Bioinformatics Questions and Answers – Comparison of SAGE and DNA Microarrays

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This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Comparison of SAGE and DNA Microarrays”.

1. Which of the following is untrue about SAGE?
a) This approach is much more efficient than the EST analysis
b) This approach is quite less efficient than the EST analysis
c) It uses a short nucleotide tag to define a gene transcript
d) It allows sequencing of multiple tags in a single clone
View Answer

Answer: b
Explanation: If an average clone has a size of 700 bp, it can contain up to 50 sequence tags (15 bp each), which means that the SAGE method can be at least fifty times more efficient than the brute force EST sequencing and counting. Therefore, the SAGE analysis has a better chance of detecting weakly expressed genes.
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2. Which of the following is untrue about SAGE?
a) Sequencing is the most costly and time-consuming step
b) Here, sequencing is economical but time-consuming step
c) Sequencing is economical but time-reducing step
d) It is difficult to know how many tags need to be sequenced to get a good coverage of the entire transcriptome
View Answer

Answer: a
Explanation: It is generally determined on a case-by-case basis. As a rule of thumb, 10,000 clones representing approximately 500,000 tags from each sample are sequenced. The scale and cost of the sequencing required for SAGE analysis are prohibitive for most laboratories. Only large sequencing centers can afford to carry out SAGE analysis routinely.

3. Which of the following is untrue about the drawbacks of SAGE?
a) One or two sequencing errors in the tag sequence can lead to ambiguous or erroneous tag identification
b) Correctly sequenced SAGE tag sometimes may correspond to several genes or no gene at all
c) Correctly sequenced SAGE tag always corresponds to several genes
d) The drawback with this approach is the sensitivity to sequencing errors
View Answer

Answer: c
Explanation: To improve the sensitivity and specificity of SAGE detection, the lengths of the tags need to be increased for the technique. There are some comprehensive software tools for SAGE analysis viz. SAGEmap, SAGExProfiler.

4. SAGEmap is a SAGE database created by NCBI.
a) True
b) False
View Answer

Answer: a
Explanation: Given a cDNA sequence, one can search SAGE libraries for possible SAGE tags and perform “virtual” Northern blots that indicate the relative abundance of a tag in a SAGE library. Each output is hyperlinked to a particular UniGene entry with sequence annotation.

5. SAGExProfiler doesn’t provide information about overexpressed or silenced genes.
a) True
b) False
View Answer

Answer: b
Explanation: It is a web-based program that allows a “virtual subtraction” of an expression profile of one library (e.g., normal tissue) from another (e.g., diseased tissue). Comparison of the two libraries can provide information about overexpressed or silenced genes in normal versus diseased tissues.
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6. Which of the following is untrue about SAGE Genie?
a) It is an NCBI web-based program
b) It allows matching of experimentally obtained SAGE tags to known genes
c) It provides an interface for visualizing human gene expression
d) It doesn’t filter out linker sequences from experimentally obtained SAGE tags
View Answer

Answer: d
Explanation: It has a filtering function that filters out linker sequences from experimentally obtained SAGE tags and allows expression pattern comparison between normal and diseased human tissues. The data output can be presented using subprograms such as the Anatomic Viewer, Digital Northern, and Digital Gene Expression Display.

7. Which of the following is an incorrect statement?
a) SAGE and DNA microarrays are both high throughput techniques that determine global mRNA expression levels
b) Studies have indicated that the gene expression measurements from these methods are highly inconsistent with each other
c) SAGE does not require prior knowledge of the transcript sequence
d) DNA microarray experiments can only detect the genes spotted on the microarray
View Answer

Answer: b
Explanation: SAGE has the potential to allow discovery of new, yet unknown gene transcripts. Because is able to measure all the mRNA expressed in a sample, it becomes possible.

8. DNA microarrays measure “absolute” mRNA expression levels without arbitrary reference standards, whereas SAGE indicates the relative expression levels.
a) True
b) False
View Answer

Answer: b
Explanation: SAGE measures “absolute” mRNA expression levels without arbitrary reference standards, whereas DNA microarrays indicate the relative expression levels. Therefore, SAGE expression data are more comparable across experimental conditions and platforms. This makes public SAGE databases more informative by allowing comparison of data from reference conditions with various experimental treatments.

9. The PCR amplification step involved in the SAGE procedure means that it requires a large quantity of sample mRNA.
a) True
b) False
View Answer

Answer: a
Explanation: The PCR amplification step involved in the SAGE procedure means that it requires only a minute quantity of sample mRNA. This compares favorably to the requirement for a much larger quantity of mRNA for microarray experiments, which may be impossible to obtain under certain circumstances.
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10. Which of the following is an incorrect statement?
a) Collecting a SAGE library is very labor intensive and expensive
b) Collecting a SAGE library is quite economical
c) SAGE is not suitable for rapid screening of cells
d) Gene identification from SAGE data is also more cumbersome
View Answer

Answer: b
Explanation: The Gene identification from SAGE data is also more cumbersome because the mRNA tags have to be extracted, compiled, and identified computationally, whereas in DNA microarrays, the identities of the probes are already known. In SAGE, comparison of gene expression profiles to discover differentially expressed genes and co-expressed genes is performed manually, whereas for microarrays, there are a large number of software algorithms to automate the process.

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Manish Bhojasia, a technology veteran with 20+ years @ Cisco & Wipro, is Founder and CTO at Sanfoundry. He is Linux Kernel Developer & SAN Architect and is passionate about competency developments in these areas. He lives in Bangalore and delivers focused training sessions to IT professionals in Linux Kernel, Linux Debugging, Linux Device Drivers, Linux Networking, Linux Storage, Advanced C Programming, SAN Storage Technologies, SCSI Internals & Storage Protocols such as iSCSI & Fiber Channel. Stay connected with him @ LinkedIn