Week 9 Flashcards
Which of the option(s) is/are true regarding Gene ontology?
A. It is a functional annotation database for genes.
B. Biological process is not one of the sub-ontologies.
C. Molecular function is one of the sub-ontologies.
D. It is partially hierarchical.
E. Compared to daughter nodes, parent nodes are better able to describe specialized functions.
A, C and D
Assume there is a bin with 30 balls in it. 12 of the balls are red, signifying the apoptotic pathway,
and the other 18 are green, signifying oxidative phosphorylation. What is the likelihood that 2
balls will come from the apoptosis pathway and 3 from the oxidative phosphorylation pathway if
5 balls are drawn at random from the bin? (Here, sampling is done without replacement).
(n) = n! / r!(n-r)!
(r)
n - total items
r - number items selceted
Probability = Favourable outcomes / Total outcomes
0.35 to 0.40
Which of the below option(s) is/are FWER correction methods?
A. Benjamini-Hochberg correction
B. Bonferroni correction
C. Holm-Bonferroni correction
D. Storey-Tibshreni correction
B and C
Which of the below option(s) is/are true?
A. FDR allows a certain number of false positives.
B. Bonferroni correction shows more type II error than Holm-Bonferroni correction.
C. FWER allows false positives.
D. FDR can control type II error.
A and B
Multiple hypothesis testing increases -
A. False negatives
B. False positives
C. True positives
D. True negatives
B
Read the given statement carefully and answer questions 6-7.
In a differential gene expression analysis of 10 genes (Gene1, Gene2, Gene3, Gene4, Gene5,
Gene6, Gene7, Gene8, Gene9, Gene10) one got 10 different p values which are
0.0001,0.001,0.06,0.0249,0.0158,0.1,0.041,0.039,0.004,0.305 respectively. (FDR cut-off is 0.1)
What will be the q value of Gene 4 according to the Benjamini-Hochberg correction?
● Arrange p values in ascending order and rank them
● Benjamini-Hochberg formula:
To calculate q value
q = (p × m)/ ranks
m - total no. Of ranks
For gene 4 :
0.0498
Read the given statement carefully and answer questions 6-7.
In a differential gene expression analysis of 10 genes (Gene1, Gene2, Gene3, Gene4, Gene5,
Gene6, Gene7, Gene8, Gene9, Gene10) one got 10 different p values which are
0.0001,0.001,0.06,0.0249,0.0158,0.1,0.041,0.039,0.004,0.305 respectively. (FDR cut-off is 0.1)
How many non-significant genes are there?
Significant genes are if p value is less than or equal to critical value
Critical value = (rank / Total no of test ) × FDR cutoff
Which of the analyses below takes just a set of genes as input?
A. Gene over-representation analysis.
B. Gene set enrichment analysis.
C. Both A and B.
D. Differential gene expression analysis.
A
Assume that there are 50 statistical tests in a multiple hypothesis test and that there is a 0.395
chance of making a single type I error. What is the statistical test’s type I error probability?
A. 0.011
B. 0.07
C. 0.002
D. 0.2
A
Gene A shows a difference in expression between diseased and healthy samples. The
significance threshold (α) is set to 0.04, and the number of genes compared between the two
samples is 2000. According to the Bonferroni method, what should be the p-value of Gene A in
order to reject the null hypothesis?
(H0 or Null-hypothesis - Gene A doesn’t have a difference in expression between diseased and
healthy sample)
A. p_value < 510-5
B. p_value > 110-5
C. p_value < 2*10-5
D. p_value < 0.05
C
Assertion: In gene set enrichment analysis, the calculation of NES (Normalized Enrichment
Score) helps in comparing results across gene sets.
Reason: By normalizing the enrichment score, GSEA corrects for biases due to gene set size
differences.
A. The assertion is false but the reason is true.
B. The assertion is true but the reason is false.
C. Both are true.
D. Both are false.
C
Which of the following databases are not used for functional enrichment analysis?
A. The cancer genome atlas (TCGA).
B. Molecular signature database (MSigDB).
C. Kyoto encyclopedia of genes and genomes (KEGG)
D. Ensembl database
A and D
Which of the below option(s) is/are true about the calculation of the ES score?
A. The score decreases if a member of a gene set for a pathway is found while traversing
through the ranked gene list.
B. Test whether the members of the gene set for a particular pathway are present at the top
or bottom of the ranked gene list
C. The final ES score is the maximum deviation from zero while traversing through the
ranked gene list.
D. Ranked gene list is not needed for the calculation of the ES score.
B and C
