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| Identifier |
000448841 |
| Title |
An extensive analysis on the linear gene clustering in Saccharomyces cerevisiae |
| Alternative Title |
Μια εκτενής ανάλυση της γονιδιακής ομαδοποίησης σε γραμμικό επίπεδο στον Saccharomyces cerevisiae |
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Author
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Σταυροπούλου, Αθανασία
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Thesis advisor
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Νικολάου, Χριστόφορος
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Reviewer
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Ηλιόπουλος, Ιωάννης
Καντεράκης, Αλέξανδρος
Γεωργουλόπουλος, Μιχαήλ
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| Abstract |
Studies from the 2000s have reported on the non-randomness of gene distribution in the
eukaryotic genome. Numerous studies have pointed out the existence of gene clustering in
all major eukaryotic kingdoms, that is thought to enable the co-regulation of functionallyrelated
and often co-expressed genes. In our current work we build on previous results
of our lab (Nikolaou (2018); Tsochatzidou et al. (2017)), in order to study the existence of
an underlying compartmentalized genomic organization in saccharomyces cerevisiae, which
correlates the topological to the functional features of the genes. In order to achieve that,
we have devised an algorithm that evaluates the existence of gene-clustering at the linear
level and can be applied on any genomic categorization. This method works on the basis
of a permutation test strategy, which assesses a) the enrichment of genes in specific chromosomes
and b) the linear intergenic distances between consecutive input genes. Starting
from a subset of genes of a specific type, the algorithm returns a set of delineated at coordinate
level sub-clusters, which enclose genes positioned in greater proximity than expected
by chance on a chromosome. We have applied this approach on a large variety
of publicly available genomic categories, which include transcription factor gene-targets,
gene ontology terms and other partitions related to evolutionary age, conservation level
and transcriptional plasticity. We have detected clustering in almost every category that we
examined. Seemingly, transcriptional regulation, expression variability and conservation
level constrain the organization of the genes at the linear level. We have also found rare
but interesting cases of sparse gene-positioning, regarding genes of a younger evolutionary
age and genes considered integral components of the membrane. In a novel approach, our
pipeline allows for the association of genomic properties through the assessment of overlapping
sub-clusters. We have identified correlated patterns between clusters of genes with
low conservation and high transcriptional plasticity, while also finding that clusters related
to the membranes overlap with such regions, implying a positional bias of such functions
towards the telomeres.
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| Language |
English |
| Subject |
Linear level |
| Issue date |
2022-07-29 |
| Collection
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School/Department--School of Medicine--Department of Medicine--Post-graduate theses
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Type of Work--Post-graduate theses
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| Permanent Link |
https://elocus.lib.uoc.gr//dlib/6/f/d/metadata-dlib-1654670589-520016-24591.tkl
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| Views |
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