Using Systems Biology to understand Immunosenescen
  • Using Systems Biology to Understand Immunosenescence
  • Background
    • Introduction
    • 1.1. Aging in Society and in the Individual
    • 1.2. Aging and its Molecular Mechanisms
    • 1.3.The Remodeling of the Immune System: Immunosenescence
    • 1.4. Changes in the Immune System Related to Immunosenescence
    • 1.5 Chronic Inflammation During Aging: Inflammaging
    • 1.6 The Immune Risk Phenotype (IRP)
    • 1.6. Systems Biology
  • Objectives
  • Methods
    • Overall Methodology
    • 3.1 Survey of Studies
    • 3.2. Reannotation of Probes in Microarrays
    • 3.3. Data acquisition and pre-processing
    • 3.4. Creation of age-representative samples: AgeCollapsed
    • 3.5. Detection of Highly Age-Related Transcripts: AgingGenes
    • 3.6. Lifetime Co-Expressed Transcript Analysis: AgingNet
    • 3.7. Detection of Change Points in Age-Related Modules
  • Results
    • 4.1. Survey and Data Acquisition
    • 4.2. Reannotation of Platforms
    • 4.3. AgeCollapsed Pre-Processing and Creation
    • 4.4. Assessment of the Agreement of the Relationships of Transcripts with Age between the Sexes
    • 4.5. AgingGenes and AgingNet Reviews
    • 4.6 Aging Co-Expression Network: AgingNet
  • Discussion
    • Main Regards
    • AgingGenes
    • Análise de Co-Expressão: AgingNet
  • Conclusions
    • Final Regards
  • Citations
    • References
  • Appendix
    • Supplementary Files
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  1. Results

4.3. AgeCollapsed Pre-Processing and Creation

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After pre-processing and quality control, 1807 samples aged between 15 and 96 years remained, most of them concentrated among young people and adults (Figure 4.4). These samples were used to build the ageCollapsed dataset (as described in Section 3.4 of the Methodology). ageCollapsed consists of a combination of all studies in a new dataset, representing the expression value of the transcripts for each age. Thus, we obtain an expression matrix where the transcripts common to all platforms (8348) are represented by the lines and the ages by the columns, with a total of 82 columns, each one representing an age between 15 and 96 years (with except age 95).

Figura 4.4. Representação da Distribuição e Representatividade das Idades. (A) Histograma das idades de todas as amostras. (B) Gráfico ilustrando a representatividade de cada idade pelas amostras encontradas em todos os estudos.