Global Gene Regulation MCQ

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• 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?
  ক

  Xi = \(\frac{Log (E_i/R_i)}{\sqrt{\sum_{j=1,N} Log_{z-2} (E_j/R_j)}}\)

  খ

  Xj = \(\frac{Log (E_j/R_i)}{\sqrt{\sum_{j=1,N} Log_z (E_j/R_j)}}\)

  গ

  Xi = \(\frac{Log (E_i/R_i)}{\sqrt{\sum_{j=1,(N-1)} Log_z (E_j/R_j)}}\)

  ঘ

  Xi = \(\frac{Log (E_i/R_i)}{\sqrt{\sum_{j=1,N} Log_z (E_j/R_j)}}\)
• SVMs (Support vector machines) are a binary classification method to discriminate one set of data points from another.
  ক

  True

  খ

  False
• In Self-organizing maps a choice is made of a number of clusters by which to organize the data.
  ক

  True

  খ

  False
• The hierarchical clustering method generates a similarity score 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.
  ক

  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. ] True

  খ

  S(X,Y)

  গ

  S(X,Y)

  ঘ

  S(X,Y)
• In cluster analysis of microarray data– For n genes, the process is repeated ________ times until a single element remains.
  ক

  n2

  খ

  n

  গ

  n-1

  ঘ

  n-4
• 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.
  ক

  lowest, frequency

  খ

  average, sequence

  গ

  lowest, number

  ঘ

  highest, number
• 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?
  ক

  S(X,Y) = \(\frac{1}{N-2}\) ∑i=1,N . (Xi – Xoffset) (Yi + Yoffset)/ϕxQY

  খ

  S(X,Y) = \(\frac{1}{N}\) ∑i=1,N . (Xi – Xoffset) (Yi – Yoffset)/ϕxQY

  গ

  S(X,Y) = \(\frac{1}{N-1}\) ∑i=1,N . (Xi + Xoffset) (Yi + Yoffset)/ϕxQY

  ঘ

  S(X,Y) = \(\frac{1}{N}\) ∑i=1,N+2 . (Xi + Xoffset) (Yi – Yoffset)/ϕxQY
• Which of the given statements is incorrect about Microarray Analysis?
  ক

  It is designed to detect global changes in transcription in a genome

  খ

  It provides information about the levels of protein products of the genes

  গ

  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

  ঘ

  Labeled protein samples may also be extracted from treated cells and separated by two-dimensional gel electrophoresis
• 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.
  ক

  True

  খ

  False
• Which of the given statements is incorrect about Microarray (or microchip) analysis?
  ক

  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

  খ

  The oligonucleotide sequences cannot be synthesized directly on the slide

  গ

  The oligonucleotides are collectively hybridized to a labeled cDNA library prepared by reverse-transcribing mRNA from cells

  ঘ

  The amount of label binding to each oligonucleotide spot reflects the amount of mRNA in the cell
• Which of the given statements is incorrect about global gene regulation?
  ক

  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

  খ

  Sets of a gene whose expression rises and falls under the same condition are likely to have a related function

  গ

  Sets of a gene whose expression rises and falls under the same condition are likely to have dissimilar functions

  ঘ

  Cell cycle is a developmental phase, or a response to the environment