Abstract:
:Large datasets from -omics studies need to be deeply investigated. The aim of this paper is to provide a new method (LEM method) for the search of transcriptome and metabolome connections. The heuristic algorithm here described extends the classical canonical correlation analysis (CCA) to a high number of variables (without regularization) and combines well-conditioning and fast-computing in "R." Reduced CCA models are summarized in PageRank matrices, the product of which gives a stochastic matrix that resumes the self-avoiding walk covered by the algorithm. Then, a homogeneous Markov process applied to this stochastic matrix converges the probabilities of interconnection between genes, providing a selection of disjointed subsets of genes. This is an alternative to regularized generalized CCA for the determination of blocks within the structure matrix. Each gene subset is thus linked to the whole metabolic or clinical dataset that represents the biological phenotype of interest. Moreover, this selection process reaches the aim of biologists who often need small sets of genes for further validation or extended phenotyping. The algorithm is shown to work efficiently on three published datasets, resulting in meaningfully broadened gene networks.
journal_name
Physiol Genomicsjournal_title
Physiological genomicsauthors
Valour D,Hue I,Grimard B,Valour Bdoi
10.1152/physiolgenomics.00139.2012subject
Has Abstractpub_date
2013-07-15 00:00:00pages
615-28issue
14eissn
1094-8341issn
1531-2267pii
physiolgenomics.00139.2012journal_volume
45pub_type
杂志文章abstract::To account for sex as a biological variable, it is sometimes necessary to identify the sex of an embryo or embryonic cell that was used to generate libraries for RNA sequencing, without the sex being known a priori. The preferred approach for this would take advantage of the mRNA data, rather than relying on other met...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00001.2018
更新日期:2018-08-01 00:00:00
abstract::Regulation of iron absorption by duodenal enterocytes is essential for the maintenance of homeostasis by preventing iron deficiency or overload. Despite the identification of a number of genes implicated in iron absorption and its regulation, it is likely that further factors remain to be identified. For that purpose,...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00297.2005
更新日期:2006-06-16 00:00:00
abstract::MicroRNAs (miRs) are small, noncoding RNAs that are emerging as crucial regulators of cardiac remodeling in left ventricular hypertrophy (LVH) and failure (LVF). However, there are no data on their role in right ventricular hypertrophy (RVH) and failure (RVF). This is a critical question given that the RV is uniquely ...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00163.2011
更新日期:2012-05-01 00:00:00
abstract::Dynamic, epigenetic mechanisms can regulate macrophage phenotypes following exposure to different stimulating conditions and environments. However, temporal patterns of microRNAs (miRNAs or miRs) across multiple macrophage polarization phenotypes have not been defined. We determined miRNA expression in bone marrow-der...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00098.2015
更新日期:2016-05-01 00:00:00
abstract::Its accessibility, unique evolutionary position, and recently assembled genome sequence have advanced the chicken to the forefront of comparative genomics and developmental biology research as a model organism. Several chicken expressed sequence tag (EST) projects have placed the chicken in 10th place for accrued ESTs...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00207.2005
更新日期:2006-05-16 00:00:00
abstract::Understanding how vertebrates respond to hypoxia can have important clinical implications. Fish have evolved the ability to survive long exposure to low oxygen levels. However, little is known about the specific changes in gene expression that result from hypoxia. In this study we used a zebrafish cDNA microarray to e...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00128.2002
更新日期:2003-04-16 00:00:00
abstract::C-reactive protein (CRP) is a sensitive marker of systemic low-grade inflammation. Increased plasma levels of CRP predict the risk of cardiovascular and metabolic diseases. Although genetic factors account for 30-40% of individual differences in plasma CRP levels, genomic regions contributing to CRP levels remain unkn...
journal_title:Physiological genomics
pub_type: 杂志文章,多中心研究
doi:10.1152/physiolgenomics.00054.2005
更新日期:2006-10-11 00:00:00
abstract::Hypertension (HTN) is a prevalent condition with complex etiology and pathophysiology. Evidence exists of significant communication between the nervous system and the immune system (IS), and there appears to be a direct role for inflammatory bone marrow (BM) cells in the pathophysiology of hypertension. However, the m...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00039.2016
更新日期:2016-07-01 00:00:00
abstract::In functional genomics, the high-throughput methods such as microarrays 1) allow analysis of the relationships between genes considering them as elements of a network and 2) lead to biological interpretations thanks to Gene Ontology. But up to now it has not been possible to find relationships between the functions an...
