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?

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

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

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

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

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

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?

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

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

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

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

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?

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

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

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

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

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

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

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

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

The oligonucleotide sequences cannot be synthesized directly on the slide

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

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?

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

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

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

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

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

16 + Mcqs in Global Gene Regulation in Bioinformatics Page 1 McqOptions

1.	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?
A.	Xi = $\frac{Log (E_i/R_i)}{\sqrt{\sum_{j=1,N} Log_{z-2} (E_j/R_j)}}$
B.	Xj = $\frac{Log (E_j/R_i)}{\sqrt{\sum_{j=1,N} Log_z (E_j/R_j)}}$
C.	Xi = $\frac{Log (E_i/R_i)}{\sqrt{\sum_{j=1,(N-1)} Log_z (E_j/R_j)}}$
D.	Xi = $\frac{Log (E_i/R_i)}{\sqrt{\sum_{j=1,N} Log_z (E_j/R_j)}}$
Answer» B. Xj = $\frac{Log (E_j/R_i)}{\sqrt{\sum_{j=1,N} Log_z (E_j/R_j)}}$

Discussion

2.	SVMs (Support vector machines) are a binary classification method to discriminate one set of data points from another.
A.	True
B.	False
Answer» B. False

Discussion

3.	In Self-organizing maps a choice is made of a number of clusters by which to organize the data.
A.	True
B.	False
Answer» B. False

Discussion

4.	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.
A.	True
B.	False
Answer» B. False

Discussion

5.	In cluster analysis of microarray data– For n genes, the process is repeated ________ times until a single element remains.
A.	n2
B.	n
C.	n-1
D.	n-4
Answer» D. n-4

Discussion

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
Answer» E.

Discussion

7.	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?
A.	S(X,Y) = $\frac{1}{N-2}$ ∑i=1,N . (Xi – Xoffset) (Yi + Yoffset)/ϕxQY
B.	S(X,Y) = $\frac{1}{N}$ ∑i=1,N . (Xi – Xoffset) (Yi – Yoffset)/ϕxQY
C.	S(X,Y) = $\frac{1}{N-1}$ ∑i=1,N . (Xi + Xoffset) (Yi + Yoffset)/ϕxQY
D.	S(X,Y) = $\frac{1}{N}$ ∑i=1,N+2 . (Xi + Xoffset) (Yi – Yoffset)/ϕxQY
Answer» C. S(X,Y) = $\frac{1}{N-1}$ ∑i=1,N . (Xi + Xoffset) (Yi + Yoffset)/ϕxQY

Discussion

8.	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
Answer» 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

Discussion

9.	SVMS_(SUPPORT_VECTOR_MACHINES)_ARE_A_BINARY_CLASSIFICATION_METHOD_TO_DISCRIMINATE_ONE_SET_OF_DATA_POINTS_FROM_ANOTHER?$
A.	True
B.	False
Answer» B. False

Discussion

10.	IN_SELF-ORGANIZING_MAPS_A_CHOICE_IS_MADE_OF_A_NUMBER_OF_CLUSTERS_BY_WHICH_TO_ORGANIZE_THE_DATA.?$
A.	True
B.	False
Answer» B. False

Discussion

11.	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?
A.	True
B.	False
Answer» B. False

Discussion

12.	In cluster analysis of microarray data‚Äö√Ñ√∂‚àö√ë‚àö¬® For n genes, the process is repeated ____ times until a single element remains.$
A.	n<sup>2</sup>
B.	n
C.	n<sup>-1</sup>
D.	n<sup>-4</sup>
Answer» D. n<sup>-4</sup>

Discussion

13.	In cluster analysis of microarray data‚Äö√Ñ√∂‚àö√ë‚àö¬® 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
Answer» E.

Discussion

14.	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.
A.	True
B.	False
Answer» B. False

Discussion

15.	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
Answer» C. The oligonucleotides are collectively hybridized to a labeled cDNA library prepared by reverse-transcribing mRNA from cells

Discussion

16.	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
Answer» D. Cell cycle is a developmental phase, or a response to the environment

Discussion

Explore topic-wise MCQs in Bioinformatics.

