| Summary: | Thesis (MSc)--Stellenbosch University, 2014. === ENGLISH ABSTRACT: This thesis involved the development and application of network approaches
for the construction, analysis and visualization of phylogenomic and transcriptomic
networks.
A co-evolutionary network model of grapevine genes was constructed based
on three mechanisms of evolution. The investigation of local neighbourhoods
of this network revealed groups of functionally related genes, illustrating that
the multi-mechanism evolutionary model was identifying groups of potentially
co-evolving genes.
An extended network definition, namely 3-way networks, was investigated,
in which edges model relationships between triplets of objects. Strategies for
weighting and pruning these 3-way networks were developed and applied to
a phylogenomic dataset of 211 bacterial genomes. These 3-way bacterial networks
were compared to standard 2-way network models constructed from the
same dataset. The 3-way networks modelled more complex relationships and
revealed relationships which were missed by the two-way network models.
Network meta-modelling was explored in which global network and node-bynode
network comparison techniques were applied in order to investigate the
effect of the similarity metric chosen on the topology of multiple types of
networks, including transcriptomic and phylogenomic networks. Two new network
comparison techniques were developed, namely PCA of Topology Profiles
and Cross-Network Topological Overlap. PCA of Topology Profiles compares networks based on a selection of network topology indices, whereas Cross-
Network Topological Overlap compares two networks on a node-by-node level,
identifying nodes in two networks with similar neighbourhood topology and
thus highlighting areas of the networks with conflicting topologies. These network
comparison methods clearly indicated how the similarity metric chosen
to weight the edges of the network influences the resulting network topology,
consequently influencing the biological interpretation of the networks. === AFRIKAANSE OPSOMMING: Hierdie tesis hou verband met die ontwikkeling en toepassing van netwerk
benaderings vir die konstruksie, analise en visualisering van filogenomiese en
transkriptomiese netwerke.
'n Mede-evolusionêre netwerk model van wingerdstok gene is gebou, gebaseerd
op drie meganismes van evolusie. Die ondersoek van plaaslike omgewings van
die netwerk het groepe funksioneel verwante gene aan die lig gebring, wat
daarop dui dat die multi-meganisme evolusionêre model groepe van potensieele
mede-evolusieerende gene identifiseer.
'n Uitgebreide netwerk definisie, naamliks 3-gang netwerke, is ondersoek, waarin
lyne die verhoudings tussen drieling voorwerpe voorstel. Strategieë vir weeg en
snoei van hierdie 3-gang netwerke was ontwikkel en op 'n filogenomiese datastel
van 211 bakteriële genome toegepas. Hierdie 3-gang bakteriële netwerke is met
die standaard 2-gang netwerk modelle wat saamgestel is uit dieselfde datastel
vergelyk. Die 3-gang netwerke het meer komplekse verhoudings gemodelleer
en het verhoudings openbaar wat deur die tweerigting-netwerk modelle gemis
is.
Verder is netwerk meta-modellering ondersoek waarby globalle netwerk en
punt-vir-punt netwerk vergelykings tegnieke toegepas is, met die doel om die
effek van die ooreenkoms-maatstaf wat gekies is op die topologie van verskeie
tipes netwerke, insluitend transcriptomic en filogenomiese netwerke, te bepaal. Twee nuwe netwerk-vergelyking tegnieke is ontwikkel, naamlik "PCA of Topology
Profiles" en"Cross-Network Topological Overlap". PCA van Topologie
Profiele vergelyk netwerke gebaseer op 'n seleksie van netwerk topologie indekse,
terwyl Cross-netwerk Topologiese Oorvleuel vergelyk twee netwerke op
'n punt-vir-punt vlak, en identifiseer punte in twee netwerke met soortgelyke
lokale topologie en dus lê klem op gebiede van die netwerke met botsende
topologieë. Hierdie netwerk-vergelyking metodes dui duidelik aan hoe die ooreenkoms
maatstaf wat gekies is om die lyne van die netwerk gewig te gee, die
gevolglike netwerk topologie beïnvloed, wat weer die biologiese interpretasie
van die netwerke kan beïnvloed.
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