The Drosophila ovary has proven to be an excellent model system for addressing many key questions in biology. Among these are questions relating to the cell cycle control of DNA replication and chromosome structure during development. Early studies of ovarian chromosome dynamics emplo ...

The genome size of an organism, commonly known as its C value, is defined as the content of DNA (measured by weight or numbers of basepairs) in a single copy of the sequence of DNA found within the cells of an organism (i.e., the amount of DNA in a haploid chromosome set, where 1n=1C) (1). A single sperm of Drosophila melan ...

Polytene chromosomes from the salivary gland cells of Drosophila melanogaster larvae have been the most useful model for studying the functional morphology of interphase eukaryotic chromosomes since their discovery almost 70 yr ago (1). The question remains as to whether the polytene ...

Identification of the transcribed regions in the newly sequenced genomes is one of the major challenges of postgenomic biology. Among different alternatives for empirical transcriptome mapping, whole-genome tiling array experiment emerged as the most comprehensive and unbi ...

A hallmark genomic feature of human brain tumors is the presence of multiple complex structural and numerical chromosomal aberrations that result in altered gene dosages. These genetic alterations lead to widespread, genome-wide gene expression changes. Both gene expression as we ...

We present a detailed method to analyze DNA copy number data generated on cDNA microarrays. A web interface is made available for those steps in the workflow that are not typically used in gene expression analysis so that these steps can be carried out online. The end result of the analysis is a list of p-valu ...

Methods are described to take a list of genes generated from a microarray experiment and interpret these results using various tools and ontologies. A workflow is described that details how to convert gene identifiers with SOURCE and MatchMiner and then use these converted gene lists to sear ...

Astrocytoma is graded as pilocytic (WHO grade I), diffuse (WHO grade II), anaplastic (WHO grade III), and glioblastoma multiforme (WHO grade IV). The progression from low- to high-grade astrocytoma is associated with distinct molecular changes that vary with patient age, yet the prognosis of ...

A tissue microarray (TMA) containing diagnostic biopsies was used to develop predictors of outcome in a group of 105 patients having advanced-stage follicular lymphoma (FL). The patients were staged and uniformly treated, and the usable cases had been randomly divided into a subgroup of 50 p ...

Typical microarray or GeneChip™ experiments now provide genome-wide measurements on gene expression across many conditions. Analysis often focuses on only a few of the genes, looking for those that are “differentially expressed” between conditions or groups of conditions. Howeve ...

DNA microarrays make it possible, for the first time, to record the complete genomic signals that guide the progression of cellular processes. Future discovery in biology and medicine will come from the mathematical modeling of these data, which hold the key to fundamental understanding of l ...

Microarray analysis results in the gathering of massive amounts of information concerning gene expression profiles of different cells and experimental conditions. Analyzing these data can often be a quagmire, with endless discussion as to what the appropriate statistical analy ...

Herein we have set forth a detailed method to analyze microarray data using artificial neural networks (ANN) for the purpose of classification, diagnosis, or prognosis. All aspects of this analysis can be carried out online via a website. The reader is guided through each step of the analysis incl ...

Recent findings of a genome-wide oscillation involving the transcriptome of the budding yeast Saccharomyces cerevisiae suggest that the most promising path to an understanding of the cell as a dynamic system will proceed from carefully designed time-series sampling followed by the d ...

Eukaryotic transcription is a complex process. A myriad of biochemical signals cause activators and repressors to bind specific cis-elements on the promoter DNA, which help to recruit the basal transcription machinery that ultimately initiates transcription. In this chapter, we d ...

DNA (mRNA) microarray, a highly promising technique with a variety of applications, can yield a wealth of data about each sample, well beyond the reach of every individual’s comprehension. A need exists for statistical approaches that reliably eliminate insufficient and uninformative ...

We present a practical guide to some of the issues involved in comparing or integrating different microarray studies. We discuss the influence that various factors have on the agreement between studies, such as different technologies and platforms, statistical analysis criteria, pr ...

Genome-wide measures of gene expression have been used to classify breast tumors into clinically relevant subtypes, as well as provide a better means of risk assessment on an individual basis for lymph node-negative (LNN) breast cancer patients. We have applied Affymetrix GeneChips of 22, ...

Double-stranded RNA (dsRNA) can suppress gene expression by inducing mRNA degradation of the homologous gene, known as RNA interference (RNAi). First, an RNase III-like dsRNA-specific endonuclease, Dicer, cleaves long dsRNA into 21- to 23-nucleotide (nt) small, interfering RNAs (siR ...

Recent work demonstrates that RNA interference (RNAi) helps coordinate the flow of information from transcription to protein expression, complicating tremendously our former understanding of how protein expression is regulated (1,2). Inhibitory RNAs can be expressed natur ...