Abstract:
BACKGROUND:Missing data is an inevitable phenomenon in gene expression microarray experiments due to instrument failure or human error. It has a negative impact on performance of downstream analysis. Technically, most existing approaches suffer from this prevalent problem. Imputation is one of the frequently used methods for processing missing data. Actually many developments have been achieved in the research on estimating missing values. The challenging task is how to improve imputation accuracy for data with a large missing rate. METHODS:In this paper, induced by the thought of collaborative training, we propose a novel hybrid imputation method, called Recursive Mutual Imputation (RMI). Specifically, RMI exploits global correlation information and local structure in the data, captured by two popular methods, Bayesian Principal Component Analysis (BPCA) and Local Least Squares (LLS), respectively. Mutual strategy is implemented by sharing the estimated data sequences at each recursive process. Meanwhile, we consider the imputation sequence based on the number of missing entries in the target gene. Furthermore, a weight based integrated method is utilized in the final assembling step. RESULTS:We evaluate RMI with three state-of-art algorithms (BPCA, LLS, Iterated Local Least Squares imputation (ItrLLS)) on four publicly available microarray datasets. Experimental results clearly demonstrate that RMI significantly outperforms comparative methods in terms of Normalized Root Mean Square Error (NRMSE), especially for datasets with large missing rates and less complete genes. CONCLUSIONS:It is noted that our proposed hybrid imputation approach incorporates both global and local information of microarray genes, which achieves lower NRMSE values against to any single approach only. Besides, this study highlights the need for considering the imputing sequence of missing entries for imputation methods.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Li H,Zhao C,Shao F,Li GZ,Wang Xdoi
10.1186/1471-2164-16-S9-S1subject
Has Abstractpub_date
2015-01-01 00:00:00pages
S1issn
1471-2164pii
1471-2164-16-S9-S1journal_volume
16 Suppl 9pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:The astounding regenerative abilities of planarian flatworms prompt steadily growing interest in examining their molecular foundation. Planarian regeneration was found to require hundreds of genes and is hence a complex process. Thus, RNA interference followed by transcriptome-wide gene expression analysis b...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6292-y
更新日期:2019-11-29 00:00:00
abstract:BACKGROUND:The Ion Torrent PGM is a popular benchtop sequencer that shows promise in replacing conventional Sanger sequencing as the gold standard for mutation detection. Despite the PGM's reported high accuracy in calling single nucleotide variations, it tends to generate many false positive calls in detecting inserti...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-516
更新日期:2014-06-24 00:00:00
abstract:BACKGROUND:There is no effective method to obtain genome information from single-celled unculturable organisms such as radiolarians. Even worse, such organisms are often very difficult to collect. Sequence analysis of 18S rDNA has been carried out, but obtaining the data has been difficult and it has provided a rather ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-135
更新日期:2006-06-02 00:00:00
abstract:BACKGROUND:GLV-1h68 is an attenuated recombinant vaccinia virus (VACV) that selectively colonizes established human xenografts inducing their complete regression. RESULTS:Here, we explored xenograft/VACV/host interactions in vivo adopting organism-specific expression arrays and tumor cell/VACV in vitro comparing VACV ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-301
更新日期:2009-07-07 00:00:00
abstract:BACKGROUND:Alternative splicing (AS) is an important regulatory mechanism that greatly contributes to eukaryotic transcriptome diversity. A substantial amount of evidence has demonstrated that AS complexity is relevant to eukaryotic evolution, development, adaptation, and complexity. In this study, six teosinte and ten...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1582-5
更新日期:2015-05-08 00:00:00
abstract:BACKGROUND:Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-137
更新日期:2012-04-16 00:00:00
abstract:BACKGROUND:Cowpea, Vigna unguiculata (L.) Walp., is one of the most important food and forage legumes in the semi-arid tropics because of its drought tolerance and ability to grow on poor quality soils. Approximately 80% of cowpea production takes place in the dry savannahs of tropical West and Central Africa, mostly b...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-103
更新日期:2008-02-27 00:00:00
abstract:BACKGROUND:Haloquadratum walsbyi represents up to 80% of cells in NaCl-saturated brines worldwide, but is notoriously difficult to maintain under laboratory conditions. In order to establish the extent of genetic diversity in a natural population of this microbe, we screened a H. walsbyi enriched metagenomic fosmid lib...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1794-8
更新日期:2015-08-13 00:00:00
abstract:BACKGROUND:Development of the soil amoeba Dictyostelium discoideum is triggered by starvation. When placed on a solid substrate, the starving solitary amoebae cease growth, communicate via extracellular cAMP, aggregate by tens of thousands and develop into multicellular organisms. Early phases of the developmental prog...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1491-7
更新日期:2015-04-13 00:00:00
abstract::Following the publication of the original article [1], the authors reported an error in Fig. 2 of the PDF version of their article. ...
