Meta-analysis of gene expression reversals in ageing brain

Dönertaş, Handan Melike
Brain ageing is characterised by disruptive changes in cognitive abilities, histology, and anatomy. The underlying molecular nature of brain ageing, on the other hand, is little understood, partly due to the stochastic and heterogeneous nature of ageing process. In this study, using published microarray studies spanning 22 brain regions with 1,015 samples, gene expression changes in ageing are analysed in comparison to those in postnatal development. A previous observation that mRNA abundance of a large number of genes in the ageing prefrontal cortex reverses toward pre-adolescent levels, is shown to be a widespread phenomenon across different brain regions. Furthermore, functional analysis reveals that gene expression reversals are consistently associated with decline in neuronal / synaptic gene expression across all studied brain regions, and thus may be linked to ageing-related phenotypes such as decline in cognitive functions. Regulatory analysis show that the genes increasing in expression in development and decreasing in expression in ageing are associated with several trans-regulators, whereas there is no consistent association with any potential trans-regulator for the genes decreasing in expression in development and increasing in expression in ageing. Overall, the results show that meta-analysis is crucial for ageing studies due to the stochastic nature of ageing and that studying gene expression change in ageing in the context of changes in development is a promising approach to discover the molecular mechanisms of ageing.


Meta analysis of alzheimer’s disease at the gene expression level
İzgi, Hamit; Somel, Mehmet; Department of Biology (2017)
In this study, publicly available microarray gene expression datasets are used to investigate common gene expression changes in different postmortem brain regions in Alzheimer’s Disease (AD) patients compared to control subjects, and to find possible functional associations related to these changes. The hypothesis is that pathogenesis of the disease converges into common patterns of dysregulation/alteration or dysfunction in molecular pathways across different brain regions in AD. In total, I studied 13 dat...
Işıldak, Ulaş; Somel, Mehmet; Department of Biology (2022-9-1)
Aging is a complex process associated with the accumulation of stochastic genetic and epigenetic alterations, leading to functional decline and increased risk for disease and death. Although some previous studies demonstrated a tendency towards increased inter-individual heterogeneity during aging, whether it is a function of time that starts at the beginning of life is unknown. Its functional consequences and regulations have also not been systematically studied. In this study, I addressed these questions ...
Prediction of protein subcellular localization using global protein sequence feature
Bozkurt, Burçin; Atalay, Mehmet Volkan; Department of Computer Engineering (2003)
The problem of identifying genes in eukaryotic genomic sequences by computational methods has attracted considerable research attention in recent years. Many early approaches to the problem focused on prediction of individual functional elements and compositional properties of coding and non coding deoxyribonucleic acid (DNA) in entire eukaryotic gene structures. More recently, a number of approaches has been developed which integrate multiple types of information including structure, function and genetic p...
Analysis and classification of spelling paradigm EEG data and an attempt for optimization of channels used
Yıldırım, Asil; Halıcı, Uğur; Department of Electrical and Electronics Engineering (2010)
Brain Computer Interfaces (BCIs) are systems developed in order to control devices by using only brain signals. In BCI systems, different mental activities to be performed by the users are associated with different actions on the device to be controlled. Spelling Paradigm is a BCI application which aims to construct the words by finding letters using P300 signals recorded via channel electrodes attached to the diverse points of the scalp. Reducing the letter detection error rates and increasing the speed of...
Investigation of age dependent contrast and T1 differences in MR images at 3.0 T: a study on MPRAGE, SPIN ECHO and FLASH protocols
Aktaş, Hayriye; Gökçay, Didem; Doğru, Ewa; Department of Biomedical Engineering (2013)
During healthy aging, the brain undergoes several structural changes such as brain atrophy, decreased volume of GM and WM and increase in CSF volume. These changes introduce prominent low contrast effects to the MRI images of the aging population, causing segmentation problems in the data processing pipeline. Measures of tissue characteristics such as T1, T2 provide unique and complementary information to widely used measures of brain atrophy. In this study, image quality metrics such as contrast, SNR, CNR ...
Citation Formats
H. M. Dönertaş, “Meta-analysis of gene expression reversals in ageing brain,” M.S. - Master of Science, Middle East Technical University, 2016.