co-expression networks
Extensive rewiring of epithelial stromal co expression networks in breast cancer
... protein’s expression in the epithelium and stroma (Additional file ...stromal expression in invasive breast cancer, 18 (75 %) showed coordinated epithelial and stromal expression in at least 50 % of ...
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Adipose Co-expression networks across Finns and Mexicans identify novel triglyceride-associated genes
... for the relatedness of the monozygotic twins, gene ex- pression values were corrected for kinship (see meth- ods). WGCNA identifies gene co-expression networks (modules), summarizing the main ...
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Selecting biologically informative genes in co-expression networks with a centrality score
... gene co- expression networks are still ...to co-expression networks that are defined with binary ...the co-expression between a pair of genes is observed above a ...
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Functional and transcriptional connectivity of communities in breast cancer co-expression networks
... gene expression data such as nonlinearity, ’delays’ ...gene co-expression ...regulatory networks from massive gene expression data is the fact that, in most cases (whenever ...
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Addressing confounding artifacts in reconstruction of gene co expression networks
... of co-expression networks from real large-scale human gene expression measurements, we applied our method to RNA-Seq data from the Genotype-Tissue Expression (GTEx) project v6p ...
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The Role of Eif6 in Skeletal Muscle Homeostasis Revealed by Endurance Training Co-expression Networks
... tional networks. First, we identified differential co-expression networks involving 8,893 unique genes, which the algorithm organized into 25 interconnected gene clusters (network mod- ules) ...
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Functional Partitioning of Yeast Co Expression Networks after Genome Duplication
... non-partitioned networks (Fig- ure 4A) which are most similar to the regulatory networks studied (which also show neither partitioning nor asymme- ...simulated networks and the regulatory ...
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An application of the Shapley value to the analysis of co-expression networks
... a co-expression network. On a co-expression network built over a dataset from the literature, we show that the Shapley value of the coalitional game introduced in the paper (Cesari et ...a ...
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ALS disrupts spinal motor neuron maturation and aging pathways within gene co-expression networks
... the expression data set that included the ALS samples so as to 1) increase the sample size of spMNs, thereby increasing the robustness of the detected modules and 2) provide some representation of ...
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Gene co expression networks shed light into diseases of brain iron accumulation
... NBIA disorders share a core set of clinicopathological features, including neurodegeneration, but not much is known about the originating cell type. According to our data and in line with NBIA histopathological features, ...
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VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer
... MCF7 cells were transfected with Smart Pool siRNA (Dharmacon, L-014515-02), siControl, GRHL2 overex- pression vector (Origene, RC214498), GRHL2 Δ425 – 437 (Origene), or empty control vector using Lipofectamine 3000 ...
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Metrics to estimate differential co-expression networks
... differential co-expression of experimental datasets is unknown and will inevitably be dependent on the metric used for ...gene expression data from normal tissues to generate artificial cancer ...
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VULCAN integrates ChIP seq with patient derived co expression networks to identify GRHL2 as a key co regulator of ERa at enhancers in breast cancer
... To enable discoveries beyond collections like EN- CODE, we are proposing a computational framework to integrate patient data in the prediction of functional protein-protein interactions. By applying machine learn- ing ...
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MicroRNA and gene co-expression networks characterize biological and clinical behavior of rhabdomyosarcomas.
... that co-expressed genes are commonly associated with similar biological function/pathways, we employed WGCNA using parallel gene expression data from the 64 RMS pa- tients [30] and identi fi ed 12 groups of ...
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gViz, a novel tool for the visualization of co expression networks
... Several programs have been designed for the analysis of biological networks, the best known of which is Cytoscape [17]. Although it is a major first class visualization pro- gram, we chose to develop gViz and to ...
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Social networks help to infer causality in the tumor microenvironment
... the co-expression of two genes) but also on the global net- work topology ...derived co-expression networks by constructing a net- work of influence and analyzing its topological ...
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Determining the transcriptional regulation pattern of PgTIP1 in transgenic Arabidopsis thaliana by constructing gene
... genome expression and bioinformatics analy- sis, including analysis of co-expression networks and transcription factors (Tfscan), were used to deter- mine the key genes that are activated ...
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A network-based signature to predict the survival of non-smoking lung adenocarcinoma
... gene co-expression modules, DEGs of each dataset were submitted to ...different co-expression networks by cluster dendrogram trees (Figure ...the co-expression modules ...
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An interactomics overview of the human and bovine milk proteome over lactation
... between co-expression networks and protein interaction networks observed based on the network alignment (Additional file 2: Figure S1 and Additional file 3: Table S2) was confirmed by ...
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Exploiting single cell expression to characterize co expression replicability
... To complement this analysis, we performed our own technically controlled scRNA-seq experiment using gen- etically targeted interneuron classes to further interro- gate data features and analysis practices that contribute ...
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