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通过管家基因鉴定微阵列和测序转录组分析中的检测偏倚。

Detection bias in microarray and sequencing transcriptomic analysis identified by housekeeping genes.

作者信息

Zhang Yijuan, Akintola Oluwafemi S, Liu Ken J A, Sun Bingyun

机构信息

Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada.

Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.

出版信息

Data Brief. 2015 Nov 27;6:121-3. doi: 10.1016/j.dib.2015.11.045. eCollection 2016 Mar.

DOI:10.1016/j.dib.2015.11.045
PMID:26858976
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4706559/
Abstract

This work includes the original data used to discover the gene ontology bias in transcriptomic analysis conducted by microarray and high throughput sequencing (Zhang et al., 2015) [1]. In the analysis, housekeeping genes were used to examine the differential detection ability by microarray and sequencing because these genes are probably the most reliably detected. The genes included here were compiled from 15 human housekeeping gene studies. The provided tables here comprise of detailed chromosomal location, detection breadth, normalized expression level, exon count, total exon length, and total intron length of each concerned gene and their related transcripts. We hope this information can help researchers better understand the differences in gene ontology-bias we discussed (Zhang et al., 2015) [1] and can encourage further improvement on these two technology platforms.

摘要

这项工作包含了用于发现通过微阵列和高通量测序进行的转录组分析中基因本体偏差的原始数据(Zhang等人,2015年)[1]。在该分析中,管家基因被用于检验微阵列和测序的差异检测能力,因为这些基因可能是检测最可靠的。此处包含的基因是从15项人类管家基因研究中汇编而来的。这里提供的表格包含了每个相关基因及其相关转录本的详细染色体位置、检测广度、标准化表达水平、外显子数量、外显子总长度和内含子总长度。我们希望这些信息能够帮助研究人员更好地理解我们所讨论的基因本体偏差差异(Zhang等人,2015年)[1],并能够鼓励对这两个技术平台进行进一步改进。

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本文引用的文献

1
Membrane gene ontology bias in sequencing and microarray obtained by housekeeping-gene analysis.通过管家基因分析在测序和微阵列中获得的膜基因本体偏差。
Gene. 2016 Jan 10;575(2 Pt 2):559-566. doi: 10.1016/j.gene.2015.09.041. Epub 2015 Sep 25.
2
Do housekeeping genes exist?管家基因存在吗?
PLoS One. 2015 May 13;10(5):e0123691. doi: 10.1371/journal.pone.0123691. eCollection 2015.
3
Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics.通过转录组学和基于抗体的蛋白质组学的全基因组整合分析人类组织特异性表达。
Mol Cell Proteomics. 2014 Feb;13(2):397-406. doi: 10.1074/mcp.M113.035600. Epub 2013 Dec 5.
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Human housekeeping genes, revisited.人类管家基因,再探。
Trends Genet. 2013 Oct;29(10):569-74. doi: 10.1016/j.tig.2013.05.010. Epub 2013 Jun 27.
5
Identification of human housekeeping genes and tissue-selective genes by microarray meta-analysis.通过微阵列荟萃分析鉴定人类管家基因和组织特异性基因。
PLoS One. 2011;6(7):e22859. doi: 10.1371/journal.pone.0022859. Epub 2011 Jul 27.
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An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data.组织转录组序列数据揭示了大量普遍表达的基因。
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Exploring the differences in evolutionary rates between monogenic and polygenic disease genes in human.探讨人类单基因疾病基因和多基因疾病基因在进化速率上的差异。
Mol Biol Evol. 2010 Apr;27(4):934-41. doi: 10.1093/molbev/msp297. Epub 2009 Dec 2.
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Definition, conservation and epigenetics of housekeeping and tissue-enriched genes.管家基因和组织富集基因的定义、保守性及表观遗传学
BMC Genomics. 2009 Jun 17;10:269. doi: 10.1186/1471-2164-10-269.
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Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.利用DAVID生物信息学资源对大型基因列表进行系统和综合分析。
Nat Protoc. 2009;4(1):44-57. doi: 10.1038/nprot.2008.211.
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Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.生物信息学富集工具:通向大型基因列表全面功能分析的途径
Nucleic Acids Res. 2009 Jan;37(1):1-13. doi: 10.1093/nar/gkn923. Epub 2008 Nov 25.