E-Locus - Ιδρυματικό Καταθετήριο Πανεπιστημίου Κρήτης - Study of gene expression regulation with spatial segregation and weak ties models

Αρχική Study of gene expression regulation with spatial segregation and weak ties models

Αποτελέσματα - Λεπτομέρειες

[Προσθήκη στο καλάθι]

Κωδικός Πόρου

000467303

Τίτλος

Study of gene expression regulation with spatial segregation and weak ties models

Άλλος τίτλος

Μελέτη της ρύθμισης της γονιδιακής έκφρασης με χωροταξικά μοντέλα διαχωρισμού και ασθενούς σύνδεσης

Συγγραφέας

Μαυρόπουλος Παπούδας, Στυλιανός Ε.

Σύμβουλος διατριβής

Σπηλιανάκης, Χαράλαμπος

Μέλος κριτικής επιτροπής

Νικολάου, Χριστόφορος
Κόλλιας, Γεώργιος
Ηλιόπουλος, Ιωάννης
Παυλίδης, Παύλος
Τσαμαρδινός, Ιωάννης
Ντίνη, Ευγενία

Περίληψη

Genes located close to each other in the linear genome often participate in common regulatory programs. This work proposes a novel approach for the study of gene expression, incorporating positional information and integrating it with functional analysis in positional- functional enrichment networks. Areas in the genome that share common expression patterns (Domains of Focal Deregulation, DFDs) are identified along with the functional enrichments of the genes located therein. This topological and functional information is combined via structures from graph theory, topological-functional bipartite networks, containing both functional and positional information. In the first part of this work, this methodology is applied to full transcriptome RNASeq data from prolonged Tnf exposure to mouse synovial fibroblasts with samples taken at 1, 3, 6 and 24 hours and 7 days along with controls. Our analysis uncovers two distinct transition phases, an early transition at 1→ 3 hrs and a late transition at 6→ 24 hrs. Early on there appears to be an inflammatory response, later converted to enrichments related to cell adhesion and developmental functions. Bipartite networks pinpoint the observed effects to specific regions in the genome. In the second part we refined and applied this method on a larger, published dataset, generalizing the core concepts to be applicable with minimal modification on various RNASeq data. The experiments were divided in the original publication into four major cell types. We attempted to classify the samples into their cell type using input from our genome segmentation, to highlight the biological significance and show that the DFDs produced by segmentation are characteristic to the system in question. Our pipeline is divided in distinct modules, allowing users to deploy the code on their own data. All the modules form a bioinformatics toolkit, called DFDgeneration, which is available on GitHub (https://github.com/stmavropoulospapoudas/DFDgeneration)

Φυσική περιγραφή

116 σ. : πίν., σχήμ., εικ. (μερ. εγχρ.) ; 30 εκ.

Γλώσσα

Αγγλικά

Θέμα

Domains of focal deregulation

Functional analysis

Positional analysis

Tnf

Topological-functional bipartite networks

Λειτουργική ανάλυση

Περιοχές εστιακής απορρύθμισης