A hybrid imputation approach for microarray missing value estimation.


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.


BMC Genomics


BMC genomics


Li H,Zhao C,Shao F,Li GZ,Wang X




Has Abstract


2015-01-01 00:00:00








16 Suppl 9


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    abstract:BACKGROUND:In many eukaryotes, microRNAs (miRNAs) bind to complementary sites in the 3'-untranslated regions (3'-UTRs) of target messenger RNAs (mRNAs) and regulate their expression at the stage of translation. Recent studies have revealed that many miRNAs are evolutionarily conserved; however, the evolution of their t...

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    authors: Takane K,Fujishima K,Watanabe Y,Sato A,Saito N,Tomita M,Kanai A

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  • Transferring knowledge of bacterial protein interaction networks to predict pathogen targeted human genes and immune signaling pathways: a case study on M. tuberculosis.

    abstract:BACKGROUND:Bacterial invasive infection and host immune response is fundamental to the understanding of pathogen pathogenesis and the discovery of effective therapeutic drugs. However, there are very few experimental studies on the signaling cross-talks between bacteria and human host to date. METHODS:In this work, ta...

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    pub_type: 杂志文章


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  • RNA sequencing identifies common pathways between cigarette smoke exposure and replicative senescence in human airway epithelia.

    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...

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    abstract:BACKGROUND:Chronic Allograft Nephropathy (CAN) is a clinical entity of progressive kidney transplant injury. The defining histology is tubular atrophy with interstitial fibrosis (IFTA). Using a meta-analysis of microarrays from 84 kidney transplant biopsies, we revealed growth factor and integrin adhesion molecule path...

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    pub_type: 杂志文章,meta分析


    authors: Dosanjh A,Robison E,Mondala T,Head SR,Salomon DR,Kurian SM

    更新日期:2013-04-23 00:00:00

  • Identification of genomic aberrations in hemangioblastoma by droplet digital PCR and SNP microarray highlights novel candidate genes and pathways for pathogenesis.

    abstract:BACKGROUND:The genetic mechanisms underlying hemangioblastoma development are still largely unknown. We used high-resolution single nucleotide polymorphism microarrays and droplet digital PCR analysis to detect copy number variations (CNVs) in total of 45 hemangioblastoma tumors. RESULTS:We identified 94 CNVs with a m...

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    pub_type: 杂志文章


    authors: Mehrian-Shai R,Yalon M,Moshe I,Barshack I,Nass D,Jacob J,Dor C,Reichardt JK,Constantini S,Toren A

    更新日期:2016-01-14 00:00:00

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    pub_type: 杂志文章


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    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...

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    authors: Culver-Cochran AE,Chadwick BP

    更新日期:2013-10-29 00:00:00