| Alzheimer's disease(AD)is a fatal neurodegenerative disease,and its clinical manifestations are progressively decline on the functions of memory and cognition and daily living,and accompanied by a variety of neuropsychiatric symptoms and behavioral disorders.Alzheimer's disease,clinically,is characterized by memory impairment,aphasia,apraxia,agnosia,executive dysfunction as well as personality and behavioral changes and other comprehensive performance features.Alzheimer's disease is the most common cause of dementia.As other neurodegenerative diseases,Alzheimer's disease is essentially a multi-factor complex disease.But its etiology is unclear,involving known risk factors including age,gender,family history,education,smoking,depression,psychological pressure,viral infections,head trauma,and many other factors.The development of AD is correlated to human aging process.With increasing age,increased neuronal death and loss of synaptic function will induce increases in the prevalence of AD.Core neuropathological feature of AD is beta-amyloid deposit consisting of extracellular senile plaques and neurofibrillary tangles consisted of by hyper-phosphorylated Tau protein accumulated in cells.The senile plaques and neurofibrillary tangles both are closely related with loss of neurons and synapse,atrophy and the expansion of the lateral ventricle of the brain,which are caused by reduced brain tissue.Neurons atrophy of the cortex,synaptic loss and dendritic atrophy may be the key pathology of Alzheimer's disease.The pathogenesis of Alzheimer's disease is still not clear.Now there are several theories to explain the molecular mechanisms,such as molecular genetics and gene theory,inflammation doctrine,oxidative stress theory,free radical theory,theory of viruses and other theory.The analysis of the expression of genes and molecular pathology of the Alzheimer's disease are effective means to explore the pathogenesis,diagnosis,prevention and treatment of the disease.The conventional genetic engineering technology and other technologies in Alzheimer's disease research have achieved fruitful results.The emergence of gene chip technology to overcome the limitations in previous studies of single gene,can grasp and understand the development of Alzheimer's from a holistic perspective.Recent studies have confirmed the efectiveness and importance of gene chip technology in the study of Alzheimer's disease.Bioinformatics is an interdisciplinary that is developed with the genome data surge.It is utilized for the collection,storage,management,annotation,analysis and mining of biological data on nucleic acids,proteins and other aspects.Bioinformatics has been widely used in various fields of life science.It has become an important means of life science and played a key role in the study on identification and functions of human genes,structure and function of proteins.Especially,in recent years,bioinformatics,by using massive amounts of data in public databases,has played an irreplaceable role in the study of human disease genes and mechanisms,regulation of gene expression,as well as drug screening,target validation and verification of biological hypotheses.The development of bioinformatics has brought new opportunities for further research of AD.In recent years,bioinformatics has been widely used for the rapid identification of AD-related genes,differential expression analysis of the gene at different stages,transcriptome analysis in different brain regions of patients with AD.Bioinformatics has also been widely applied for the analysis of association between AD and aging,age and gender.Bioinformatics provided profound insight into the molecular mechanisms in the development of AD.Due to the complexity of living systems,biological phenotypes and genotypes is not a single correspondence relationship.The complex relationship between them can't be explained by a change of a single gene.The tens of thousands of proteins in the cell are organized to participate in the biological processes and the complete physiological activity and,such as signal transduction,metabolism pathways,and the detailed functions in the processes are involved in a variety of proteins with related functions.A gene system functionally consists of the synergic and interdependent molecular modules.In physiological and pathological processes of nerve cells,changes in cell functions often involve changes in multiple genes or proteins module.The genes in the same module are often involved in the same biological processes or have similar biological functions,especially,co-regulated and co-expressed phenomena often occur among the genes with related functions.Researches on co-expression and co-regulation of the genes as well as the altered relations among them in the nerve cells of normal and AD brain tissue are helpful to better explore and understand the molecular mechanisms of Alzheimer's disease.To futher understand the molecular mechanisms of Alzheimer's disease,the present study integrated a variety of bioinformatics methods to analyze Alzheimer's disease-related data from GEO database and investigated the gene changes correlated with Alzheimer's disease in the multi-level perspectives.First,the analysis of the overall on gene expression was implemented on the brain tissues in the normal and AD group.Then,we assessed the functions of the co-expressed modules identified in two groups.Further,we checked the functionally similarity between the modules and their expression model in different tissues in groups.From the modules,we identified the subset correlated with age and their expression patterns in two groups.Finally,the regulation and co-regulation of genes correlated with age in each module were studied.Meanwhile,protein-protein interactive relationships were analyzed and the interactive network was constructed in the entorhinal cortex.From the interactive network,11 key genes were identified by network analysis,which expressed dynamic may represent the progression of AD.This study is divided into four parts:Part ?:Treatment of Alzheimer's disease-related microarray data sets and analysis of gene expression:First of all,Alzheimer's disease-related dataset,GSE48350,was download from the GEO databases that United States National Center for biotechnology information(NCBI)created and maintained.Next,the R/Bioconductor package was used to the background correction,normalization,log processing of the raw dataset,and filtering and annotations of the pre-processed data.Self-organizing mapping analysis of the all genes obtained after preprocessing of the dataset was executed for survey of expression distribution of the genes in various regions of the brain in the normal control and AD samples.By self-organizing map analysis,there was a significant difference of genes expression between normal control samples and Alzheimer's samples.The discrepancy in patterns of genes expression in different tissues in the same group shows the complex of the gene expression in the brain and of molecular mechanism in AD.Part ?:Identification and functional analysis of co-expressed gene modules in brain tissueFirst,for the processed microarray data,the co-expressed gene modules were identified by an unsupervised learning "attractor" algorithm in AD and normal brain,respectively.After several iterations,three co-expressed genes module were obtained from the control group and five co-expressed genes module were obtained from Alzheimer's group.Within the set threshold range,the first co-expression module includes 513 genes,the second module includes 