The document is a series of multiple choice questions and answers focused on microarray-based approaches, detailing key concepts such as microarray design, data collection, clustering analysis, and bioinformatics applications. It discusses incorrect statements related to microarrays, techniques like hierarchical clustering and k-means, and various bioinformatics tools and methodologies. Additionally, it covers historical context and examples relevant to the field.

1. Multiple Choice Questions & Answers (MCQs) focuses on “Microarray-Based Approaches”.
Author: Dr. R.N. Chavhan, Department of Zoology, RMG College, Nagbhid
1. Which of the following is incorrect about a microarray?
a) It is a slide attached with a high-density array of immobilized DNA oligomers
representing the entire genome of the species under study
b) Array of immobilized DNA oligomers cannot be cDNAs
c) Each oligomer is spotted on the slide and serves as a probe for binding to a unique
complementary cDNA
d) It is the most commonly used global gene expression profiling method
Answer: b)
Explanation: The entire cDNA population, labeled with fluorescent dyes or
radioisotopes, is allowed to hybridize with the oligo probes on the chip. The amount of
fluorescent or radiolabels at each spot position reflects the amount of corresponding
mRNA in the cell. Using this analysis, patterns of global gene expression in a cell can
be examined.
2. Which of the following is incorrect about Oligonucleotide Design in A microarray?
a) DNA microarrays are generated by fixing oligonucleotides onto a solid support
b) The oligonucleotide array slide represents thousands of preselected genes from an
organism
c) The length of oligonucleotides is typically in the range of twenty-five to seventy
bases long
d) The oligonucleotides don’t react with cDNA samples
Answer: d)
Explanation: The oligonucleotides are called probes that hybridize to labeled cDNA
samples. Shorter oligo probes tend to be more specific in hybridization because they
are better at discriminating perfect complementary sequences fromsequences
containing mismatches. However, longer oligos can be more sensitive in binding
cDNAs.
3. Which of the following is incorrect about Data Collection?
a) The two-color microarray uses multiple dyes at times
b) The most common type of microarray protocol is the two-color microarray
c) The cDNAs are obtained by extracting total RNA or mRNA from tissues or cells
and incorporating fluorescent dyes in the DNA strands during the cDNA
biosynthesis
d) The expression of genes is measured via the signals from cDNAs hybridizing with
the specific oligonucleotide probes on the microarray
Answer: a
Explanation: The most common type of microarray protocol is the two-color
microarray, which involves labeling one set of cDNA from an experimental
condition with one dye (Cy5, red fluorescence) and another set of cDNA from a
reference condition (the controls) with another dye (Cy3, green fluorescence).
When the two differently labeled cDNA samples are mixed in equal quantity and
allowed to hybridize with the DNA probes on the chips, gene expression patterns
of both samples can be measured simultaneously.
4. In the analysis of microarray data–If replicated datasets are available, rigorous
statistical tests such as t-test and analysis of variance (ANOVA) can be performed to
test the null hypothesis that a given data point is not significantly different from the
mean of the data distribution.
a) True

2. b) False
Answer: a
Explanation: For such tests, it is common to use a P-value cutoff of .05, which
means a confidence level of 95% to distinguish the data groups. This level also
corresponds to a gene expression level with two standard deviations from the mean
of distribution.
5. Which of the following is incorrect about Classification of microarray data?
a) For microarray data, clustering analysis identifies coexpressed and coregulated
genes
b) For microarray data, clustering analysis identifies coexpressed but not
coregulated genes
c) For microarray data, clustering analysis identifies and coregulated but not
coexpressed genes
d) Genes within a category have more similarity in expression than genes from
different categories.
Answer: a
Explanation: When genes are co-regulated, they normally reflect related
functionality. Through gene clustering, functions of previously uncharacterized
genes may be discovered. Clustering methods include hierarchical clustering and
partitioning clustering (e.g., k-means, self-organizing maps [SOMs]).
6. A supervised analysis refers to classification of data into a set of predefined categories.
For example, depending on the purpose of the experiment, the data can be classified
into predefined ‘diseased’ or ‘normal’ categories.
a) True
b) False
Answer: a
Explanation: Similarly, an unsupervised analysis does not assume predefined
categories, but identifies data categories according to actual similarity patterns. The
unsupervised analysis is also called clustering, which is to group patterns into clusters
of genes with correlated profiles.
7. Which of the following is incorrect about Hierarchical Clustering?
a) The tree-branching pattern illustrates a higher degree of relationship between related
gene groups
c) It is not similar to the distance phylogenetic tree-building method
c) It produces a treelike structure that represents a hierarchy or relative relatedness
of data groups
d) d) In the tree leaves, similar gene expression profiles are placed more closely
together than dissimilar gene expression profiles
Answer: b
Explanation: A hierarchical clustering method is in principle similar to the distance
phylogenetic tree-building method. When genes with similar expression profiles are
grouped in such a way, functions for unknown genes can often be inferred.
Hierarchical clustering uses the agglomerative approach that works in much the
same way as the UPGMA method, in which the most similar data pairs are joined
first to form a cluster.
8. Which of the following is incorrect about k-Means Clustering?
a) k-means clustering produces a dendrogram
b) It classifies data through a single step partition
c) It is a divisive approach

