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Big Data and Biological Networks · Quiz 2 · Jan 2026

Big Data and Biological Networks · Quiz 2 · Jan 2026

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Question 2 MCQ · 1.0 marks

If currency metabolites like ATP and NADH are not removed from a substrate graph, shortest path analysis between two metabolite nodes will likely:
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Overestimate path lengths due to the presence of many edges
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Underestimate path length due to artificial shortcuts
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Fail to compute paths
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Give identical results

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Question 3 MCQ · 1.0 marks

What is the reason for the stuck reactions getting relieved in a microbial community?
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New genes appear in the organisms
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Reaction stoichiometry changes
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Enzymes are removed from the organisms
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Metabolites can be exchanged between organisms

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Question 4 MCQ · 1.0 marks

In a community, organism A relieves 5 stuck reactions in organism B, and organism B relieves 5 stuck reactions in organism A. Which of the following is true?
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MSI(A) = MSI(B)
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MSI(A) > MSI(B)
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MSI(A) < MSI(B)
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MSI(A) and MSI(B) cannot be determined without knowing the initial number of stuck reactions

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Question 5 MCQ · 1.0 marks

In a disease-spread bipartite network model with people and locations as nodes, what do the two projections of the bipartite network represent?
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Vaccination and quarantine networks
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People-people interactions and location-location interaction networks
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Susceptible-infected and infected-recovered populations
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Disease-disease networks in different populations

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Question 6 MCQ · 1.0 marks

A scale-free network has a characteristic path length of L = 3.5. After a targeted attack on the single highest-degree hub, L jumps to 8.2. If a random node was removed instead, what is the most likely new value for L?
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8.2
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15.0
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3.6
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1.2

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Question 7 MCQ · 1.0 marks

If a metabolite acting as a global “hub” in a metabolic network is knocked out, the most likely immediate consequence is:
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A decrease in the pairwise disconnectivity index.
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The fragmentation of metabolic pathways, potentially disrupting essential functions.
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A significant increase in the network's resilience.
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No change, as metabolic networks always have alternative redundant routes.

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Question 8 MCQ · 1.0 marks

In a hierarchical agglomerative clustering process, what happens at the very final step?
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Every point remains in its own individual cluster.
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The network is split into two factions like the Karate Club.
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All nodes are coalesced into a single, massive cluster.
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The betweenness centrality of all edges becomes equal.

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Question 9 MCQ · 1.0 marks

What is the primary reason for using Erdős–Rényi graph when identifying network motifs?
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To determine if the characteristic path length is significantly larger than would be expected by chance
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To demonstrate that the network’s robustness to random failure is significantly higher than would be expected by chance
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To ensure that the network possesses a significantly higher density than would be expected by chance
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To determine if a specific pattern occurs significantly more than would be expected by chance

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Question 10 MCQ · 1.0 marks

In a Gene Regulatory Network (GRN) with
Source diagram or notation
genes where self-regulation of genes is allowed, the number of possible directed interactions is:
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6406536641942.Source diagram or notation
6406536641943.Source diagram or notation
6406536641944.Source diagram or notation

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Question 11 MCQ · 1.0 marks

Which of the following cannot be a node in signalling network?
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Ligands
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Receptors
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Transcription factors
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Enzymes

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Question 12 MCQ · 1.0 marks

How many solutions are possible for a string reconstruction problem with 10 words?
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6406536641983.Source diagram or notation
6406536641984.Source diagram or notation
6406536641985.Source diagram or notation

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Question 13 MCQ · 1.0 marks

What is the number of 3-mers generated from the sequence : CAAACTACCACGGATACACCACTTGG?
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20
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24
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15
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21

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Question 14 MCQ · 2.0 marks

What is the average degree (regardless of the direction) of the 3-mer overlap graph constructed from “CAAACTA”?
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4.1
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2.4
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3.4
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2

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Question 15 MCQ · 2.0 marks

What is the total number of edges of the De-Bruijn Graph generated from the 3-mers obtained from “CAAACTACCACG”?
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10
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14
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16
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8

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Question 16 MCQ · 2.0 marks

What is the total number of nodes of the Overlap Graph generated from the 4-mers obtained from “CAAACTACCACGGATACA”?
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13
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15
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16
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14

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Question 17 MCQ · 3.0 marks

Given the two sequences “AGAGCTTA”, “AAGAGTTGA”, and the scoring paradigm: matches: “
Source diagram or notation
”, mismatches: “
Source diagram or notation
” and gap: “
Source diagram or notation
”, find the final score for the best global alignment between the two sequences.
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10
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11
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2
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8

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Question 18 MCQ · 3.0 marks

Given the k-mers : ’CAAA’, ’AACT’, ’AAAC’, ’ACTA’, ’CTAC’, ’TACC’, ’ACCA’, ’CCAC’, ’CACG’, ’CGGA’, ’ACGG’, ’GGAT’, ’GATA’, ’TACA’, ’ATAC’, ’ACAC’, ’CACC’, reconstruct the sequence from which the k-mers were generated.
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CAAACTACCACGGATACAGC
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CTATGCCGTAGGCGGTACTAA
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ATCGGTACAACGGTTA
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CAAACTACCACGGATACACC