1771 genes,and the third module includes 205 genes in the normal group.In Alzheimer's group the five co-expression modules obtained contain 327,1467,246,43 and 21 genes,respectively.In the process of attractor identification,the meta-genes in two pairs of modules that were negatively correlated with each other were found in normal and AD group,respectively.Gene members in co-expressed modules obtained by attractor algorithm are highly co-expressed between each other and functionally synergic in cell physiology.The DAVID tool was used for the functional analysis of the genes in co-expressed modules.The result indicated the functions of the gene members of the modules were closely associated with the neurological function and the dynamic of the genes may reflect the changes in neurological function.Part ?:Identifying of modules with similar functions and analysis of their expression pattern in the brain tissues in normal samples and Alzheimer's samplesFirst of all,the functional similarity between the modules in AD and normal group was calculated by pairwise comparison method.According to the functional similarity calculated between the modules in the two groups,the similar modules were matched.The similarity between the first module of the Alzheimer's group and the first one in normal control group is 0.684,the similarity between the second module of the Alzheimer's group and the second in normal control group is 0.567,the similarity between the third module of the Alzheimer's group and the third in normal control group is 0.51.The similarity between three pairs of modules above is higher than that between them and other modules.Therefore,the first,second and third module in Alzheimer's group corresponds to the first,second and third module in the normal control group,respectively.The common genes in the matched modules were extracted.There were 255 genes shared in the first pair modules,and 1057 genes shared in the second pair modules and 202genes shared in the third pair modules.The common functions of the genes in the first pair modules include protein binding,biological control,cell process control and the negative regulation of the cell process,and so on.The common functions of the genes in the second pair modules involved in synapses,synaptic transmission,neuronal map,mitochondria,nerve impulse transfer,ion transport,protein combination,oxidative phosphorylation,and some signaling pathways such as Huntington disease,calcium signaling pathway,Alzheimer's signaling pathway,axon guidance and Parkinson's disease(PD)signaling pathway.Most of the genes in the second pair of similar modules have typical neurological features.Next,expression patterns of those genes in functionally similar modules were analyzed in brain tissue of the normal samples with age over 60 years old and Alzheimer's group.The polynomial regression method was used to analyze the relationship between age and expression level of the genes shared in similar modules matched.After filtering by statistical significance(p<0.05)and adjusted R2,the age-related genes were obtained.The results showed that the distribution of age-related genes in three modules varied widely in different tissues,and this indicated the susceptibility of genes to age is not the same indifferent tissues.In the same tissue,the distribution of the gene in Alzheimer's group also has many differences,compared with normal control group.Only Quantitatively,Alzheimer's disease affects both the expression of genes in every tissue.In addition,according to changes in the number of genes from the same tissue,the remarkable changes were in the post-central gyrus and hippocampal tissue.Many age-related genes were identified in the post-central gyrus and hippocampal tissue in the normal group,while only few genes in the post-central gyrus and hippocampal tissue in the AD group.But in AD group,there were many age-related genes in the entorhinal cortex.These indicated that the genes in different modules were affected differentially in different tissues.The number and expressed change of those genes could influence the functions of the brain and may be associated with AD by direct or indirect ways.In normal hippocampus tissue,the age-related genes in the first module were correlated nonlinearly with age,and the expression levels of these genes were down-regulated with age,while in the second module,the expression of age-related gene was showed to an increasing trend with age increasing.Expression of synapse-related genes and mitochondrial-related genes showed consistent trends.This indicated that the nervous system function-related genes and mitochondrion-related gene have a close relationship.The trend of the age-related genes of the two gene modules in normal hippocampus was just the opposite.It can be observed that the expression of age-related genes in the two modules was negatively correlated in the two tissues.In the normal post-central gyrus,the expression level of age-related genes in the module A increased with age,and the age-related genes in the module B were negatively correlated with age.Their expression is non-linear.In entorhinal cortex in Alzheimer's disease group,the expression of age-related genes in two modules showed a linear relationship with age,and their trends were just opposite.The analysis revealed that there were the highest numbers of age-related genes in the normal post-central gyrus and hippocampus.This indicated that functional changes of both organizations most likely reflect the aging process of the brain.However,the study found that,the changes on the number of age-related gene also were the most significant in the two tissues due to the impact of Alzheimer's disease.This indicated that the functions of the two tissues were most severely damaged by Alzheimer's disease.Altered expression patterns of age-related gene in hippocampus and post-central gyrus between Alzheimer's group and normal group reflected that the normal aging process of these two tissues was interfered and disturbed by Alzheimer's disease.Part ?:Inference of the regulatory network of age-related gene in the hippocampal tissue and the post-central gyrus and construction and analysis of protein interaction network of aged-related genes in the entorhinal corticalIn order to compare the regulatory changes among age-related genes in the hippocampus and the post-central gyrus between normal group and Alzheimer's disease group,LICORN learning algorithm was used for inference of regulatory networks among age-related gene in same tissue in two groups,respectively.We have identified some transcriptional regulators and the regulated relationship between the transcriptional regulators and their potential targets.Meanwhile,the co-regulation network among the identified regulators were constructed and analyzed.Comparison of the regulators and co-regulated relationship in the post-central gyrus and the hippocampus between AD and normal group showed that the changes in the regulators and co-regulated relationship may be associated with AD pathology.In addition,three regulators such as TFEB,TCF12 and PTMA were conservative in the two groups.Finally,the protein-protein interactive network among age-related genes in the entorhinal cortex in AD group was constructed to identify the dynamic modules and the key molecules.After network analysis,11 key genes were identified that reflected the progress and severity of Alzheimer's disease.A few genes of them may become therapeutic targets of Alzheimer's disease. |
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