Differential gene expression and apoptosis are key processes in development beca

Question

Differential gene expression and apoptosis are key processes in development because they _____.

have provided theories as to how cells specialize and proliferate have provided hypotheses on mechanisms in which gene activation controls cell death and apoptosis promotes cell division provide a plausible explanation as to how controlled DNA replication controls cell death in a regulated fashion offer an explanation as to how transcription controls development and how loss of specific cells can facilitate formation of mature organs

Explanation / Answer

Whether you’re comparing disease to normal tissue, tumor samples with and without drug treatment, cultured cells before and after exposure to environmental stimuli, or any number of other experimental conditions, measured changes in the pattern of gene expression between experimental and control samples can provide a view into what is happening in the cell. But how do you make sense of the data, translating measured expression values into evidence for the biological mechanism at work? There are two ways to approach analysis of differential gene expression: through traditional downstream analysis approaches and through the more recently described upstream analysis approach. Since 2008, BIOBASE has been spreading the word about the added value offered by upstream analysis compared to traditional downstream analysis alone, but why is upstream analysis so important? Traditional downstream analysis looks at enrichment of functional categories within differentially expressed gene sets—categories that include Gene Ontology’s molecule function, biological process and cellular component, disease-associated genes, biomarkers and therapeutic targets, and signaling pathways. Further methods search for network modules or cluster co-regulated genes over a time course. Downstream methods rely solely on the subset of genes that are differentially expressed—genes that provide evidence of the effect, much like ripples in a lake provide evidence of the effect of the stone that penetrated the surface—but which do not themselves necessarily identify the cause of the differential gene expression. What if the causal molecule, the stone, is not differentially expressed? What if, for example, increased activity of a growth factor sets off a signaling cascade, but the gene expression of the growth factor itself, or of components of its pathway, do not change? In such situations the causal signal can be completely lost when looking at differentially expressed genes only. Click Image To Enlarge + . ExPlain identifies downstream effects and upstream causes of differential gene expression. Upstream analysis, on the other hand, does not assume that causal molecules should undergo expression changes and finds the cause by applying biological principles. Upstream analysis uses the promoter sequences of upregulated genes to identify the pattern of transcription factors that are most likely to be responsible for the coordinated experimental observations. Once the unique set of responsible transcription factors has been identified, the entire network of signaling reactions is used to reveal causative upstream key nodes that have activated the important transcription factors (Apoptosis (play /?æp?'to?s?s/) is the process of programmed cell death (PCD) that may occur in multicellular organisms.Biochemical events lead to characteristic cell changes (morphology) and death. These changes include blebbing, cell shrinkage, nuclear fragmentation, chromatin condensation, and chromosomal DNA fragmentation. (See also apoptotic DNA fragmentation.) In contrast to necrosis, which is a form of traumatic cell death that results from acute cellular injury, apoptosis, in general, confers advantages during an organism's life cycle. For example, the differentiation of fingers and toes in a developing human embryo occurs because cells between the fingers apoptose; the result is that the digits are separate. Unlike necrosis, apoptosis produces cell fragments called apoptotic bodies that phagocytic cells are able to engulf and quickly remove before the contents of the cell can spill out onto surrounding cells and cause damage. Between 50 and 70 billion cells die each day due to apoptosis in the average human adult. For an average child between the ages of 8 and 14, approximately 20 billion to 30 billion cells die a day. Research in and around apoptosis has increased substantially since the early 1990s. In addition to its importance as a biological phenomenon, defective apoptotic processes have been implicated in an extensive variety of diseases. Excessive apoptosis causes atrophy, whereas an insufficient amount results in uncontrolled cell proliferation, such as cancer.

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