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CorSig: a general framework for estimating statistical significance of correlation and its application to gene co-expression analysis.

Identifieur interne : 002747 ( Main/Exploration ); précédent : 002746; suivant : 002748

CorSig: a general framework for estimating statistical significance of correlation and its application to gene co-expression analysis.

Auteurs : Hong-Qiang Wang [République populaire de Chine] ; Chung-Jui Tsai

Source :

RBID : pubmed:24194884

Descripteurs français

English descriptors

Abstract

UNLABELLED

With the rapid increase of omics data, correlation analysis has become an indispensable tool for inferring meaningful associations from a large number of observations. Pearson correlation coefficient (PCC) and its variants are widely used for such purposes. However, it remains challenging to test whether an observed association is reliable both statistically and biologically. We present here a new method, CorSig, for statistical inference of correlation significance. CorSig is based on a biology-informed null hypothesis, i.e., testing whether the true PCC (ρ) between two variables is statistically larger than a user-specified PCC cutoff (τ), as opposed to the simple null hypothesis of ρ = 0 in existing methods, i.e., testing whether an association can be declared without a threshold. CorSig incorporates Fisher's Z transformation of the observed PCC (r), which facilitates use of standard techniques for p-value computation and multiple testing corrections. We compared CorSig against two methods: one uses a minimum PCC cutoff while the other (Zhu's procedure) controls correlation strength and statistical significance in two discrete steps. CorSig consistently outperformed these methods in various simulation data scenarios by balancing between false positives and false negatives. When tested on real-world Populus microarray data, CorSig effectively identified co-expressed genes in the flavonoid pathway, and discriminated between closely related gene family members for their differential association with flavonoid and lignin pathways. The p-values obtained by CorSig can be used as a stand-alone parameter for stratification of co-expressed genes according to their correlation strength in lieu of an arbitrary cutoff. CorSig requires one single tunable parameter, and can be readily extended to other correlation measures. Thus, CorSig should be useful for a wide range of applications, particularly for network analysis of high-dimensional genomic data.

SOFTWARE AVAILABILITY

A web server for CorSig is provided at http://202.127.200.1:8080/probeWeb. R code for CorSig is freely available for non-commercial use at http://aspendb.uga.edu/downloads.


DOI: 10.1371/journal.pone.0077429
PubMed: 24194884
PubMed Central: PMC3806744


Affiliations:


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Le document en format XML

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   |area=    PoplarV1
   |flux=    Main
   |étape=   Exploration
   |type=    RBID
   |clé=     pubmed:24194884
   |texte=   CorSig: a general framework for estimating statistical significance of correlation and its application to gene co-expression analysis.
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i   -Sk "pubmed:24194884" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd   \
       | NlmPubMed2Wicri -a PoplarV1 

Wicri

This area was generated with Dilib version V0.6.37.
Data generation: Wed Nov 18 12:07:19 2020. Site generation: Wed Nov 18 12:16:31 2020