This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Global Gene Regulation”.
1. Which of the given statements is incorrect about global gene regulation?
a) One way to obtain useful information about a genome is to determine which genes are induced or repressed in response to a phase of the cell cycle
b) Sets of a gene whose expression rises and falls under the same condition are likely to have a related function
c) Sets of a gene whose expression rises and falls under the same condition are likely to have dissimilar functions
d) Cell cycle is a developmental phase, or a response to the environment
Explanation: In addition, a pattern of gene expression may also be an indicator of abnormal cellular regulation and is a useful tool in cancer diagnosis. Because genomes, especially eukaryotic genomes, are so large, a new technology has been developed for studying the regulation of thousands of genes on a microscope slide.
2. Which of the given statements is incorrect about Microarray (or microchip) analysis?
a) It is a new technology in which all of the genes of an organism are represented by oligonucleotide sequences spread out in an 80 x 80 array on microscope slides
b) The oligonucleotide sequences cannot be synthesized directly on the slide
c) The oligonucleotides are collectively hybridized to a labeled cDNA library prepared by reverse-transcribing mRNA from cells
d) The amount of label binding to each oligonucleotide spot reflects the amount of mRNA in the cell
Explanation: The oligonucleotide sequences can also be synthesized directly on the slide at densities of up to one million per square centimeter. Genes that are responding the same way to an environmental signal, in this case the addition of serum to serum-starved skin cells are clustered together in a display. From this analysis, a set of genes that responds in an identical manner may be identified.
3. Once a set of genes that are co-regulated has been found, the promoter regions of these genes may be analyzed for conserved patterns that represent sites of interaction with specific transcription factors.
Explanation: Automatic methods for clustering related sets of genes have been devised. The first of these methods, hierarchical clustering, is commonly used, but the other two methods are better designed to detect differences in patterns over a set of time points or samples.
4. Which of the given statements is incorrect about Microarray Analysis?
a) It is designed to detect global changes in transcription in a genome
b) It provides information about the levels of protein products of the genes
c) The proteins are first separated in a column on the basis of size and then across a second dimension on a slab on the basis of charge
d) Labeled protein samples may also be extracted from treated cells and separated by two-dimensional gel electrophoresis
Explanation: Microarray analysis is designed to detect global changes in transcription in a genome but does not provide information about the levels of protein products of the genes, which may also be subject to translational regulation. This method also can resolve thousands of proteins based on size and charge. There are databases of the patterns found in different organisms.
5. In cluster analysis of microarray data– If Xi is the log odds value for gene X at time i, then for two genes X and Y and N observations, a similarity score is calculated. S(X,Y) is also known as the Pearson correlation coefficent. Xoffset and Yoffset can be the mean of the observations on X or Y, respectively, in which case is the standard deviation, or else Xoffset and Yoffset can be set to zero when a reference state is used.Which of the following best represents it?
Explanation: After values of S(X,Y) have been calculated for all gene combinations, the most closely related pairs are identified in an above-diagonal scoring matrix. The object of clustering is to identify genes that respond the same way to the environmental treatment. Each gene is compared to every other gene and a gene similarity score (metric) is produced.
6. In cluster analysis of microarray data– A node is created between the _____ scoring pair, and the gene expressed profiles of these two genes are averaged and the joined elements are weighted by the _____ of elements they contain.
a) lowest, frequency
b) average, sequence
c) lowest, number
d) highest, number
Explanation: The node is created as mentioned. The matrix is then updated replacing the two joined elements by the node.
7. In cluster analysis of microarray data– For n genes, the process is repeated ____ times until a single element remains.
Explanation: This number of iterations gives the best results. In the final dendrogram, the order of genes within a cluster is determined by simple weighting schemes, e.g., average dendrogram level.
8. The hierarchical clustering method generates a similarity score [S(X,Y)] for all gene combinations, places the scores in a matrix, joins those genes that have the highest score, and then continues to join progressively less similar pairs.
Explanation: The disadvantage of this method is that it fails to discriminate between different patterns of variation. For example, a gene expression pattern for which a high value is found at an intermediate time point will be clustered with another for which a high value is found at a late time point in the experiment. These variations have to be separated in a subsequent step.
9. In Self-organizing maps a choice is made of a number of clusters by which to organize the data.
Explanation: The object is to move each node to the center of a cluster of data points. At each iteration a data point P is selected, and the node closest to that point is identified.
10. SVMs (Support vector machines) are a binary classification method to discriminate one set of data points from another
Explanation: They are similar to the types of discriminant analyses. For microarray analysis, sets of genes are identified that represent a target pattern of gene expression.
11. In SVMs (Support vector machines) Data points are log-transformed and normalized as in method A, where for N observations of a gene i, the log transform Xi of the expression level Ei and reference level Ri is _____
Explanation: SVMs were used to categorize genes based on 79 different sets of data points from studies of the yeast cell cycle and are particularly useful for such complex data sets. Gene combinations averaged over all experimental conditions are then examined by a multidimensional analysis.
Sanfoundry Global Education & Learning Series – Bioinformatics.
To practice all areas of Bioinformatics, here is complete set of 1000+ Multiple Choice Questions and Answers.