日期:2010-04-22 00:00:00
abstract:BACKGROUND:Identifying the genotypes underlying human disease phenotypes is a fundamental step in human genetics and medicine. High-throughput genomic technologies provide thousands of genetic variants per individual. The causal genes of a specific phenotype are usually expected to be functionally close to each other. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-256
更新日期:2014-04-03 00:00:00
abstract:BACKGROUND:Salinity is an abiotic stress that negatively affects soybean [Glycine max (L.) Merr.] seed yield. Although a major gene for salt tolerance was identified and consistently mapped to chromosome (Chr.) 3 by linkage mapping studies, it does not fully explain genetic variability for tolerance in soybean germplas...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5662-9
更新日期:2019-04-25 00:00:00
abstract:BACKGROUND:In livestock species like the chicken, high throughput single nucleotide polymorphism (SNP) genotyping assays are increasingly being used for whole genome association studies and as a tool in breeding (referred to as genomic selection). To be of value in a wide variety of breeds and populations, the success ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-274
更新日期:2011-05-31 00:00:00
abstract:BACKGROUND:Secondary structure in the target is a property not usually considered in software applications for design of optimal custom oligonucleotide probes. It is frequently assumed that eliminating self-complementarity, or screening for secondary structure in the probe, is sufficient to avoid interference with hybr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-6-31
更新日期:2005-03-08 00:00:00
abstract:BACKGROUND:Gonadotropin releasing hormone (GnRH) is responsible for stimulation of gonadotropic hormone (GtH) in the hypothalamus-pituitary-gonadal axis (HPG). The regulatory mechanisms responsible for brain specificity make the promoter attractive for in silico analysis and reporter gene studies in zebrafish (Danio re...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-3-25
更新日期:2002-08-21 00:00:00
abstract:BACKGROUND:Bombyx mori was domesticated from the Chinese wild silkworm, Bombyx mandarina. Wild and domestic silkworms are good models in which to investigate genes related to silk protein synthesis that may be differentially expressed in silk glands, because their silk productions are very different. Here we used the m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1287-9
更新日期:2015-02-06 00:00:00
abstract:BACKGROUND:Despite the known importance of somatic cells for oocyte developmental competence acquisition, the overall mechanisms underlying the acquisition of full developmental competence are far from being understood, especially in non-mammalian species. The present work aimed at identifying key molecular signals fro...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-560
更新日期:2012-10-19 00:00:00
abstract:BACKGROUND:Many tools exist to predict structural variants (SVs), utilizing a variety of algorithms. However, they have largely been developed and tested on human germline or somatic (e.g. cancer) variation. It seems appropriate to exploit this wealth of technology available for humans also for other species. Objective...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1376-9
更新日期:2015-03-25 00:00:00
abstract:BACKGROUND:Horses have been strongly selected for speed, strength, and endurance-exercise traits since the onset of domestication. As a result, highly specialized horse breeds have developed with many modern horse breeds often representing closed populations with high phenotypic and genetic uniformity. However, a great...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5484-9
更新日期:2019-02-04 00:00:00
abstract:BACKGROUND:Microsatellites are extremely common in plant genomes, and in particular, they are significantly enriched in the 5' noncoding regions. Although some 5' noncoding microsatellites involved in gene regulation have been described, the general properties of microsatellites as regulatory elements are still unknown...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-323
更新日期:2006-12-25 00:00:00
abstract:BACKGROUND:Glandular trichomes produce a wide variety of commercially important secondary metabolites in many plant species. The most prominent anti-malarial drug artemisinin, a sesquiterpene lactone, is produced in glandular trichomes of Artemisia annua. However, only limited genomic information is currently available...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-465
更新日期:2009-10-09 00:00:00
abstract:BACKGROUND:Over the last decade, emerging research methods, such as comparative genomic analysis and phylogenetic study, have yielded new insights into genotypes and phenotypes of closely related bacterial strains. Several findings have revealed that genomic structural variations (SVs), including gene gain/loss, gene d...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1259-0
更新日期:2015-02-14 00:00:00
abstract:BACKGROUND:In the postgenome era, a prediction of response to treatment could lead to better dose selection for patients in radiotherapy. To identify a radiosensitive gene signature and elucidate related signaling pathways, four different microarray experiments were reanalyzed before radiotherapy. RESULTS:Radiosensiti...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-348
