Co-expressed genes network
Optimal Function Prediction of Key Aberrant Genes in Early-onset Preeclampsia Using a Modified Network-based Guilt by Association Method
... differentially expressed genes (DEGs) were extracted using linear models for microarray data (LIMMA) ...assess co-expressed strength of each interaction between DEGs, based on which the ...
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Identification of novel biomarkers affecting the metastasis of colorectal cancer through bioinformatics analysis and validation through qRT-PCR
... gene co-expression network analysis; DEGs: Dif- ferentially expressed genes; DELs: Differentially expressed lncRNAs; COAD: Colon adenocarcinoma; READ: Rectal adenocarcinoma; GO: Gene ...
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A co-expression network for differentially expressed genes in bladder cancer and a risk score model for predicting survival
... differentially expressed genes, which were analyzed by the WGCNA to identify the brown co-expression module comprised of 77 patho- logical stage-specific ...six genes (DCN, EMILIN1, FBLN5, ...
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RETRACTED ARTICLE: Ranking candidate genes of esophageal squamous cell carcinomas based on differentially expressed genes and the topological properties of the co-expression network
... Microarray analysis has been widely used to investigate gene expression in various diseases, such as breast tumors [7], brain cancer [8], endometrial cancer [9], and renal cell carcinoma [10]. In previous studies of ...
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Integrated genomic characterization of cancer genes in glioma
... values expressed as Fragments per kilobase of exon per million fragments mapped (FPKM) were compared between glioma and normal brain tissues for all driver genes with t test, P values were adjusted using ...
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Transcriptome analyses of tumor-adjacent somatic tissues reveal genes co-expressed with transposable elements
... the co-factor KAP1 (TRIM28), the KZFP-KAP1 complex has been shown to silence both ex- ogenous retroviruses and endogenous retroelements dur- ing embryonic development [66, ...of co-evolution of retroviral ...
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Do sputum or circulating blood samples reflect the pulmonary transcriptomic differences of COPD patients? A multi-tissue transcriptomic network META-analysis
... gene co-expression network correlation- based analysis (WGCNA) is a particular type of network analysis that allows the identification of modules of co-expressed genes in a given ...
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Identification of novel gene and pathway targets for human epilepsy treatment
... (PPI) network and co- expression modules associated with ...and co-expression modules analyses can provide new insights into protein function, besides, they may help to uncover the generic ...
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Human gene correlation analysis (HGCA): A tool for the identification of transcriptionally co expressed genes
... WGCNA [16] is a collection of R functions for net- work analysis. In terms of data visualisation and inter- activity, WGCNA comes with static images to present data clustering which can be exported to Cytoscape. As it ...
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Regulation of rumen development in neonatal ruminants through microbial metagenomes and host transcriptomes
... 399 genes (CPM > 1) expressed in the calf rumen ...differentially expressed (DE) genes were observed when comparing between newborn (0-day) and 1W calves (36) and 1W and 3W calves (147), ...
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Identification of novel long non-coding RNAs deregulated in hepatocellular carcinoma using RNA-sequencing
... differentially expressed in the three ...gene network analysis identified a cluster of 18 upregulated lncRNAs co-expressed with protein-coding genes involved in cell cycle ...novel ...
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Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery
... a co-expression network of 320 genes (M30), which is significantly enriched for non-synonymous de novo mutations ascertained from patients with monogenic epilepsy and for common variants associated ...
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Quantitative proteomics reveals the novel co-expression signatures in early brain development for prognosis of glioblastoma multiforme
... gene co-expression network analysis (WGCNA) on protein expression data of brain development to identify co-expressed modules that highly expressed on distinct development stages, ...
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<p><em>CYP1B1</em>, <em>VEGFA</em>, <em>BCL2</em>, and <em>CDKN1A</em> Affect the Development of Chronic Obstructive Pulmonary Disease</p>
... gene co-expression network analysis ...differentially expressed genes (DEGs) between COPD and healthy sam- ...metabolite network analysis were also performed, which were not mentioned ...
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Identification of gene co-regulatory modules and associated cis-elements involved in degenerative heart disease
... A non-canonical initiator motif (YYCTTTYY) appears to be a nearly universal feature of translation promoter sequences. In addition to its sequence, the motif is highly specific to the positive strand and the area ...
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Genomic positions of co expressed genes: echoes of chromosome organisation in gene expression data
... While the patterns of the three-dimensional orga- nization of the chromosomes in the nucleus are not solved, the involvement of several chromosome structure features influencing the organisation (e.g. gene density or ...
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Effect of hyperoside on cervical cancer cells and transcriptome analysis of differentially expressed genes
... these genes are closely related to the occurrence and development of ...PPI network analysis identified CCNA2, CLTC, DVL2, HIST1H2BD, HIST1H2BN, HSPA8, PRKACA, and TFRC as candidate ...regulatory ...
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Renna, Alessio (2018): Using differential MNase-seq to dissect nucleosome organization around promoters and enhancers in D.melanogaster. Dissertation, LMU München: Fakultät für Chemie und Pharmazie
... S.cerevisiae genes are housekeeping, characterized by a constant transcription rate and low expression ...stress-responsive genes do not contain these elements and they are characterized by higher intrinsic ...
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Analyses of gene expression profiles in the rat dorsal horn of the spinal cord using RNA sequencing in chronic constriction injury rats
... PPI network analysis showed that Cd68, C1qc, C1qa, Laptm5, and Fcgr3a were crucial nodes with high connectivity ...these genes which have previously been linked to immune and inflammation-related pathways ...
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Identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysis
... dysregulated genes along with changes in processing conditions [untreated—treated with X-ray—X-ray + treated with HPD]) and 464 DEGs in the gene set G2 (significantly dysregulated between X-ray + HPD-treated group ...
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