journal_title:BMC genomics
pub_type: 杂志文章,已发布勘误
doi:10.1186/s12864-019-6419-1
更新日期:2019-12-31 00:00:00
abstract:BACKGROUND:Gene expression technologies have the ability to generate vast amounts of data, yet there often resides only limited resources for subsequent validation studies. This necessitates the ability to perform sorting and prioritization of the output data. Previously described methodologies have used functional pat...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-5-58
更新日期:2004-08-20 00:00:00
abstract:BACKGROUND:The ascomycete fungus Ceratocystis cacaofunesta is the causal agent of wilt disease in cacao, which results in significant economic losses in the affected producing areas. Despite the economic importance of the Ceratocystis complex of species, no genomic data are available for any of its members. Given that ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-91
更新日期:2013-02-11 00:00:00
abstract:BACKGROUND:Phenomics provides new technologies and platforms as a systematic phenome-genome approach. However, few studies have reported on the systematic mining of shared genetics among clinical biochemical indices based on phenomics methods, especially in China. This study aimed to apply phenomics to systematically e...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6363-0
更新日期:2019-12-16 00:00:00
abstract:BACKGROUND:Transcription factor (TF) GAMYB, belonging to MYB family (named after the gene of the avian myeloblastosis virus) is a master gibberellin (GA)-induced regulatory protein that is crucial for development and germination of cereal grain and involved in anther formation. It activates many genes including high-mo...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06991-3
更新日期:2020-08-24 00:00:00
abstract:BACKGROUND:Obesity affects quality of life and life expectancy and is associated with cardiovascular disorders, cancer, diabetes, reproductive disorders in women, prostate diseases in men, and congenital anomalies in children. The use of single nucleotide polymorphism (SNP) markers of diseases and drug responses (i.e.,...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-16-S13-S5
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Bananas (Musa spp.) are an important crop worldwide. Most modern cultivars resulted from a complex polyploidization history that comprised three whole genome duplications (WGDs) shaping the haploid Musa genome, followed by inter- and intra-specific crosses between Musa acuminata and M. balbisiana (A and B ge...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5618-0
更新日期:2019-03-27 00:00:00
abstract:BACKGROUND:The question of whether bacterial species objectively exist has long divided microbiologists. A major source of contention stems from the fact that bacteria regularly engage in horizontal gene transfer (HGT), making it difficult to ascertain relatedness and draw boundaries between taxa. A natural way to defi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5099-6
更新日期:2018-10-03 00:00:00
abstract:BACKGROUND:The gut of phloem feeding insects is critical for nutrition uptake and xenobiotics degradation. However, partly due to its tiny size, genomic information for the gut of phloem feeding insects is limited. RESULTS:In this study, the gut transcriptomes of two species of invasive whiteflies in the Bemisia tabac...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-370
更新日期:2014-05-15 00:00:00
abstract:BACKGROUND:Lactose provides an easily-digested energy source for neonates, and is the primary carbohydrate in milk in most species. Bovine lactose is also a key component of many human food products. However, compared to analyses of other milk components, the genetic control of lactose has been little studied. Here we ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4320-3
更新日期:2017-12-15 00:00:00
abstract:BACKGROUND:Arsenic (As) exposure is a significant worldwide environmental health concern. Low dose, chronic arsenic exposure has been associated with a higher than normal risk of skin, lung, and bladder cancer, as well as cardiovascular disease and diabetes. While arsenic-induced biological changes play a role in disea...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1295-9
更新日期:2015-03-19 00:00:00
abstract:BACKGROUND:The pattern of point mutation is important for studying mutational mechanisms, genome evolution, and diseases. Previous studies of mutation direction were largely based on substitution data from a limited number of loci. To date, there is no genome-wide analysis of mutation direction or methylation-dependent...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-316
更新日期:2006-12-13 00:00:00
abstract:BACKGROUND:Many species of the genus Prevotella are pathogens that cause oral diseases. Prevotella intermedia is known to cause various oral disorders e.g. periodontal disease, periapical periodontitis and noma as well as colonize in the respiratory tract and be associated with cystic fibrosis and chronic bronchitis. I...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1272-3
更新日期:2015-02-25 00:00:00
abstract:BACKGROUND:The gonad is the major factor affecting animal reproduction. The regulatory mechanism of the expression of protein-coding genes involved in reproduction still remains to be elucidated. Increasing evidence has shown that ncRNAs play key regulatory roles in gene expression in many life processes. The roles of ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06826-1
更新日期:2020-06-29 00:00:00
abstract:BACKGROUND:Whole-genome sequencing is an important method to understand the genetic information, gene function, biological characteristics and survival mechanisms of organisms. Sequencing large genomes is very simple at present. However, we encountered a hard-to-sequence genome of Pseudomonas aeruginosa phage PaP1. Sho...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-803
更新日期:2014-09-19 00:00:00
abstract:BACKGROUND:Volvox carteri (V. carteri) is a multicellular green alga used as model system for the evolution of multicellularity. So far, the contribution of small RNA pathways to these phenomena is not understood. Thus, we have sequenced V. carteri Argonaute 3 (VcAGO3)-associated small RNAs from different developmental...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3202-4
更新日期:2016-11-02 00:00:00
abstract:BACKGROUND:Elucidating gut microbiota among gallstone patients as well as the complex bacterial colonization of cholesterol gallstones may help in both the prediction and subsequent lowered risk of cholelithiasis. To this end, we studied the composition of bacterial communities of gut, bile, and gallstones from 29 gall...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-669
更新日期:2013-10-01 00:00:00
abstract:BACKGROUND:Milkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L.)...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-211
更新日期:2011-05-04 00:00:00
abstract:BACKGROUND:Insect mitochondrial genomes (mitogenomes) are the most extensively used genetic marker for evolutionary and population genetics studies of insects. The Pentatomoidea superfamily is economically important and the largest superfamily within Pentatomomorpha with over 7,000 species. To better understand the div...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1679-x
更新日期:2015-06-16 00:00:00
abstract:BACKGROUND:While the gargantuan multi-nation effort of sequencing T. aestivum gets close to completion, the annotation process for the vast number of wheat genes and proteins is in its infancy. Previous experimental studies carried out on model plant organisms such as A. thaliana and O. sativa provide a plethora of gen...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1496-2
更新日期:2015-04-15 00:00:00
abstract:BACKGROUND:Citrus shoot tips abscise at an anatomically distinct abscission zone (AZ) that separates the top part of the shoots into basal and apical portions (citrus self-pruning). Cell separation occurs only at the AZ, which suggests its cells have distinctive molecular regulation. Although several studies have looke...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-892
更新日期:2014-10-13 00:00:00