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BIOL > Microarray I and II > Flashcards

Microarray I and II Flashcards

1
Q

What is a transcriptome?

A

A complete set of the transcripts encoded from the genome

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2
Q

What can the transcriptome tell you?

A

Genes that exhibit cell and tissue specific expression

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3
Q

What can a transcriptome tell you about a disease?

A

The molecular basis behind it

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4
Q

How can an unknown drug impact genes?

A

Genes that are expressed in response to environmental toxins or drugs

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5
Q

What are genes expressed in response to?

A

Pathogens, diseases, and any mode of infection

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6
Q

What is northern blotting?

A

This is a method od visualizing and detecting RNA transcripts

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7
Q

What is western blotting?

A

A method of detecting proteins

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8
Q

What is southern blotting?

A

A method of detecting DNA

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9
Q

What is the goal of a DNA microarray?

A

To detect which genes are turned on and off depending on the environment

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10
Q

What does the chip contain?

A
  • Many ss probes
  • Fluorescent-labelled mRNAs or cDNAs to bind to the probe
  • The fluorescent intensity tells us the mRNA levels binding to probes
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11
Q

How is the probe design specific?

A

It does not allow for cross hybridization

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12
Q

How is the probe design homogeneous?

A

Binds to complementary DNA at the same melting temperature

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13
Q

How is the probe design sensitive?

A

Does not form secondary structures that could interfere with the hybridization between the probe and mRNA

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14
Q

What is the microarray procedure?

A
  1. Isolate mRNA
  2. Reverse transcribe to cDNA
  3. Label with Cy3 (green) and Cy5 (red)
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15
Q

What is the agilent method?

A

Ink-jet print-head uniformly deposits small, accurate volumes of nucleic acids which builds the oligonucleotide probes one base at a time

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16
Q

What is the affymetric method?

A

The probes are synthesized on wafer and a photomask covers the the silicon wafer and light shines through the holes the light removes blocking compounds which prevents the base addition then you flood with a base (A, T, C, or G) that binds to the uncovered area and continue

17
Q

How do you label the nucleic acids?

A
  1. Random priming of dsDNA
  2. Directly labeling the mRNA with fluorescent molecules
  3. Poly-T primed cDNA
  4. Amplification by transcription
18
Q

What are Cy3 and Cy5?

A

Water-soluble fluorescent dyes of the cyanine family that is excited by green and red lasers respectively

19
Q

To quantify the segmentation which central tendency should you use?

A

Median: it is less likely to be skewed compared to the mean it is robust and tells you the outliers

20
Q

Why do we normalize the data?

A

We do this so we can compare the magnitude of up and down regulation equally rather than treating the quantity as less 2 fold Vs. 1/2

21
Q

What is an MA plot?

A

It shows the intensity dependent effect on log expression ratios

22
Q

What is differential expression?

A

Genes that are turned on or rather have a higher or lower than normal expression

23
Q

How do we identify the genes that are differentially expressed?

A

We use a cut-off value

24
Q

What is clustering?

A

Grouping data based on similiarities which makes it easier to analyze

25
Q

What can the similarities be based on?

A
  1. Euclidean distance - Distance between 2 points
  2. Correlation distance - Similarity of the diretions in which 2 vectors point
26
Q

What is hierarchichal clustering?

A

Clustering based on similarity

27
Q

What is partitional clustering?

A

When you cluster based on K groups

28
Q

What is agglomerative clustering?

A

Start with a single gene and build up to a super-cluster

29
Q

What is divisive clustering?

A

Start with a group of genes and build to a single gene

30
Q

What is 2D clustering?

A

This organizes rows and columns of genes together so you can determine co-regulated genes

31
Q

What is an ORF microarray?

A

Probing for sequence of known genes about 10 nucleotides at a time

32
Q

What is tiling microarray?

A

Tile the entire genome with probes rather than just the coding sequence

33
Q

What do longer UTR regions tell us?

A

That the gene undergoes more gene regulation

34
Q

What do shorter UTR regions tell us?

A

Reduced need for regulation

35
Q
A

BIOL (3 decks)

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