更新日期:2012-07-30 00:00:00
abstract:BACKGROUND:Genes, RNAs, and proteins play important roles during germline development. However, the functions of non-coding RNAs (ncRNAs) on germline development remain unclear in avian species. Recent high-throughput techniques have identified several classes of ncRNAs, including micro RNAs (miRNAs), small-interfering...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-757
更新日期:2014-09-04 00:00:00
abstract:BACKGROUND:In silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical,...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-356
更新日期:2014-05-12 00:00:00
abstract:BACKGROUND:Descriptive hierarchical Poisson models and population-genetic coalescent mixture models are used to describe the observed variation in single-nucleotide polymorphism (SNP) density from samples of size two across the human genome. RESULTS:Using empirical estimates of recombination rate across the human geno...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-146
更新日期:2007-06-06 00:00:00
abstract:BACKGROUND:Rapeseed (Brassica napus) is an important oil seed crop in the Brassicaceae family. Chemical induced male sterility (CIMS) is one of the widely used method to produce the hybrids in B. napus. Identification of the key genes and pathways that involved in CIMS were important to understand the underlying molecu...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5203-y
更新日期:2018-11-07 00:00:00
abstract:BACKGROUND:Rare genetic variation in the human population is a major source of pathophysiological variability and has been implicated in a host of complex phenotypes and diseases. Finding disease-related genes harboring disparate functional rare variants requires sequencing of many individuals across many genomic regio...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-683
更新日期:2012-12-06 00:00:00
abstract:BACKGROUND:Lipoxygenases (LOXs), a type of non-haem iron-containing dioxygenase, are ubiquitous enzymes in plants and participate in the formation of fruit aroma which is a very important aspect of fruit quality. Amongst the various aroma volatiles, saturated and unsaturated alcohols and aldehydes provide the character...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-444
更新日期:2014-06-07 00:00:00
abstract:BACKGROUND:Williams syndrome transcription factor (WSTF) is a multifaceted protein that is involved in several nuclear processes, including replication, transcription, and the DNA damage response. WSTF participates in a chromatin-remodeling complex with the ISWI ATPase, SNF2H, and is thought to contribute to the mainte...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-740
更新日期:2013-10-29 00:00:00
abstract:BACKGROUND:With its genome sequence and other experimental attributes, Populus trichocarpa has become the model species for genomic studies of wood development. Wood is derived from secondary growth of tree stems, and begins with the development of a ring of vascular cambium in the young developing stem. The terminal r...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-150
更新日期:2010-03-04 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:The genus Populus includes poplars, aspens and cottonwoods, which will be collectively referred to as poplars hereafter unless otherwise specified. Poplars are the dominant tree species in many forest ecosystems in the Northern Hemisphere and are of substantial economic value in plantation forestry. Poplar h...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-57
更新日期:2008-01-29 00:00:00
abstract:BACKGROUND:Retrogenes are processed copies of other genes. This duplication mechanism produces a copy of the parental gene that should not contain introns, and usually does not contain cis-regulatory regions. Here, we computationally address the evolutionary origin of promoter and other cis-regulatory regions in retrog...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-241
更新日期:2008-05-22 00:00:00
abstract:BACKGROUND:Succinate is produced petrochemically from maleic anhydride to satisfy a small specialty chemical market. If succinate could be produced fermentatively at a price competitive with that of maleic anhydride, though, it could replace maleic anhydride as the precursor of many bulk chemicals, transforming a multi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-680
更新日期:2010-11-30 00:00:00
abstract:BACKGROUND:The plastome of medicinal and endangered species in Kingdom of Saudi Arabia, Barleria prionitis was sequenced. The plastome was compared with that of seven Acanthoideae species in order to describe the plastome, spot the microsatellite, assess the dissimilarities within the sampled plastomes and to infer the...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06798-2
更新日期:2020-06-06 00:00:00
abstract:BACKGROUND:Restriction-modification (R-M) systems protect bacteria and archaea from attacks by bacteriophages and archaeal viruses. An R-M system specifically recognizes short sites in foreign DNA and cleaves it, while such sites in the host DNA are protected by methylation. Prokaryotic viruses have developed a number ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5324-3
更新日期:2018-12-07 00:00:00