Big Data and Biological Networks Quiz 1: 26 February 2023, Set QPE3 (January 2023 term)

1. A

   RNA-Seq

2. B

   Transcriptomics

3. C

   Epigenomics

4. D

   Metabolomics

1. A

   Purified fragments of DNA cut from plasmid/phage clones or amplified bypolymerase chain reaction (PCR)

2. B

   Clones of DNA fragments are denatured to single strands, and one of thestrands is hybridized to an oligonucleotide primer

3. C

   Reverse transcriptase is used to create DNA fragments during DNAsequencing

4. D

   New strands of DNA are synthesized from the end of the primer

1. A

   The number of false-positive errors in detecting differentially expressed geneswill increase

2. B

   The number of false-negative errors in detecting differentially expressedgenes will increase

3. C

   No statistical analysis of the significance of the observed changes will bepossible

4. D

   All of these

1. A

   Real-time PCR

2. B

   ChiP-seq

3. C

   Microarray analysis

4. D

   RNA-seq

1. A

   SAM file

2. B

   BAM file

3. C

   FASTQ file

4. D

   CRAM file

1. A

   Frameshift mutation involves the insertion or deletion of a single base in aDNA molecule

2. B

   Mutagen is a substance or energy form that can cause a mutation in DNA

3. C

   Point Mutation involves substitution of a single nucleotide in a DNA molecule

4. D

   Frameshift mutation involves the insertion or deletion of a single base in aDNA molecule, Mutagen is a substance or energy form that can cause a mutation in DNA andPoint Mutation involves substitution of a single nucleotide in a DNA molecule

5. E

   None of these

1. A

   Single nucleotides

2. B

   Joined sugar and phosphates

3. C

   Joined nitrogenous base and phosphates

4. D

   Paired nucleotides

1. A

   Lack of a hydroxyl group on the 2' carbon

2. B

   Lack of a hydroxyl group on the 3' carbon

3. C

   Lack of a triphosphate moiety on the 5' carbon

4. D

   Presence of a hydroxyl group on the 3' carbon

1. A

   Only Graph A

2. B

   Only Graph B

3. C

   Both Graph A and Graph B

4. D

   Neither of them

1. A

   0.125

2. B

   0.25

3. C

   0.40

4. D

   0.50

1. A

   If A represents an undirected graph, then n is always an even number

2. B

   If A represents a directed graph, then n is always an even number

3. C

   If self-loops are allowed, then n is always an even number

4. D

   In a weighted graph, the sum of all the elements in A equals n

1. A

   0.52

2. B

   0.7

3. C

   0.43

4. D

   0.23

1. A

   It is a connected graph

2. B

   The degree distribution of the graph follows the binomial distribution

3. C

   The clustering coefficient is the same for all the nodes

4. D

   The number of neighbours for all the nodes remains the same

1. A

   3

2. B

   10

3. C

   8

4. D

   6

1. A

   45

2. B

   55

3. C

   35

4. D

   25

1. A

   300

2. B

   400

3. C

   100

4. D

   200

1. A

   1/4, 1/4, 1/4, 1/4

2. B

   3/4, 2/4, 2/4, 1/4

3. C

   1/8, 1/8, 1/8, 1/8

4. D

   3/8, 2/8, 2/8, 1/8

1. A

   2.17

2. B

   4.35

3. C

   0.92

4. D

   1.24

1. A

   (1,2)

2. B

   (1,2), (2,1), (1,1), (2,2)

3. C

   (1,2), (1,1), (2,2)

4. D

   (1,2), (2,1)

Select all that apply.

1. A

   Is the abundance of the tumour suppressor p-53 affected by growth of ahuman cell line in the presence of penicillin?

2. B

   Which genes are upregulated in response to lower temperatures in a cultureof S. cerevisiae?

3. C

   Which proteins are localised to the Golgi apparatus in mouse liverhepatocytes?

4. D

   Which SNPs are associated with Breast Cancer?

Select all that apply.

1. A

   Identification of disease biomarkers

2. B

   Mass production of essential proteins and metabolites

3. C

   Determination of SNPs associated with a disease

4. D

   To study gene-expression pattern in a context-specific manner

Select all that apply.

1. A

   Sequence a single DNA fragment at a time

2. B

   Short fragment reads (100-150 bp) are ligated to the flow cell surface

3. C

   Ability to sequence hundreds to thousands of genes or gene regionssimultaneously

4. D

   None of these

Select all that apply.

1. A

   The maximum value of n is 20

2. B

   n is always an even number

3. C

   The number of non-zero elements in A[:5 , :5] is 10

4. D

   The minimum value of n is 10

Select all that apply.

1. A

   Metabolic network

2. B

   Citation network from a biological journal

3. C

   Signaling network

4. D

   People from a Facebook group “Big data in biology”

Select all that apply.

1. A

   Number of parameters required for generating a Erdos-Renyi graph is 2

2. B

   Number of parameters required for generating a Watts-Strogatz graph is 3

3. C

   Number of parameters required for generating a power-law graph is 1

4. D

   Neither of them are correct

Select all that apply.

1. A

   It can capture the degree distribution of the real-world network

2. B

   It can capture the small-world properties of the real-world network

3. C

   It has a long-tail degree distribution

4. D

   It can capture the characteristic path length of the real-world network

Select all that apply.

1. A

   Bulk RNA-seq captures only an “average” of the expression profiles ofthousands of cells

2. B

   Single cell RNA-seq (scRNA-seq) allows the capture of individual measurementsacross dozens and up to thousands of single cells

3. C

   RNA transcripts generated are identical across all the cell-types.

4. D

   Post-translational modifications can be studied using RNA-seq approach.

Select all that apply.

1. A

   It combines genomic data with data from other modalities such astranscriptomics, epigenetics, and proteomics

2. B

   It enables a more comprehensive understanding of molecular changescontributing to normal development, cellular response, and disease

3. C

   It focuses on one aspect of the biological system

4. D

   It allows the systematic understanding of information flow across differentomics layers

Select all that apply.

1. A

   GWAS test hundreds of thousands of genetic variants across many genomes tofind those statistically associated with a specific trait or disease

2. B

   GWAS can be used to predict an individual’s risk for physical and mentaldisease based on their genetic profile

3. C

   If a variant is found to be associated with a trait, it means that a variant in thatgenomic region may cause a difference in the trait

4. D

   If a variant is found to be associated with a trait, it means that a variant in thatgenomic region certainly causes a difference in the trait

Select all that apply.

1. A

   Nanopore is long read sequencing technique, whereas, Illumina sequencing isshort read sequencing technique.

2. B

   Nanopore has 99% accuracy whereas Illumina has 92-95% accuracy

3. C

   Nanopore sequencing technology uses change in current in protein nanoporewhen DNA is passed through it

4. D

   Illumina sequencing uses reversible dye terminator technology to detect thesequence of DNA molecules

1. A

   0.597

2. B

   0.041

3. C

   0.055

4. D

   0.122

1. A

   0.66

2. B

   0.33

3. C

   0.86

4. D

   0.46