Ashwani Kumar and Tiratha Raj Singh*

Slides:



Advertisements
Similar presentations
TCGA(The cancer genome atlas) catalogue genetic mutations responsible for cancer, using genome sequencing and bioinformatics The TCGA is sequencing the.
Advertisements

Microarrays Dr Peter Smooker,
By Russell Armstrong Supervisor Mrs Wei Ji Diagnosis Analysis of Lung Cancer by Genome Expression Profiles.
Microarrays and Cancer Segal et al. CS 466 Saurabh Sinha.
Cluster Analysis Hierarchical and k-means. Expression data Expression data are typically analyzed in matrix form with each row representing a gene and.
Why microarrays in a bioinformatics class? Design of chips Quantitation of signals Integration of the data Extraction of groups of genes with linked expression.
Comprehensive Gene Expression Analysis of Prostate Cancer Reveals Distinct Transcriptional Programs Associated With Metastatic Disease Kevin Paiz-Ramirez.
Systematic Analysis of Interactome: A New Trend in Bioinformatics KOCSEA Technical Symposium 2010 Young-Rae Cho, Ph.D. Assistant Professor Department of.
Introduction The goal of translational bioinformatics is to enable the transformation of increasingly voluminous genomic and biological data into diagnostics.
Supplementary Material Epigenetic histone modifications of human transposable elements: genome defense versus exaptation Ahsan Huda, Leonardo Mariño-Ramírez.
Cancer is heterogeneous disease! -> enabled characterization of new tumor subtypes for improving personalized treatment and ultimately achieving better.
Gene expression analysis
Ranjit Ganta, Raj Acharya, Shruthi Prabhakara Department of Computer Science and Engineering, Penn State University DATA WAREHOUSE FOR BIO-GEO HEALTH CARE.
Differential analysis of Eigengene Networks: Finding And Analyzing Shared Modules Across Multiple Microarray Datasets Peter Langfelder and Steve Horvath.
Pan-cancer analysis of prognostic genes Jordan Anaya Omnes Res, In this study I have used publicly available clinical and.
Case Study: Characterizing Diseased States from Expression/Regulation Data Tuck et al., BMC Bioinformatics, 2006.
Finding genes in the genome
 Cancer  Compound perturbations  Gene perturbations  Tumor development  Cancer metastasis  Cancer treatments Altered Caspase-8 Expression.
miRNA-targets cross-talks: key players in glioblastoma multiforme
1. SELECTION OF THE KEY GENE SET 2. BIOLOGICAL NETWORK SELECTION
Clustering Manpreet S. Katari.
MicroRNA-34a: a key regulator in the hallmarks of renal cell carcinoma
Monica Britton, Ph.D. Sr. Bioinformatics Analyst June 2016 Workshop
Combinatorial impact of SNPs & regulatory RNAs in the aetiology of late onset Alzheimer’s disease The 3’ un‐translated regions (UTRs) of mRNAs being the.
Gene expression.
Global Transcriptional Dysregulation in Breast Cancer
Functional Genomics Analysis Reveals a MYC Signature Associated with a Poor Clinical Prognosis in Liposarcomas  Dat Tran, Kundan Verma, Kristin Ward,
 The human genome contains approximately genes.  At any given moment, each of our cells has some combination of these genes turned on & others.
Nat. Rev. Neurol. doi: /nrneurol
RNA Sequencing Approaches to Identify Novel Biomarkers for Venous Thromboembolism (VTE) in Lung Cancer Tamara A. Sussman MD1, Mohamed Abazeed MD PhD1,
Dynamic epigenetic enhancer signatures reveal key transcription factors associated with monocytic differentiation states by Thu-Hang Pham, Christopher.
A bioinformatic analysis of microRNAs role in osteoarthritis
In Silico Analysis of Transposable Elements Expression in Human Cancer
Rasoul Godini, Hossein Fallahi
Loyola Marymount University
Gene expression analysis
Transcriptional Signature of Histone Deacetylases in Breast cancer
Volume 17, Issue 1, Pages (January 2010)
Lecture 7: Biological Network Crosstalk Y. Z
Transcriptional Landscape of Cardiomyocyte Maturation
Genomic characterization of the inflammatory response initiated by surgical intervention and the effect of perioperative cyclooxygenase 2 blockade  Keith.
Divergent Whole-Genome Methylation Maps of Human and Chimpanzee Brains Reveal Epigenetic Basis of Human Regulatory Evolution  Jia Zeng, Genevieve Konopka,
Integrative Multi-omic Analysis of Human Platelet eQTLs Reveals Alternative Start Site in Mitofusin 2  Lukas M. Simon, Edward S. Chen, Leonard C. Edelstein,
Volume 22, Issue 13, Pages (March 2018)
Volume 63, Issue 4, Pages (August 2016)
Molecular Mechanisms Regulating the Defects in Fragile X Syndrome Neurons Derived from Human Pluripotent Stem Cells  Tomer Halevy, Christian Czech, Nissim.
Microarray Gene Expression Analysis of Fixed Archival Tissue Permits Molecular Classification and Identification of Potential Therapeutic Targets in Diffuse.
Cluster analysis and pathway-based characterization of differentially expressed genes and proteins from integrated proteomics. Cluster analysis and pathway-based.
A systems view of genetics in chronic kidney disease
Genome-wide promoter methylation of hairy cell leukemia
Gene Expression Analysis
Triple‐negative human breast cancers specifically express high levels of nuclear HMGA2, whose expression has clinical relevance and predicts recurrence‐free.
Volume 10, Issue 10, Pages (October 2017)
Samirkumar B. Amin, Roel G.W. Verhaak  Cell Systems 
HER-2/neu mRNA detection by gene expression profiling
Volume 7, Issue 2, Pages (August 2010)
Significant differences in translational efficiencies of DNA damage repair pathway genes between patient clusters. Significant differences in translational.
Loyola Marymount University
Anh Pham Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease.
Altered Caspase-8 Expression
Loyola Marymount University
Figure 1. Identification of three tumour molecular subtypes in CIT and TCGA cohorts. We used CIT multi-omics data ( Figure 1. Identification of.
Loyola Marymount University
CD4+CLA+CD103+ T cells from human blood and skin share a transcriptional profile. CD4+CLA+CD103+ T cells from human blood and skin share a transcriptional.
Whole-genome microarray analysis of gene expression in the livers of control mice and STAM mice subjected to NASH-derived hepatocarcinogenesis. Whole-genome.
Loyola Marymount University
Partial alteration of the Treg gene signature by the p.A384T mutation.
Genome-wide Functional Analysis Reveals Factors Needed at the Transition Steps of Induced Reprogramming  Chao-Shun Yang, Kung-Yen Chang, Tariq M. Rana 
Figure 1 Relationships between genetic variants, quantitative traits and diseases Figure 1 | Relationships between genetic variants, quantitative traits.
Pancreatic adenocarcinoma, chronic pancreatitis, and normal pancreas samples can be distinguished on the basis of gene expression profiling. Pancreatic.
Presentation transcript:

Computational Analysis of Transcription Profiling Gene Expression Data of Alzheimer’s Brain Ashwani Kumar and Tiratha Raj Singh* Department of Biotechnology and Bioinformatics Jaypee University of Information Technology Waknaghat, Solan, H.P *tiratharaj.singh@juit.ac.in Introduction The pathogenesis of incipient Alzheimer’s disease (AD) has been difficult to analyse because of the complexity of AD and the overlap of its early-stage markers with normal aging. Genome-wide transcription profiling is a powerful diagnostic technique applied to disease tissue that may reveal quantitative and qualitative alterations in gene expression, that give information about genetics and pathogenesis of disease. This transcription level analysis could provide essential clues regarding expression of genes associated to AD and further reduce the complexity in understanding the involved mechanism. Methodology START Cluster Heatmap are generated according to Hierarchical gene mapping using uncentered correlation distance and complete linkage algorithm. High expression and low expression gene are shown with varied color. Group the sample according to expression value of genes in samples and then ranked according to adj.P value and logFC value. Compare Two or more sets of samples using GEO2R tool contain different genes using two tailed T-test at significance level of 0.01 Hippocampus Gene Expression Data of 9 control and 22 postmortem subjects with AD at various stage of severity whose series id is GSE1297 taken from GEO. Results Figure 3: Cluster Heat Map for Hierarchial cluster Conclusion It has been observed that the over expression data based on low adj.P value and high log fold change value, there was frequent occurrence of major histocampatibilty complex I and complex II related genes, PSAT1 and FGFR2, etc. while for the under expression genes are RAB25 and ATG5 and few transcription factors were also found. From these studies we can attempt to define therapeutic strategies that would prevent the loss of specific components of neuronal functions. Control Incipient AD Moderate AD Severe AD Figure 1: Gene expression changes with number of counts and percentile rank Table 1: GEO2R result show expression of genes are ranked on basis of adj.P .value and log FC value ID Adj.P.Value Log FC Gene Symbol Gene Expression 211911_x_at 0.0037 1.209915 HLA-B High 220892_S_at 0.00337 1.33895 PSAT1 203639_s_at 1.680364 FGFR2 214953_s_at 0.068 0.511453 APP Medium 203460_s_at 0.109 0.440217 PSEN1 203382_s_at 0.13049 -0.5282 APOE 218186_s_at 0.29694 -0.8267 RAB25 Low 210639_s_at 0.27035 ATG5 References Ricciarelli, Roberta, et al. "Microarray analysis in Alzheimer's disease and normal aging." IUBMB life 56.6 (2004): 349-354. Augustin, Regina, et al. "Bioinformatics identification of modules of transcription factor binding sites in Alzheimer's disease-related genes by in silico promoter analysis and microarrays." International Journal of Alzheimer’s Disease 2011 (2011). Kumar, Ashwani, and Singh, T.R.,” Systems biology approach for gene set enrichment and topological analysis of Alzheimer’s disease pathway.,” BSB, International Conference on. IEEE,2016. Verhaak, Roel GW, et al. ”Integral genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1.” Cancer cell 17.1 (2010): 98.-110. Discussion These studies reveal that widespread change in genomic regulation of genes in multiple pathways are majorly correlated to AD. Transcriptional microarray analysis provide correlation of many genes through cluster heat mapping and profiling. However major coordination seen in AD may provide a new perspective on the possible origins of these harmful processes in various stage of AD pathogenesis. STOP