Coexpression analysis of human genes across many microarray data sets.

By Homin K. Lee, Amy K. Hsu, J. Sajdak, J. Qin, Paul Pavlidis. Genome Research, 2004

795 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/ef8161b95ba86b2644b56bfffa54f0926843376a

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In Molecular Biology

Citations in the corpus

Global Testing and Large-Scale Multiple Testing for High-Dimensional Covariance Structures (2017, neutral): “Lee, H. K., A. K. Hsu, J. Sajdak, J. Qin, and P. Pavlidis (2004).”
A human functional protein interaction network and its application to cancer data analysis (2010, methodology): “…( Caenorhabditis ele-Figure Human PPI [45-47] Fly PPI [45] Domain Interaction [52] Prieto(cid:3)s Gene Expression [50] Lee(cid:3)s Gene Expression [49] GO BP Sharing [51] Yeast PPI [45] Worm PPI [45] PPIs from GeneWays [53] Human PPI [45-47] Fly PPI [45] Domain Interaction [52] Prieto(cid:3)s…”
Semantic Similarity in Biomedical Ontologies (2009, background): “However, it can also be used to link and compare results from different assays [30], to improve data quality [70], and to validate gene selection for biomedical purposes [71].”
NCBI GEO: mining millions of expression profiles—database and tools (2004, result): “Cross-comparison of independently generated but experimentally similar datasets can corroborate interesting gene expression trends that may be overlooked in one experiment alone ( 11 ).”
Network visualization and analysis of gene expression data using BioLayout Express3D (2009, background): “The idea of transforming gene expression data into a network graph based on correlation measures is not ne”
Using graph theory to analyze biological networks (2011, methodology): “As an example, relations whose importance varies are frequently assigned to biological data to capture the relevance of co-occurrences identified by text mining, sequence or structural similarities between proteins or co-expression of genes [23,60].”
Large-scale mapping of human protein–protein interactions by mass spectrometry (2007, methodology): “Integration of the gene co-expression compendium (Lee et al, 2004) was performed by cross-referencing gene symbols.”
Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks (2005, background): “Analyses of gene coexpression [3-7] have demonstrated that clusters with similar overall expression are often enriched for genes with similar functions, consistent with the hypothesis of modularly-behaving gene programs, where sets of genes are activated in concert to carry out functions.”
Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network (2011, background): “However, owing to the vast amount of ‘noise’ in microarray data, a co-expression network should be constructed using multiple microarray data sets, since genes with similar expression patterns under multiple, but resembling experimental conditions have a higher probability of sharing similar functio”
Visualization of omics data for systems biology (2010, methodology): “Network clustering of gene expression data is done using so-called 'correlation networks', in which each gene is a node and each edge indicates coexpression of two genes under the conditions of the experimen”
Network-based prediction of protein function (2007, methodology): “Following the success of several methods integrating expression data from multiple studies (Ihmels et al, 2002; Lee et al, 2004; Segal et al, 2005; Tanay et al, 2005), we expect that techniques based on large compendia of expression data and protein interaction networks will significantly increase”
Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. (2006, methodology): “To ensure that the quality of the intensity measurements was reliable, various filtering steps were performed to exclude spots with low signal-to-noise ratios.(31) Within the SMD data sets, intensity spots were filtered out that were either missing or contaminated, and the mean intensity of spots ha”