Network-Based Analysis of Cognitive Impairment and Memory Deficits from Transcriptome Data

Emanetci, Elif; Çakır, Tunahan

doi:10.1007/s12031-021-01807-9

Cited by 4 publications

(1 citation statement)

References 87 publications

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“…WGCNA (Emanetci & Çakır, 2021; Langfelder & Horvath, 2008) is an algorithm that detects modules from expression data by using Pearson correlation. This algorithm can be used to find highly correlated gene clusters from expression data, and interactions between them.…”

Section: Methodsmentioning

confidence: 99%

A co‐expression network based molecular characterization of genes responsive for Braak stages in Parkinson's disease

Emanetci

Çakır

2022

Eur J of Neuroscience

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The progression of Parkinson's disease (PD) is defined by six Braak stages. We used transcriptome data from PD patients with Braak stage information to understand underlying molecular mechanisms for the progress of the disease. We created networks of genes with continuously decreased/increased co‐expression from control group to Braak 5–6 stages. These networks are significantly associated with PD‐related mechanisms such as mitochondrial dysfunction and synaptic signalling among others. Applying weighted gene co‐expression network analysis (WGCNA) algorithm to the co‐expression networks led to more specific modules enriched with neurodegeneration‐related disease pathways, seizure, abnormality of coordination, and hypotonia. Furthermore, we showed that one of the co‐expression networks is clustered into three major communities with dedicated molecular functions: (i) tubulin folding pathway, gap junction‐related mechanisms, neuronal system; (ii) synaptic vesicle, intracellular vesicle, proteasome complex, PD genes; (iii) energy metabolism, mitochondrial mechanisms, oxidative phosphorylation, TCA cycle, PD genes. The co‐expression relations we identified in this study as crucial players in the disease progression cover several known PD‐associated genes and genes whose products are known to physically interact with alpha‐synuclein protein.

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Section: Methodsmentioning

confidence: 99%

A co‐expression network based molecular characterization of genes responsive for Braak stages in Parkinson's disease

Emanetci

Çakır

2022

Eur J of Neuroscience

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Personalized Protein-Protein Interaction Networks Towards Unraveling the Molecular Mechanisms of Alzheimer’s Disease

CEYLAN,

DÜZ,

ÇAKIR

2023

Mol Neurobiol

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Transcriptional landscape of cellular networks reveal interactions driving the dormancy mechanisms in cancer

Uzuner

Akkoç

Peker

et al. 2021

Sci Rep

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Primary cancer cells exert unique capacity to disseminate and nestle in distant organs. Once seeded in secondary sites, cancer cells may enter a dormant state, becoming resistant to current treatment approaches, and they remain silent until they reactivate and cause overt metastases. To illuminate the complex mechanisms of cancer dormancy, 10 transcriptomic datasets from the literature enabling 21 dormancy–cancer comparisons were mapped on protein–protein interaction networks and gene-regulatory networks to extract subnetworks that are enriched in significantly deregulated genes. The genes appearing in the subnetworks and significantly upregulated in dormancy with respect to proliferative state were scored and filtered across all comparisons, leading to a dormancy–interaction network for the first time in the literature, which includes 139 genes and 1974 interactions. The dormancy interaction network will contribute to the elucidation of cellular mechanisms orchestrating cancer dormancy, paving the way for improvements in the diagnosis and treatment of metastatic cancer.

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Network-Based Analysis of Cognitive Impairment and Memory Deficits from Transcriptome Data

Cited by 4 publications

References 87 publications

A co‐expression network based molecular characterization of genes responsive for Braak stages in Parkinson's disease

A co‐expression network based molecular characterization of genes responsive for Braak stages in Parkinson's disease

Personalized Protein-Protein Interaction Networks Towards Unraveling the Molecular Mechanisms of Alzheimer’s Disease

Transcriptional landscape of cellular networks reveal interactions driving the dormancy mechanisms in cancer

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