Download Reading assessment for Unit 2

Reading assessment for Unit 2.3: Introduction to DNA microarrays
1. With microarrays, it is possible
a. to look the expression of only a single gene at a time
b. to look globally at the expression of all genes
c. to pinpoint all of the cis-regulatory sequences for all genes in one
experiment
d. distinguish between transcription rate and RNA stability
2. Oligonucleotide arrays made by Affymetrix
a. allow direct comparisons of two samples on a single array
b. have high chip-to-chip reproducibility
c. allow only one sample per array
d. b and c only
e. none of the above
3. Microarray based methods may soon become eclipsed by
a. Northern blot technology
b. purely computational approaches to biological research
c. cloning experiments
d. next-generation sequencing methods
4. In addition to gene expression studies, microarrays can be used for
a. investigating DNA copy number
b. looking at sites of in vivo protein-DNA binding
c. identifying transcription factor binding sites
d. looking at single nucleotide polymorphisms (SNPs)
e. all of the above
f. a and d only
5. Key findings from microarray experiments
a. should be validated by other means
b. can always be accepted as being accurate
c. are impossible to verify using RT-PCR
d. never need to be accompanied by statistical analysis
6. When analyzing microarray results, there is typically
a. a trade-off between specificity and sensitivity
b. not a need to use statistics
c. only one really good method to use
d. never a reason to think that a percentage of the results might be in error
7. The following are important considerations for design of microarray experiments
a. number of technical replicates
b. number of biological replicates
c. available starting amount of nucleic acid
d. all of the above
e. none of the above
f. b and c only
8. The following is NOT a data mining method usually used for microarray analysis
a. hierarchical clustering
b. k-means clustering
c. pseudo clustering
d. principal components analysis
e. self organizing maps
9. The following steps should be taken in order to perform a clustering analysis
a. compare pairwise distances, generate expression summaries, cluster
b. create ROC curves, cluster, perform Bonferroni correction
c. generate expression summaries, compare pairwise distances, cluster
d. cluster, then compare pairwise distances
10. When analyzing microarray data, some sort of statistical correction should be
made to account for
a. multiple testing problem
b. cross-hybridization artifacts
c. user induced error
d. RNA-DNA interactions
e. both b and c
11. Which of the following statements is true?
a. there is only one appropriate way to cluster microarray data
b. there are no incorrect ways to cluster data
c. although there are many correct ways to perform clustering, there are also
incorrect ways
d. clustering of data should be avoided whenever possible
e. the only acceptable way of analyzing microarray data is by cluster analysis
12. The False Discovery Rate
a. provides a poor tradeoff in balancing sensitivity and specificity
b. is a reasonable answer to the multiple testing problem
c. is much more conservative than the Bonferroni correction
d. is identical to the p-value
e. none of the above
13. With respect to microarrays, MIAME refers to
a. the city where microarrays were invented
b. a 1980s TV show that once featured microarray experiments
c. an Ohio university where the first microarray experiments took place
d. a common clustering application used for data analysis
e. a minimal set of information that should be reported with publication of
microarray data