Nonparametric methods for analyzing replication origins in genomewide data.

Debashis Ghosh

doi:10.1007/s10142-004-0122-1

Home/Archive/PubMed

PubMed · 15599787

Nonparametric methods for analyzing replication origins in genomewide data.

Debashis Ghosh

View original source ↗Export metadata ↓

Abstract

Due to the advent of high-throughput genomic technology, it has become possible to monitor cellular activities on a genomewide basis. With these new methods, scientists can begin to address important biological questions. One such question involves the identification of replication origins, which are regions in the chromosomes where DNA replication is initiated. One hypothesis is that their locations are nonrandom throughout the genome. In this article, we analyze data from a recent yeast study in which candidate replication origins were profiled using cDNA microarrays to test this hypothesis. We find no evidence for such clustering.

Explore related subjects

DNA, Complementary Genome Oligonucleotide Array Sequence Analysis Replication Origin Statistics, Nonparametric Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Debashis Ghosh. 2004-09-09. Nonparametric methods for analyzing replication origins in genomewide data.. https://doi.org/10.1007/s10142-004-0122-1

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2006

Identification of genes differentially expressed during ripening of banana.

The banana (Musa acuminata, subgroup Cavendish 'Grand Nain') is a climacteric fruit of economic importance. A better understanding of the banana ripening process is needed to improve fruit quality and to extend shelf life. Eighty-four up-regulated unigenes were identified by differential screening of a banana fruit cDNA subtraction library at a late ripening stage. The ripening stages in this study were defined according to the peel color index (PCI). Unigene sequences were analyzed with different databases to assign a putative identification. The expression patterns of 36 transcripts confirmed as positive by differential screening were analyzed comparing the PCI 1, PCI 5 and PCI 7 ripening stages. Expression profiles were obtained for unigenes annotated as orcinol O-methyltransferase, putative alcohol dehydrogenase, ubiquitin-protein ligase, chorismate mutase and two unigenes with non-significant matches with any reported sequence. Similar expression profiles were observed in banana pulp and peel. Our results show differential expression of a group of genes involved in processes associated with fruit ripening, such as stress, detoxification, cytoskeleton and biosynthesis of volatile compounds. Some of the identified genes had not been characterized in banana fruit. Besides providing an overview of gene expression programs and metabolic pathways at late stages of banana fruit ripening, this study contributes to increasing the information available on banana fruit ESTs.

DNA, Complementary↗

PubMed2006

Gene expression analysis of primary normal human hepatocytes infected with human hepatitis B virus.

AIM: To find the relationship between hepatitis B virus (HBV) and hepatocytes during the initial state of infection by cDNA microarray. METHODS: Primary normal human hepatocytes (PNHHs) were isolated and infected with HBV. From the PNHHs, RNA was isolated and inverted into complement DNA (cDNA) with Cy3- or Cy5- labeled dUTP for microarray analysis. The labeled cDNA was hybridized with microarray chip, including 4224 cDNAs. From the image of the microarray, expression profiles were produced and some of them were confirmed by RT-PCR, immunoblot analysis, and NF-kappaB luciferase reporter assay. RESULTS: From the cDNA microarray, we obtained 98 differentially regulated genes. Of the 98 genes, 53 were up regulated and 45 down regulated. Interestingly, in the up regulated genes, we found the TNF signaling pathway-related genes: LT-alpha, TRAF2, and NIK. By using RT-PCR, we confirmed the up-regulation of these genes in HepG2, Huh7, and Chang liver cells, which were transfected with pHBV1.2x, a plasmid encoding all HBV messages. Moreover, these three genes participated in HBV-mediated NF-kappaB activation. CONCLUSION: During the initial state of HBV infection, hepatocytes facilitate the activation of NF-kappaB through up regulation of LT-alpha, TRAF2, and NIK.

DNA, Complementary↗

PubMed2006

EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6,000 genes from a basal eudicot.

The Floral Genome Project (FGP) selected California poppy (Eschscholzia californica Cham. ssp. Californica) to help identify new florally-expressed genes related to floral diversity in basal eudicots. A large, non-normalized cDNA library was constructed from premeiotic and meiotic floral buds and sequenced to generate a database of 9,079 high quality Expressed Sequence Tags (ESTs). These sequences clustered into 5,713 unigenes, including 1,414 contigs and 4,299 singletons. Homologs of genes regulating many aspects of flower development were identified, including those for organ identity and development, cell and tissue differentiation, cell cycle control, and secondary metabolism. Over 5% of the transcriptome consisted of homologs to known floral gene families. Most are the first representatives of their respective gene families in basal eudicots and their conservation suggests they are important for floral development and/or function. App. 10% of the transcripts encoded transcription factors and other regulatory genes, including nine genes from the seven major lineages of the important MADS-box family of developmental regulators. Homologs of alkaloid pathway genes were also recovered, providing opportunities to explore adaptive evolution in secondary products. Furthermore, comparison of the poppy ESTs with the Arabidopsis genome provided support for putative Arabidopsis genes that previously lacked annotation. Finally, over 1,800 unique sequences had no observable homology in the public databases. The California poppy EST database and library will help bridge our understanding of flower initiation and development among higher eudicot and monocot model plants and provide new opportunities for comparative analysis of gene families across angiosperm species.

DNA, Complementary↗