ArticleBMC genomics2008
A novel method of differential gene expression analysis using multiple cDNA libraries applied to the identification of tumour endothelial genes.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it, 54 citations in OpenAlex.
- The Role of RhoJ in Endothelial Cell Biology and Tumor Pathology.BioMed research international · 2016Pooled it
- Endothelial cell-specific chemotaxis receptor (ECSCR) enhances vascular endothelial growth factor (VEGF) receptor-2/kinase insert domain receptor (KDR) activation and promotes proteolysis of internalized KDR.The Journal of biological chemistry · 2013Trial
- ELTD1 is present in extracellular vesicles derived from endothelial cells as a cleaved extracellular domain which induces in vivo angiogenesis.Journal of extracellular biology · 2022Article
- ADGRL4/ELTD1 Expression in Breast Cancer Cells Induces Vascular Normalization and Immune Suppression.Molecular cancer research : MCR · 2021Article
- Elevated expression of the adhesion GPCR ADGRL4/ELTD1 promotes endothelial sprouting angiogenesis without activating canonical GPCR signalling.Scientific reports · 2021Article
- Rho GTPases in Retinal Vascular Diseases.International journal of molecular sciences · 2021Review
- MCAM and LAMA4 Are Highly Enriched in Tumor Blood Vessels of Renal Cell Carcinoma and Predict Patient Outcome.Cancer research · 2016Article
- Identification of novel vascular targets in lung cancer.British journal of cancer · 2015Article
- AtMYB93 is a novel negative regulator of lateral root development in Arabidopsis.The New phytologist · 2014Article
- Changes in the gene expression pattern induced by 2-methoxyestradiol in the mouse uterus.Endocrine · 2013Article
- Impaired angiogenesis and tumor development by inhibition of the mitotic kinesin Eg5.Oncotarget · 2013Article
- De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana.BMC genomics · 2013Article
- A core human primary tumor angiogenesis signature identifies the endothelial orphan receptor ELTD1 as a key regulator of angiogenesis.Cancer cell · 2013Article
- Mapping the extracellular and membrane proteome associated with the vasculature and the stroma in the embryo.Molecular & cellular proteomics : MCP · 2013Article
- Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment.BMC genomics · 2013Article
- Hepatic sinusoidal endothelium avidly binds platelets in an integrin-dependent manner, leading to platelet and endothelial activation and leukocyte recruitment.American journal of physiology. Gastrointestinal and liver physiology · 2013Article
- Rho GTPases and regulation of cell migration and polarization in human corneal epithelial cells.PloS one · 2013Article
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Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundIn this study, differential gene expression analysis using complementary DNA (cDNA) libraries has been improved. Firstly by the introduction of an accurate method of assigning Expressed Sequence Tags (ESTs) to genes and secondly, by using a novel likelihood ratio statistical scoring of differential gene expression between two pools of cDNA libraries. These methods were applied to the latest available cell line and bulk tissue cDNA libraries in a two-step screen to predict novel tumour endothelial markers. Initially, endothelial cell lines were in silico subtracted from non-endothelial cell lines to identify endothelial genes. Subsequently, a second bulk tumour versus normal tissue subtraction was employed to predict tumour endothelial markers.
resultsFrom an endothelial cDNA library analysis, 431 genes were significantly up regulated in endothelial cells with a False Discovery Rate adjusted q-value of 0.01 or less and 104 of these were expressed only in endothelial cells. Combining the cDNA library data with the latest Serial Analysis of Gene Expression (SAGE) library data derived a complete list of 459 genes preferentially expressed in endothelium. 27 genes were predicted tumour endothelial markers in multiple tissues based on the second bulk tissue screen.
conclusionThis approach represents a significant advance on earlier work in its ability to accurately assign an EST to a gene, statistically measure differential expression between two pools of cDNA libraries and predict putative tumour endothelial markers before entering the laboratory. These methods are of value and available http://www.compbio.ox.ac.uk/data/diffex.html to researchers that are interested in the analysis of transcriptomic data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.