Πλοήγηση ανά Συγγραφέας "Atsalaki, Xanthoula"

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    Pathway analysis for ChIP-seq data.
    (Τ.Ε.Ι. Κρήτης, Σχολή Τεχνολογικών Εφαρμογών (Σ.Τ.Εφ), ΠΜΣ Πληροφορική και Πολυμέσα, 2018-01-22) Atsalaki, Xanthoula; Ατσαλάκη, Ξανθούλα
    With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements and the interactions among them through different phenotypes. Epigenetics is a field of biology that studies these interactions. On one hand, an important issue in deciphering the epigenetic code is whether two given histone modifications, transcription factors or chromatin modifiers are co-enriched on the same locus [1]. To resolve these issues, ChIP-seq has been developed, where one protein is immunoprecipitated from a chromatin sample, and a second protein is subsequently immunoprecipitated from chromatin eluted from the first ChIP [1]. On the other hand, analysis of GRN can help in identifying important or core regulatory genes (TFs and miRNAs) that play significant role in controlling the specificity of gene expression during a biological process [2]. These two keys, can unravel the mystery behind diseases and their treatment, and can be a powerful tool when combined in software tools in the hands of biologists. The objective of the thesis is to explore the effect of ChIP-seq data, coming from specific proteins under specific conditions, in functional sub-pathways for specific phenotype. A Shiny application combined with R programming language was developed for the download and analysis of ChIP-seq data from the ENCODE Experiment ChIP-seq Matrix and the extended version of the open source pathway analysis tool MinePath was used for the identification and visualization of functional sub-pathways.