journal_title:Physiological genomics
pub_type: 杂志文章,meta分析
doi:10.1152/physiolgenomics.00008.2008
更新日期:2008-06-12 00:00:00
abstract::ATP-sensitive K+ (KATP) channels play a crucial role in coupling cellular metabolism to membrane potential. In addition to the orthologs corresponding to Kir6.1 and Kir6.2 of mammals, we have identified a novel member, designated Kir6.3 (zKir6.3), of the inward rectifier K+ channel subfamily Kir6.x in zebrafish. zKir6...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00228.2005
更新日期:2006-02-14 00:00:00
abstract::Obesity is influenced by genetics and diet and has wide ranging comorbidities, including anxiety and depressive disorders. Outbred heterogeneous stock (HS) rats are used for fine-genetic mapping of complex traits and may be useful for understanding gene by diet interactions. In this study, HS rats were fed diets conta...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00018.2020
更新日期:2020-09-01 00:00:00
abstract::Vasopressin is a peptide hormone that regulates renal water excretion in part through its actions on the collecting duct. The regulation occurs in part via control of transcription of genes coding for the water channels aquaporin-2 (Aqp2) and aquaporin-3 (Aqp3). To identify transcription factors expressed in collectin...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00148.2009
更新日期:2010-02-04 00:00:00
abstract::Using CRISPR-Cas9 technology, we created a 5-HT7 receptor global knockout (KO) rat, on a Sprague-Dawley background, for use in cardiovascular physiology studies focused on blood pressure regulation. A stable line carrying indels in exons 1 and 2 of the rat Htr7 locus was established and validated. Surprisingly, 5-HT7 ...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00030.2019
更新日期:2019-07-01 00:00:00
abstract::Cardiac microvascular endothelial cells (CMVECs) are the most numerous cells in the myocardium and orchestrate cardiogenesis during development, regulate adult cardiac function, and modulate pathophysiology of heart failure. It has been shown that the transcriptome of CMVECs differs from other endothelial cell types, ...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00002.2019
更新日期:2019-06-01 00:00:00
abstract::Consumption of a protein-containing meal by a fasted animal promotes protein accretion in skeletal muscle, in part through leucine stimulation of protein synthesis and indirectly through repression of protein degradation mediated by its metabolite, α-ketoisocaproate. Mice lacking the mitochondrial branched-chain amino...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00055.2015
更新日期:2015-11-01 00:00:00
abstract::Peripheral blood cells are an accessible environment in which to visualize exercise-induced alterations in global gene expression patterns. We aimed to identify a peripheral blood mononuclear cell (PBMC) signature represented by alterations in gene expression, in response to a standardized endurance exercise training ...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00072.2014
更新日期:2015-02-01 00:00:00
abstract::To further define genes that are differentially expressed during cysteine deprivation and to evaluate the roles of amino acid deprivation vs. oxidative stress in the response to cysteine deprivation, we assessed gene expression in human hepatoma cells cultured in complete or cysteine-deficient medium. Overall, C3A cel...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00263.2007
更新日期:2008-04-22 00:00:00
abstract::The human miR-29 family of microRNAs has three mature members, miR-29a, miR-29b, and miR-29c. miR-29s are encoded by two gene clusters. Binding sites for several transcriptional factors have been identified in the promoter regions of miR-29 genes. The miR-29 family members share a common seed region sequence and are p...
