Network-based identification of reliable bio-markers for cancers

Deng, Shiguo; Qi, Jingchao; Stephen, Mutua; Qiu, Lu; Yang, Huijie

doi:10.1016/j.jtbi.2015.07.026

Cited by 11 publications

(9 citation statements)

References 40 publications

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“…Cancer is a complex disease, and is triggered by genetic factors as well as environmental impact (UV exposure), gene interactions, and lifestyle (e.g., smoking, drinking alcohol, and diet) [63–71]. Interaction between environmental factors and VDR gene is also a possibility [70, 72].…”

Section: Discussionmentioning

confidence: 99%

Role of vitamin D receptor gene Cdx2 and Apa1 polymorphisms in prostate cancer susceptibility: a meta-analysis

Wang

et al. 2016

BMC Cancer

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BackgroundVitamin D receptor (VDR) gene polymorphisms affect the risk of prostate cancer. However, studies investigating the relationship between VDR gene polymorphisms (Cdx2 and ApaI) and prostate cancer risk are equivocal. Therefore, we conducted a meta-analysis of all the studies to review the evidence available.MethodsA comprehensive search of PubMed, EMBASE, and ISI Web of Science for studies published until September 2015 was conducted. Odds ratios (ORs) and 95 % confidence intervals (CIs) were analyzed to determine the association between VDR Cdx2 and ApaI polymorphisms, and prostate cancer risk.ResultsThe meta-analysis included 10 studies involving 4979 cases and 4380 controls to analyze the VDR Cdx2 polymorphism. An additional 11 studies involving 2837 cases and 2884 controls were analyzed for the VDR ApaI polymorphism. Evidence failed to support the role of VDR Cdx2 and ApaI polymorphisms in prostate cancer. For Cdx2, the pooled OR was 1.11 (95 % CI = 0.93–1.33) for AA vs. GG genotypes, 0.97 (95 % CI = 0.88–1.06) for GA vs. AA genotypes, 0.99 (95 % CI = 0.91–1.08) for AA + GA vs. GG, and 1.12 (95 % CI = 0.95–1.31) for AA vs. GA + GG. No significant relationship was observed in any subgroup analysis based on ethnicity, controls, and Hardy–Weinberg equilibrium (HWE). ORs for the ApaI polymorphism were similar.ConclusionsVDR Cdx2 and ApaI polymorphisms are not associated with prostate cancer. Additional evidence is required to confirm this conclusion.

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Section: Discussionmentioning

confidence: 99%

Role of vitamin D receptor gene Cdx2 and Apa1 polymorphisms in prostate cancer susceptibility: a meta-analysis

Wang

et al. 2016

BMC Cancer

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“…The advent of networks and systems biology has revolutionized the transcriptomic and genomic approach to biology and influenced every aspect of biological research. Network-based methods have turned out to be more powerful and informative in studying the disease mechanism [14] [15]. In the genomics era, high-throughput researches have generated huge biological networks of interacting molecules.…”

Section: Introductionmentioning

confidence: 99%

Identification of key regulatory genes connected to NF-κB family of proteins in visceral adipose tissues using gene expression and weighted protein interaction network

et al. 2019

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Obesity is connected to the activation of chronic inflammatory pathways in both adipocytes and macrophages located in adipose tissues. The nuclear factor (NF)-κB is a central molecule involved in inflammatory pathways linked to the pathology of different complex metabolic disorders. Investigating the gene expression data in the adipose tissue would potentially unravel disease relevant gene interactions. The present study is aimed at creating a signature molecular network and at prioritizing the potential biomarkers interacting with NF-κB family of proteins in obesity using system biology approaches. The dataset GSE88837 associated with obesity was downloaded from Gene Expression Omnibus (GEO) database. Statistical analysis represented the differential expression of a total of 2650 genes in adipose tissues (p = <0.05). Using concepts like correlation, semantic similarity, and theoretical graph parameters we narrowed down genes to a network of 23 genes strongly connected with NF-κB family with higher significance. Functional enrichment analysis revealed 21 of 23 target genes of NF-κB were found to have a critical role in the pathophysiology of obesity. Interestingly, GEM and PPP1R13L were predicted as novel genes which may act as potential target or biomarkers of obesity as they occur with other 21 target genes with known obesity relationship. Our study concludes that NF-κB and prioritized target genes regulate the inflammation in adipose tissues through several molecular signaling pathways like NF-κB, PI3K-Akt, glucocorticoid receptor regulatory network, angiogenesis and cytokine pathways. This integrated system biology approaches can be applied for elucidating functional protein interaction networks of NF-κB protein family in different complex diseases. Our integrative and network-based approach for finding therapeutic targets in genomic data could accelerate the identification of novel drug targets for obesity.

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“…We briefly summarize the data generation aspects relevant to the novel developments, and refer the readers for further details on HOS and RB treatments to our previous work (10,11). Here, we embrace networks for inference purposes, and following known techniques (12)(13)(14).…”

Section: Methodsmentioning

confidence: 99%

Immuno-regulated common markers but different network signatures in two associated cancers: evidences from epigenetic treatment

Capobianco

2016

Ann. Transl. Med.

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Network-based identification of reliable bio-markers for cancers

Cited by 11 publications

References 40 publications

Role of vitamin D receptor gene Cdx2 and Apa1 polymorphisms in prostate cancer susceptibility: a meta-analysis

Role of vitamin D receptor gene Cdx2 and Apa1 polymorphisms in prostate cancer susceptibility: a meta-analysis

Identification of key regulatory genes connected to NF-κB family of proteins in visceral adipose tissues using gene expression and weighted protein interaction network

Immuno-regulated common markers but different network signatures in two associated cancers: evidences from epigenetic treatment

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