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SpeCond：一种检测条件特异性基因表达的方法。

SpeCond: a method to detect condition-specific gene expression.

机构信息

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.

出版信息

Genome Biol. 2011 Oct 18;12(10):R101. doi: 10.1186/gb-2011-12-10-r101.

DOI:10.1186/gb-2011-12-10-r101
PMID:22008066
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3333772/
Abstract

Transcriptomic studies routinely measure expression levels across numerous conditions. These datasets allow identification of genes that are specifically expressed in a small number of conditions. However, there are currently no statistically robust methods for identifying such genes. Here we present SpeCond, a method to detect condition-specific genes that outperforms alternative approaches. We apply the method to a dataset of 32 human tissues to determine 2,673 specifically expressed genes. An implementation of SpeCond is freely available as a Bioconductor package at http://www.bioconductor.org/packages/release/bioc/html/SpeCond.html.

摘要

转录组研究通常会在众多条件下测量表达水平。这些数据集可以识别在少数条件下特异性表达的基因。然而，目前还没有用于识别这些基因的统计上稳健的方法。在这里，我们提出了 SpeCond，这是一种用于检测条件特异性基因的方法，其性能优于其他方法。我们将该方法应用于 32 个人类组织的数据集，以确定 2673 个特异性表达的基因。SpeCond 的实现可作为 Bioconductor 软件包在 http://www.bioconductor.org/packages/release/bioc/html/SpeCond.html 上免费获得。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3dc/3333772/2b839d934f69/gb-2011-12-10-r101-7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3dc/3333772/cb95365503d9/gb-2011-12-10-r101-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3dc/3333772/1b385eeb4f32/gb-2011-12-10-r101-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3dc/3333772/b775aca9d746/gb-2011-12-10-r101-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3dc/3333772/1a59585766cd/gb-2011-12-10-r101-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3dc/3333772/48c6104e384f/gb-2011-12-10-r101-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3dc/3333772/4779497f2cc1/gb-2011-12-10-r101-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3dc/3333772/2b839d934f69/gb-2011-12-10-r101-7.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3dc/3333772/cb95365503d9/gb-2011-12-10-r101-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3dc/3333772/1b385eeb4f32/gb-2011-12-10-r101-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3dc/3333772/b775aca9d746/gb-2011-12-10-r101-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3dc/3333772/1a59585766cd/gb-2011-12-10-r101-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3dc/3333772/48c6104e384f/gb-2011-12-10-r101-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3dc/3333772/4779497f2cc1/gb-2011-12-10-r101-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d3dc/3333772/2b839d934f69/gb-2011-12-10-r101-7.jpg

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本文引用的文献

[1]
The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes.

Nucleic Acids Res. 2011-1

[2]
Systematical detection of significant genes in microarray data by incorporating gene interaction relationship in biological systems.

PLoS One. 2010-10-29

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Differential expression analysis for sequence count data.

Genome Biol. 2010-10-27

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Nat Biotechnol. 2010-4

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A census of human transcription factors: function, expression and evolution.

Nat Rev Genet. 2009-4

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ATF5 is a highly abundant liver-enriched transcription factor that cooperates with constitutive androstane receptor in the transactivation of CYP2B6: implications in hepatic stress responses.

Drug Metab Dispos. 2008-6

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BMC Bioinformatics. 2007-6-29

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Nucleic Acids Res. 2007-7

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