Literature DB >> 21156727

Missing value imputation for gene expression data: computational techniques to recover missing data from available information.

Alan Wee-Chung Liew1, Ngai-Fong Law, Hong Yan.   

Abstract

Microarray gene expression data generally suffers from missing value problem due to a variety of experimental reasons. Since the missing data points can adversely affect downstream analysis, many algorithms have been proposed to impute missing values. In this survey, we provide a comprehensive review of existing missing value imputation algorithms, focusing on their underlying algorithmic techniques and how they utilize local or global information from within the data, or their use of domain knowledge during imputation. In addition, we describe how the imputation results can be validated and the different ways to assess the performance of different imputation algorithms, as well as a discussion on some possible future research directions. It is hoped that this review will give the readers a good understanding of the current development in this field and inspire them to come up with the next generation of imputation algorithms.

Mesh:

Year:  2010        PMID: 21156727     DOI: 10.1093/bib/bbq080

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN: 1467-5463            Impact factor:   11.622


  43 in total

1.  A NEW METHOD OF PEAK DETECTION FOR ANALYSIS OF COMPREHENSIVE TWO-DIMENSIONAL GAS CHROMATOGRAPHY MASS SPECTROMETRY DATA.

Authors:  Seongho Kim; Ming Ouyang; Jaesik Jeong; Changyu Shen; Xiang Zhang
Journal:  Ann Appl Stat       Date:  2014-06       Impact factor: 2.083

2.  Data Imputation in Epistatic MAPs by Network-Guided Matrix Completion.

Authors:  Marinka Žitnik; Blaž Zupan
Journal:  J Comput Biol       Date:  2015-02-06       Impact factor: 1.479

3.  Identifications of genetic differences between metastatic and non-metastatic osteosarcoma samples based on bioinformatics analysis.

Authors:  Baoyong Sun; Fangxin Wang; Min Li; Mingshan Yang
Journal:  Med Oncol       Date:  2015-04-02       Impact factor: 3.064

4.  Long non-coding RNA transcriptome of uncharacterized samples can be accurately imputed using protein-coding genes.

Authors:  Aritro Nath; Paul Geeleher; R Stephanie Huang
Journal:  Brief Bioinform       Date:  2020-03-23       Impact factor: 11.622

5.  Sstack: an R package for stacking with applications to scenarios involving sequential addition of samples and features.

Authors:  Kevin Matlock; Raziur Rahman; Souparno Ghosh; Ranadip Pal
Journal:  Bioinformatics       Date:  2019-09-01       Impact factor: 6.937

6.  Imputing Gene Expression in Uncollected Tissues Within and Beyond GTEx.

Authors:  Jiebiao Wang; Eric R Gamazon; Brandon L Pierce; Barbara E Stranger; Hae Kyung Im; Robert D Gibbons; Nancy J Cox; Dan L Nicolae; Lin S Chen
Journal:  Am J Hum Genet       Date:  2016-03-31       Impact factor: 11.025

7.  Comparative analysis of codon usage bias in Crenarchaea and Euryarchaea genome reveals differential preference of synonymous codons to encode highly expressed ribosomal and RNA polymerase proteins.

Authors:  Vishwa Jyoti Baruah; Siddhartha Sankar Satapathy; Bhesh Raj Powdel; Rocktotpal Konwarh; Alak Kumar Buragohain; Suvendra Kumar Ray
Journal:  J Genet       Date:  2016-09       Impact factor: 1.166

Review 8.  Genomic Approaches to Posttraumatic Stress Disorder: The Psychiatric Genomic Consortium Initiative.

Authors:  Caroline M Nievergelt; Allison E Ashley-Koch; Shareefa Dalvie; Michael A Hauser; Rajendra A Morey; Alicia K Smith; Monica Uddin
Journal:  Biol Psychiatry       Date:  2018-02-02       Impact factor: 13.382

9.  Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data.

Authors:  Jason E McDermott; Jing Wang; Hugh Mitchell; Bobbie-Jo Webb-Robertson; Ryan Hafen; John Ramey; Karin D Rodland
Journal:  Expert Opin Med Diagn       Date:  2013-01

10.  Techniques to cope with missing data in host-pathogen protein interaction prediction.

Authors:  Meghana Kshirsagar; Jaime Carbonell; Judith Klein-Seetharaman
Journal:  Bioinformatics       Date:  2012-09-15       Impact factor: 6.937

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