journal_title:Physiological genomics
pub_type: 杂志文章,评审
doi:10.1152/physiolgenomics.00141.2011
更新日期:2012-02-27 00:00:00
abstract::The purpose of this study was to identify novel transcriptional events occurring in the aortic wall before angiogenesis. We used a defined tissue culture system that takes advantage of the capacity of rat aortic rings to generate neovessels ex vivo in response to angiogenic factor stimulation. Total RNA isolated from ...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00048.2006
更新日期:2006-10-03 00:00:00
abstract::To examine differences in cytokine profiles that may confer tolerance/susceptibility to bovine African trypanosomiasis, N'Dama (trypanotolerant, n = 8) and Boran (trypanosusceptible, n = 8) cattle were experimentally challenged with Trypanosoma congolense. Blood samples were collected over a 34-day period, and RNA was...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00100.2006
更新日期:2006-12-13 00:00:00
abstract::Experimental rat models of arthritis are extensively studied with a view to understand the genetic underpinnings of rheumatoid arthritis (RA). Genome scans using these models have led to the detection of arthritis regulatory quantitative trait loci (QTLs) on all but three chromosomes of the rat. Whereas some of the QT...
journal_title:Physiological genomics
pub_type: 杂志文章,评审
doi:10.1152/physiolgenomics.00034.2005
更新日期:2006-10-03 00:00:00
abstract::Following vascular injury medial smooth muscle cells dedifferentiate and migrate through the internal elastic lamina where they form a neointima. The goal of the current study was to identify changes in gene expression that occur before the development of neointima and are associated with the early response to injury....
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00095.2016
更新日期:2017-03-01 00:00:00
abstract::Hypoxia-inducible factor-1alpha (HIF-1alpha) is a transcription factor that regulates the oxygen-dependent expression of a number of genes. This transcription factor may contribute to the abundant expression of many genes in renal medullary cells that function normally under hypoxic conditions. The present study was d...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.2001.6.3.159
更新日期:2001-08-28 00:00:00
abstract::Mesodermal and epidermal precursor cells undergo phenotypic changes during differentiation to the smooth muscle cell (SMC) lineage that are relevant to pathophysiological processes in the adult. Molecular mechanisms that underlie lineage determination and terminal differentiation of this cell type have received much a...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00148.2004
更新日期:2004-11-17 00:00:00
abstract::Megakaryocyte (MK) development is critically informed by plasma membrane-localized receptors that integrate a multiplicity of environmental cues. Given that the current understanding about receptors and ligands involved in megakaryocytopoiesis is based on single targets, we performed a genome-wide search to identify a...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00056.2012
更新日期:2013-03-18 00:00:00
abstract::Previously we demonstrated that aging in coronary arteries is associated with proinflammatory phenotypic changes and decreased NO bioavailability, which, we hypothesized, promotes vascular disease by enhancing endothelial apoptosis. To test this hypothesis we characterized proapoptotic alterations in the phenotype of ...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00136.2003
更新日期:2004-03-12 00:00:00
abstract::Epistasis effects (gene interactions) have been increasingly recognized as important genetic factors underlying complex traits. The existence of a large number of single nucleotide polymorphisms (SNPs) provides opportunities and challenges to screen DNA variations affecting complex traits using a candidate gene analys...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00096.2006
更新日期:2006-12-13 00:00:00
abstract::The zebrafish has become a popular model system for the study of vertebrate developmental biology because of its numerous strengths as a molecular genetic and embryological system. To determine the requirement for specific genes during embryogenesis, it is necessary to generate organisms carrying loss-of-function muta...
journal_title:Physiological genomics
pub_type: 杂志文章,评审
doi:10.1152/physiolgenomics.2000.2.2.37
更新日期:2000-03-13 00:00:00
abstract::A microarray study of the effect of senescence in mice on gene expression in muscle has been published recently. The present analysis was done to evaluate the extent to which the age-related differences in gene expression in murine muscle are also evident in human muscle. RNA extracted from muscle of young (21-24 yr) ...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.2001.5.2.67
更新日期:2001-03-08 00:00:00
abstract::Elastic fibers provide reversible elasticity to the large arteries and are assembled during development when hemodynamic forces are increasing. Mutations in elastic fiber genes are associated with cardiovascular disease. Mice lacking expression of the elastic fiber genes elastin ( Eln-/-), fibulin-4 ( Efemp2-/-), or l...
journal_title:Physiological genomics
pub_type: 杂志文章
doi:10.1152/physiolgenomics.00080.2018
更新日期:2018-11-01 00:00:00