3. d) In this method, data are partitioned into k-clusters, which are prespecified at the
outset
Answer: a
Explanation: In contrast to hierarchical clustering algorithms, k-means clustering
does not produce a dendrogram, but instead classifies data through a single step
partition. The value of k is normally randomly set but can be adjusted if results are
found to be unsatisfactory.
9. Which of the following is incorrect about Self-Organizing Maps?
a) Clustering by SOMs is in principle similar to the k-means method
b) It doesn’t involve neural networks
c) The data points are initially assigned to the nodes at random
d) It starts by defining a number of nodes
Answer: b
Explanation: This pattern recognition algorithm employs neural networks. The
distance between the input data points and the centroids are calculated. The data
points are successively adjusted among the nodes, and their distances to the
centroids are recalculated. After many iterations, a stabilized clustering pattern are
reached with the minimum distances of the data points to the centroids. The
differences between SOM and k-means are that, in SOM, the nodes are not treated
as isolated entities, but as connected to other nodes.
10. TIGR TM4 is a suite of multiplatform programs for analyzing microarray data.
a) True
b) False
Answer: a
Explanation: This comprehensive package includes four interlinked programs, TIGR
spot finder (for image analysis), MIDAS (for data normalization), MeV (for clustering
analysis and visualization), and MADAM (for data management). The package
provides different data normalization schemes and clustering options. Other Similar
Clustering Programs are EPCLUST, SOTA.
MCQs on Bioinformatics
1. Which of the following is an example of Homology and similarity tool?
(a) BLAST
(b) RasMol
(c) EMBOSS
(d) PROSPECT
Sol:(a) BLAST.
2. In which year did the SWISSPROT protein sequence database begin?
(a) 1988
(b) 1985
(c) 1986
(d) 1987
Sol: (d) 1987.
3.Which of the following scientists created the first Bioinformatics database?

4. (a) Dayhoff
(b) Pearson
(c) Richard Durbin
(d) Michael.J.Dunn
Sol:(a) Dayhoff.
4. The human genome contains approximately__________.
(a) 6 billion base pairs
(b) 5 billion base pairs
(c) 3 billion base pairs
(d) 4 billion base pairs
Sol: (c) 3 billion base pairs.
5. Which of the following tools is used for the identification of motifs?
(a) BLAST
(b) COPIA
(c) PROSPECT
(d) Pattern hunter
Sol: (b) COPIA.
6. The first molecular biology server expasy was in the year __________.
(a) 1992
(b) 1993
(c) 1994
(d) 1995
Sol: (b) 1993.
7. What is the deposition of cDNA into the inert structure called?
(a) DNA probes
(b) DNA polymerase
(c) DNA microarrays
(d) DNA fingerprinting
Sol: (c) DNA microarrays.
8. The identification of drugs through the genomic study is called__________.
(a) Genomics
(b) Pharmacogenomics
(c) Pharmacogenetics

5. (d) Cheminformatics
Sol: (b) Pharmacogenomics.
9. Which of the following compounds has desirable properties to become a drug?
(a) Fit drug
(b) Lead
(c) Fit compound
(d) All of the above
Sol:(b) Lead.
10. Proteomics refers to the study of __________.
(a) Set of proteins in a specific region of the cell
(b) Biomolecules
(c) Set of proteins
(d) The entire set of expressed proteins in the cell
Sol: (d) The entire set of expressed proteins in the cell.
11. The process of finding the relative location of genes on a chromosome is called
__________.
(a) Gene tracking
(b) Genome walking
(c) Genome mapping
(d) Chromosome walking
Sol:(c) Genome mapping.
12. The computational methodology that tries to find the best matching between two
molecules, a receptor and ligand are called __________.
(a) Molecular fitting
(b) Molecular matching
(c) Molecular docking
(d) Molecule affinity checking
Sol: (c) Molecular docking.
13. Which of the following are not the application of bioinformatics?
(a) Drug designing
(b) Data storage and management
(c) Understand the relationships between organisms
(d) None of the above

6. Sol: (d) None of the above.
14. The term “invitro” is the Latin word which refers to__________.
(a) Within the lab
(b) Within the glass
(c) Outside the lab
(d) Outside the glass
Sol: (b) Within the glass.
15. The stepwise method for solving problems in computer science is called__________.
(a) Flowchart
(b) Algorithm
(c) Procedure
(d) Sequential design
Sol:(b) Algorithm.
16. The term Bioinformatics was coined by __________.
(a) J.D Watson
(b) Pauline Hogeweg
(c) Margaret Dayhoff
(d) Frederic Sanger
Sol: (b) Pauline Hogeweg.
17. The laboratory work using computers and associated with web-based analysis
generally online is referred to as __________.
(a) In silico
(b) Dry lab
(c) Wet lab
(d) All of the above
Sol: (c) In silico.
18. Which of the following is the first completed and published gene sequence?
(a) ΦX174
(b) T4 phage
(c) M13 phage
(d) Lambda phage
Sol: (a) ΦX174.

7. 19. The laboratory work using computers and computer-generated models generally
offline is referred to as __________.
(a) Insilico
(b) Wet lab
(c) Dry lab
(d) All of the above
Sol: (c) Dry lab.
20. The computer simulation refers to __________.
(a) Dry lab
(b) Invitro
(c) In silico
(d) Wet lab
Sol:(c) In silico.