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?

SVMs (Support vector machines) are a binary classification method to discriminate one set of data points from another.

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

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.

In cluster analysis of microarray data– For n genes, the process is repeated ________ times until a single element remains.

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.

Which of the given statements is incorrect about Microarray Analysis?

SVMS_(SUPPORT_VECTOR_MACHINES)_ARE_A_BINARY_CLASSIFICATION_METHOD_TO_DISCRIMINATE_ONE_SET_OF_DATA_POINTS_FROM_ANOTHER?$

IN_SELF-ORGANIZING_MAPS_A_CHOICE_IS_MADE_OF_A_NUMBER_OF_CLUSTERS_BY_WHICH_TO_ORGANIZE_THE_DATA.?$

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?

In cluster analysis of microarray data‚Äö√Ñ√∂‚àö√ë‚àö¬® For n genes, the process is repeated ____ times until a single element remains.$

In cluster analysis of microarray data‚Äö√Ñ√∂‚àö√ë‚àö¬® 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.$

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.

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

Which of the given statements is incorrect about global gene regulation?

1.	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?
A.	Xi = \(\frac{Log (E_i/R_i)}{\sqrt{\sum_{j=1,N} Log_{z-2} (E_j/R_j)}}\)
B.	Xj = \(\frac{Log (E_j/R_i)}{\sqrt{\sum_{j=1,N} Log_z (E_j/R_j)}}\)
C.	Xi = \(\frac{Log (E_i/R_i)}{\sqrt{\sum_{j=1,(N-1)} Log_z (E_j/R_j)}}\)
D.	Xi = \(\frac{Log (E_i/R_i)}{\sqrt{\sum_{j=1,N} Log_z (E_j/R_j)}}\)
Answer» B. Xj = \(\frac{Log (E_j/R_i)}{\sqrt{\sum_{j=1,N} Log_z (E_j/R_j)}}\)

7.	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?
A.	S(X,Y) = \(\frac{1}{N-2}\) ∑i=1,N . (Xi – Xoffset) (Yi + Yoffset)/ϕxQY
B.	S(X,Y) = \(\frac{1}{N}\) ∑i=1,N . (Xi – Xoffset) (Yi – Yoffset)/ϕxQY
C.	S(X,Y) = \(\frac{1}{N-1}\) ∑i=1,N . (Xi + Xoffset) (Yi + Yoffset)/ϕxQY
D.	S(X,Y) = \(\frac{1}{N}\) ∑i=1,N+2 . (Xi + Xoffset) (Yi – Yoffset)/ϕxQY
Answer» C. S(X,Y) = \(\frac{1}{N-1}\) ∑i=1,N . (Xi + Xoffset) (Yi + Yoffset)/ϕxQY

Explore topic-wise MCQs in Bioinformatics.

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?

SVMs (Support vector machines) are a binary classification method to discriminate one set of data points from another.

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

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.

In cluster analysis of microarray data– For n genes, the process is repeated ________ times until a single element remains.

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.

Which of the given statements is incorrect about Microarray Analysis?

SVMS_(SUPPORT_VECTOR_MACHINES)_ARE_A_BINARY_CLASSIFICATION_METHOD_TO_DISCRIMINATE_ONE_SET_OF_DATA_POINTS_FROM_ANOTHER?$

IN_SELF-ORGANIZING_MAPS_A_CHOICE_IS_MADE_OF_A_NUMBER_OF_CLUSTERS_BY_WHICH_TO_ORGANIZE_THE_DATA.?$

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?

In cluster analysis of microarray data‚Äö√Ñ√∂‚àö√ë‚àö¬® For n genes, the process is repeated ____ times until a single element remains.$

In cluster analysis of microarray data‚Äö√Ñ√∂‚àö√ë‚àö¬® 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.$

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.

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

Which of the given statements is incorrect about global gene regulation?

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.

In cluster analysis of microarray data‚Äö√Ñ√∂‚àö√ë‚àö¬® 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.$