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Question 19 MCQ · 3.0 marks

Consider the following two statements: **Statement 1**: Reads from the genome sequencing are prone to error. **Statement 2**: Sequence alignment can be used to overcome this problem. Based on your observations, which of the following statements is true?
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Both statements are true and statement 2 is a potential solution for statement 1
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Both statements are true but statement 2 is not a solution to statement 1
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Both statements are false
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Statement 1 is false but Statement 2 is true

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Question 20 MSQ · 2.0 marks

Considering a metabolic system with 50 metabolites and 120 reactions, which of the following statements are correct?
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The corresponding substrate graph will contain 50 nodes and 120 edges
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The corresponding reaction graph will contain 120 nodes and 120 edges
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The corresponding bipartite graph will contain 170 nodes
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The corresponding substrate graph will contain 50 nodes

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Question 21 MSQ · 2.0 marks

In a community of two organisms, A and B, what are the possible scenarios in which Metabolic Support Index (MSI) will be 0 for organism A?
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All stuck reactions in A are relieved in the presence of B
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All stuck reactions in B are relieved in the presence of A
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Number of stuck reactions in A remains unchanged in the presence of B
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No stuck reactions are present in A initially
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No metabolites are exchanged between organisms

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Question 22 MSQ · 2.0 marks

Two genes A and B belong to two different metabolic pathways producing the same essential metabolite. Removing either of these genes separately does not affect cell survival but deleting them together leads to cell death. Which of the following are true:
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Gene products of A and B interact physically
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Genes A and B must be located adjacent to each other in the genome
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Both genes compensate for each other
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There is redundancy in the metabolic pathway

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Question 23 MSQ · 2.0 marks

Consider the following network and identify the possible gene regulatory interactions: (arrows in the option indicates a directed interaction)
Source diagram or notation
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Gene 1 → Gene 2
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Gene 1 → Gene 3
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Gene 3 → Gene 2
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Gene 2 → Gene 3

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Question 24 MSQ · 2.0 marks

We have a graph that was constructed by comparing n DNA sequences. If the two sequences can be aligned with a score greater than a threshold value, we assign an edge between the two in the graph. Given this, which of the following are true:
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Inserting a new node to the graph requires n comparisons
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Inserting a new node is a node level task
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If all the alignments have the same score, the resultant graph is a complete graph
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There will be two connected components in the resultant graph

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Question 25 MSQ · 2.0 marks

Which of the following makes appropriate pairs?
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Node classification – Predicting drug-drug interaction
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Graph classification – Predicting toxicity of a chemical compound
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Link Prediction – Predicting function of novel proteins
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Graph regression – Predicting free energy of hydration

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Question 26 MSQ · 3.0 marks

Which of these are challenges one might encounter in the process of genome assembly?
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Erroneous reads
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Large volumes of data
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Duplicate sequences
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Incomplete graph

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Question 27 MCQ · 2.0 marks

Consider an adjacency matrix of 7-node network. Nodes are indexed as N1 to N7. A value of 1 indicates an edge, and 0 indicates no direct edge.
Source diagram or notation
Based on the above data, answer the given subquestions.
In similarity-based clustering (e.g., Jaccard or Cosine similarity), why are nodes N1, N4, and N5 most likely to be grouped into the same cluster?
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They have the lowest degree centrality in the network.
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They share a high number of common neighbors (Nodes N2 and N3) and are directly connected.
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They are "bridge" nodes (high betweenness) connecting N6 and N7 to the rest of the graph.
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They are isolated from the rest of the network's path redundancy.

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Question 28 MCQ · 2.0 marks

Consider an adjacency matrix of 7-node network. Nodes are indexed as N1 to N7. A value of 1 indicates an edge, and 0 indicates no direct edge.
Source diagram or notation
Based on the above data, answer the given subquestions.
To find the number of paths of **length 2** between Node N1 and Node N4, which mathematical operation should a student perform on the matrix provided?
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Calculate the Eigenvector Centrality of the adjacency matrix.
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Look at the value at index (1, 4) of the squared adjacency matrix (
Source diagram or notation
).
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Sum the total number of 1s in the first row.
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Identify the shortest path using the Girvan-Newman algorithm.

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Question 29 MCQ · 2.0 marks

Consider an adjacency matrix of 7-node network. Nodes are indexed as N1 to N7. A value of 1 indicates an edge, and 0 indicates no direct edge.
Source diagram or notation
Based on the above data, answer the given subquestions.
If you wanted to partition this network into two communities using the Girvan-Newman algorithm, which edge would be the first to be removed?
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Edge (N1,N5)
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Edge (N4,N5)
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Edge (N6,N7)
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Edge (N5,N6)

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Question 30 MCQ · 2.0 marks

Consider an adjacency matrix of 7-node network. Nodes are indexed as N1 to N7. A value of 1 indicates an edge, and 0 indicates no direct edge.
Source diagram or notation
Based on the above data, answer the given subquestions.
After applying the Girvan-Newman algorithm for the first necessary edge removal, what is the most appropriate property of the largest resulting component?
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Sparsely connected component
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Component consists of 10 edges
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Component forms a clique
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Component consists of 7 nodes

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