Bioinformatics Study on Relationship of Hyperlipidemia and Phospholipids Based on Cytoscape Software

Shi, Zhongfeng; Feng, Yifan; Rui, Wen; Guo, Jian

doi:10.2991/meic-14.2014.80

Cited by 2 publications

(4 citation statements)

References 10 publications

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“…The overall abundance of methyltransferases in Δ omcBESTZ was significantly higher when compared to wild-type strain ( p value = 1.894 × 10 –5 ) (Figure b), whereas the differences between Δ hgcAB and the wild-type strain were statistically insignificant ( p value = 0.3537). These findings agree with experimental results that show Hg methylation activity follows the order Δ omcBESTZ > wild-type > Δ hgcAB and are thus indicative of elevated C1 metabolic activity in the Δ omcBESTZ mutant. , …”

Section: Resultssupporting

confidence: 91%

“…These findings agree with experimental results 19 that show Hg methylation activity follows the order ΔomcBESTZ > wildtype > ΔhgcAB and are thus indicative of elevated C1 metabolic activity in the ΔomcBESTZ mutant. 44,45 Impact of Gene Deletions on Carbon Metabolism in G. sulf urreducens PCA As described above, Hg methylation is predicted to be linked to cellular C1 metabolism and possibly part of the acetyl-CoA pathway. 8 Analysis of homologous genes required for the C1 metabolism reveals that G. sulf urreducens PCA encodes an incomplete acetyl-CoA pathway (Table 1); only genes corresponding to the folate branch of the reductive acetyl-CoA pathway are present in the genome.…”

Section: Increased Abundance Of Pila-c and C-type Cytochromes After D...supporting

confidence: 88%

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Global Proteome Response to Deletion of Genes Related to Mercury Methylation and Dissimilatory Metal Reduction Reveals Changes in Respiratory Metabolism in Geobacter sulfurreducens PCA

et al. 2016

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Geobacter sulfurreducens PCA can reduce, sorb, and methylate mercury (Hg); however, the underlying biochemical mechanisms of these processes and interdependent metabolic pathways remain unknown. In this study, shotgun proteomics was used to compare global proteome profiles between wild-type G. sulfurreducens PCA and two mutant strains: a ΔhgcAB mutant, which is deficient in two genes known to be essential for Hg methylation and a ΔomcBESTZ mutant, which is deficient in five outer membrane c-type cytochromes and thus impaired in its ability for dissimilatory metal ion reduction. We were able to delineate the global response of G. sulfurreducens PCA in both mutants and identify cellular networks and metabolic pathways that were affected by the loss of these genes. Deletion of hgcAB increased the relative abundances of proteins implicated in extracellular electron transfer, including most of the c-type cytochromes, PilA-C, and OmpB, and is consistent with a previously observed increase in Hg reduction in the ΔhgcAB mutant. Deletion of omcBESTZ was found to significantly increase relative abundances of various methyltransferases, suggesting that a loss of dissimilatory reduction capacity results in elevated activity among one-carbon (C1) metabolic pathways and thus increased methylation. We show that G. sulfurreducens PCA encodes only the folate branch of the acetyl-CoA pathway, and proteins associated with the folate branch were found at lower abundance in the ΔhgcAB mutant strain than the wild type. This observation supports the hypothesis that the function of HgcA and HgcB is linked to C1 metabolism through the folate branch of the acetyl-CoA pathway by providing methyl groups required for Hg methylation.

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Section: Resultssupporting

confidence: 91%

Section: Increased Abundance Of Pila-c and C-type Cytochromes After D...supporting

confidence: 88%

Global Proteome Response to Deletion of Genes Related to Mercury Methylation and Dissimilatory Metal Reduction Reveals Changes in Respiratory Metabolism in Geobacter sulfurreducens PCA

et al. 2016

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“…The Search Tool for the Retrieval of Interacting Genes (STRING; ) includes verified and predicted interactions ( 19 ). Cytoscape software (version 3.2.0; Institute for Systems Biology, Seattle, WA, USA) was used to construct a unified framework by integrating gene expression data with biomolecular interaction networks ( 20 ). The interactions among the DEGs were searched for using the STRING database (version 10.0) ( 19 ), with a combined score >0.8 as the threshold.…”

Section: Methodsmentioning

confidence: 99%

“…The interactions among the DEGs were searched for using the STRING database (version 10.0) ( 19 ), with a combined score >0.8 as the threshold. Subsequently, the PPI network was visualized using Cytoscape software (version 3.2.0) ( 20 ). The number of interactions associated with a given node corresponded to the degree for the node.…”

Section: Methodsmentioning

confidence: 99%

Identification and analysis of key genes in osteosarcoma using bioinformatics

Diao

Yang²,

Xiao

2017

Oncol Lett

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Osteosarcoma (OS) is an invasive malignant neoplasm of the bones. The present study identified and analyzed key genes associated with OS. Expression profiling of the dataset GSE49003, which included 6 metastatic and 6 non-metastatic OS cell lines and was obtained from the Gene Expression Omnibus, was performed. Following data preprocessing, the differentially expressed genes (DEGs) were selected using the limma package in R. Subsequently, bidirectional hierarchical clustering using the pheatmap package in R and an unpaired Students' t-test was performed for the DEGs. Based on the Search Tool for the Retrieval of Interacting Genes database and Cytoscape software, a protein-protein interaction (PPI) network for the DEGs was constructed. Using Database for Annotation, Visualization and Integrated Discovery software and the Kyoto Encyclopedia of Genes and Genomes Orthology Based Annotation System server, functional and pathway enrichment analyses were performed for the DEGs corresponding to the proteins of the network. In addition, the transcription factors (TFs) and CpG islands of the gene promoter were searched for using the TRANSFAC database and CpG Island Searcher software, respectively. A total of 323 DEGs were identified between the metastatic and non-metastatic samples. In the PPI network, upregulated epidermal growth factor receptor (EGFR) exhibits a high degree and was therefore highly interconnected with other proteins. Enrichment analysis revealed that EGFR was enriched in cytoskeleton organization, organic substance response and the signaling pathway of focal adhesion. The TFs early growth response 1, nuclear factor-κB complex subunits, peroxisome proliferator activated receptor α, signal transducer and activator of transcription 3 and MYC proto-oncogene were identified in the EGFR promoter region. Furthermore, multiple CpG islands, starting from the 400 bp of the EGFR promoter sequence, were predicted. Methylated modification of the CpG islands in the EGFR promoter may help to regulate EGFR expression. The TFs identified in the EGFR promoter may function in the progression of OS.

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Bioinformatics Study on Relationship of Hyperlipidemia and Phospholipids Based on Cytoscape Software

Cited by 2 publications

References 10 publications

Global Proteome Response to Deletion of Genes Related to Mercury Methylation and Dissimilatory Metal Reduction Reveals Changes in Respiratory Metabolism in Geobacter sulfurreducens PCA

Global Proteome Response to Deletion of Genes Related to Mercury Methylation and Dissimilatory Metal Reduction Reveals Changes in Respiratory Metabolism in Geobacter sulfurreducens PCA

Identification and analysis of key genes in osteosarcoma using bioinformatics

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