published_or_final_version / Medical Sciences / Master / Master of Medical Sciences

published_or_final_version / Medical Sciences / Master / Master of Medical Sciences

published_or_final_version / Statistics / Master / Master of Philosophy

published_or_final_version / Pathology / Doctoral / Doctor of Philosophy

No description available.

Motivation: RNA-Sequence or RNA-Seq experiments produce millions of discrete DNA sequence reads, as a measure of gene expression levels. It enable researchers to investigate complex aspects of the genomic studies. These include but not limited to identi cation of di erentially expressed (DE) genes in two or more treatment conditions and detection of novel transcripts. One of the common assumptions of RNA-Seq data is that, all gene counts follow an overdispersed Poisson or negative binomial (NB) distribution which is sometimes misleading because some genes may have stable transcription levels with no overdispersion. Thus, a more realistic assumption in RNA-Seq data is to consider two sets of genes: overdispersed and non-overdispersed. Method: We propose a new two step integrated approach to detect di erentially expressed (DE) genes in RNA-Seq data using standard Poisson model for non-overdispersed genes and NB model for overdispersed genes. This is an integrated approach because this method can be combined with any other NB based methods for detecting DE genes. Results: We evaluate the proposed approach using two simulated and two real RNA-Seq data sets. We compare the performance of our proposed method combined with the four popular R-software packages edgeR, DESeq, sSeq, and NBPSeq with their default settings. For both the simulated and real data sets, integrated approaches perform better or at least equally well compared to the regular methods embedded in these R-packages. / Access to thesis permanently restricted to Ball State community only.

C. cinereus, any two of which are sufficient to promote B-regulated development following cell fusion. The isolation of the B42 locus is described along with the DNA sequence analysis that identified nine B mating type genes within a 27kb B42 -specific DNA sequence. Six of the genes, with small transcripts of 800-900nt, encode the mating pheromone precursors and the other three, with 1.9 to 2-5kb transcripts, encode the transmembrane pheromone receptors. The genes are arranged in three groups, designated group 1, 2 and 3, each consisting of one receptor gene and two pheromone genes. B42 and B6 share the same alleles of the group 1 genes, but not those of groups 2 and 3. This was demonstrated by DNAsequence analysis and Southern blot analysis. None of the group 1 genes from B42 were able to activate B -regulated development in a B6 host when introduced by transformation but with one exception, all genes from group 2 and group 3 were able to do so. This analysis led to the recognition that the three genes in any one group are held together in an allele-specific DNA sequence and that Southern blot analysis and transformation can be used to identify shared alleles in uncloned loci. Extensive Southern analyses using cloned genes to probe genomic DNAs from strains having other B mating specificites showed that different B loci may share identical alleles of two groups of genes. Mating partners thus require different alleles of only one group of genes to generate a compatible B mating interaction. Transformation analyses with the same cloned genes confirmed the conclusions derived from the hybridisation data. Multiple B mating specificities thus appear to be derived from three groups of multiallelic and functionally redundant genes. A tenth gene located within the B42- specific DNA sequence encodes a putative transporter protein belonging to the major facilitator superfamily (MFS). In other genomic backgrounds this gene lies in homologous flanking sequences and its presence within the B42 locus is unlikely to be related to mating type function.

Thesis (Ph. D.)--University of Hawaii at Manoa, 1996. / Includes bibliographical references (leaves 185-196). / Microfiche. / xii, 196 leaves, bound ill. (some col.) 29 cm

Bibliography: leaves 147-165 / iv, 165 leaves, [31] leaves of plates : ill ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Biochemistry, 1986

Thesis (Ph. D.)--University of Adelaide, Dept. of Biochemistry, 1986. / Includes bibliographical references.