ArticleProceedings of the National Academy of Sciences of the United States of America2004
A system for enhancing genome-wide coexpression dynamics study.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers, 1 of them a synthesis that pooled it.
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Who cites it
33 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide.Bioinformatics (Oxford, England) · 2009Pooled it
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- Flexible copula model for integrating correlated multi-omics data from single-cell experiments.Biometrics · 2023Article
- Generalized Liquid Association Analysis for Multimodal Data Integration.Journal of the American Statistical Association · 2023Article
- Modeling dynamic correlation in zero-inflated bivariate count data with applications to single-cell RNA sequencing data.Biometrics · 2022Article
- A hypergraph-based method for large-scale dynamic correlation study at the transcriptomic scale.BMC genomics · 2019Article
- A new dynamic correlation algorithm reveals novel functional aspects in single cell and bulk RNA-seq data.PLoS computational biology · 2018Article
- Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels.BMC plant biology · 2017Article
- StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data.Bioinformatics (Oxford, England) · 2017Article
- Meta-analytic framework for liquid association.Bioinformatics (Oxford, England) · 2017Article
- Detecting subnetwork-level dynamic correlations.Bioinformatics (Oxford, England) · 2017Article
- UNCLES: method for the identification of genes differentially consistently co-expressed in a specific subset of datasets.BMC bioinformatics · 2015Article
- K-Profiles: A Nonlinear Clustering Method for Pattern Detection in High Dimensional Data.BioMed research international · 2015Article
- An efficient algorithm to explore liquid association on a genome-wide scale.BMC bioinformatics · 2014Article
- Lignin, mitochondrial family, and photorespiratory transporter classification as case studies in using co-expression, co-response, and protein locations to aid in identifying transport functions.Frontiers in plant science · 2014Review
- High-Dimensional Heteroscedastic Regression with an Application to eQTL Data Analysis.Biometrics · 2012Article
- Identification of markers associated with global changes in DNA methylation regulation in cancers.BMC bioinformatics · 2012Article
- Capturing changes in gene expression dynamics by gene set differential coordination analysis.Genomics · 2011Article
- Improving gene expression data interpretation by finding latent factors that co-regulate gene modules with clinical factors.BMC genomics · 2011Article
- A penalized likelihood approach for bivariate conditional normal models for dynamic co-expression analysis.Biometrics · 2011Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Statistical similarity analysis has been instrumental in elucidation of the voluminous microarray data. Genes with correlated expression profiles tend to be functionally associated. However, the majority of functionally associated genes turn out to be uncorrelated. One conceivable reason is that the expression of a gene can be sensitively dependent on the often-varying cellular state. The intrinsic state change has to be plastically accommodated by gene-regulatory mechanisms. To capture such dynamic coexpression between genes, a concept termed "liquid association" (LA) has been introduced recently. LA offers a scoring system to guide a genome-wide search for critical cellular players that may interfere with the coexpression of a pair of genes, thereby weakening their overall correlation. Although the LA method works in many cases, a direct extension to more than two genes is hindered by the "curse of dimensionality." Here we introduce a strategy of finding an informative 2D projection to generalize LA for multiple genes. A web site is constructed that performs on-line LA computation for any user-specified group of genes. We apply this scoring system to study yeast protein complexes by using the Saccharomyces cerevisiae protein complexes database of the Munich Information Center for Protein Sequences. Human genes are also investigated by profiling of 60 cancer cell lines of the National Cancer Institute. In particular, our system links the expression of the Alzheimer's disease hallmark gene APP (amyloid-beta precursor protein) to the beta-site-cleaving enzymes BACE and BACE2, the gamma-site-cleaving enzymes presenilin 1 and 2, apolipoprotein E, and other Alzheimer's disease-related genes.
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