000007906 001__ 7906
000007906 005__ 20240124114253.0
000007906 0247_ $$2DOI$$a10.6083/bc386j87q
000007906 037__ $$aETD
000007906 245__ $$aIterative graph perturbation to identify high impact nodes with application to genetic regulation of onset of puberty
000007906 260__ $$bOregon Health and Science University
000007906 269__ $$a2020-04-27
000007906 336__ $$aDissertation
000007906 502__ $$bPh.D.
000007906 520__ $$aComplex networks that connect hundreds or thousands of nodes together can function properly through the use of nodes interacting, affecting and regulating one another. Genetic networks underlying high-level hormonal changes are also believed to be complex and most of the time are not yet very well understood. There are also different networks with common genes that start to activate or deactivate at the same time, which also adds to the difficulty of the problem of understanding genetic networks. Therefore, finding genes transcriptionally active in a gene set that are responsible for a change in the human body is a key point in reaching the underlying network structure. Here, we present a new technique that searches for these nodes in a set of variables that connect to form a network. It is a stepwise greedy search that investigates the change in a chosen network when one node is taken out at a time. Our simulated genetic data results show that our method is successful for differentiating between transcriptionally active nodes and background nodes with a p-value of less than 0.05. As real biological data, we used rat RNA-seq data taken for initiation-of-puberty research. Our method found new genes as well as confirming previously known genes with significant enrichment results taking charge in functions such as transcriptional binding, histone modifications, and reproductive development.
000007906 542__ $$fIn copyright - single owner
000007906 650__ $$aGene Regulatory Networks$$037326
000007906 650__ $$aPuberty$$024878
000007906 6531_ $$apartial correlation networks
000007906 691__ $$aSchool of Medicine$$041369
000007906 692__ $$aDepartment of Computer Science and Engineering$$041405
000007906 7001_ $$aSelcuk, Basak
000007906 8564_ $$9ea9e9bb9-391c-4f42-b1c4-1d6032e0d483$$s2404110$$uhttps://digitalcollections.ohsu.edu/record/7906/files/Selcuk.Basak.2020.pdf
000007906 905__ $$a/rest/prod/bc/38/6j/87/bc386j87q
000007906 909CO $$ooai:digitalcollections.ohsu.edu:7906$$pstudent-work
000007906 980__ $$aTheses and Dissertations