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Flashcards in Genomics Deck (15)
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1
Q

The study of an entire genome or genomes

A

Genomics

2
Q

Two major subfields of genomics:

A
  1. Functional Genomics

2. Comparative Genomics

3
Q

The global analysis of the function of sequences in a genome.

  • Understand genome and phenotype of an organism
  • Useful when considering complex traits.
A

Functional genomics

4
Q

Comparison of entire genomes from different species, individuals, or groups.

  • Studies genetic variation, evolutionary relatedness
  • Asks “what sequences are different and what are similar?”
A

Comparative Genomics

5
Q

An example of genomics: identification of genes linked to drought tolerance in plants:

  • Tomato plants grown in high vs. low water conditions
  • Performed microarray to identify genes that are differentially transcribed in these conditions
A

An example of genomics: identification of genes that make us human:

  • HAR-1= Human Accelerated Region 1
  • Chicken and chimp HAR-1 nearly identical
  • Chimp and human HAR-1 a lot different
  • HAR-1 encodes a small noncoding RNA (fxn unknown)
  • Expressed in a region of the brain that undergoes a unique deelopmental process in humans
  • Other genes: FOXP2 (speech) and ASPM (brain size)
6
Q

An example of genomics: identification of genes hat make certain cancers aggressive

A
  • Sequence DNA from different breast cancers, some with good prognosis (less aggressive and easily treatable) and some from patients with poor prognosis (from highly aggressive tumors)
  • Identify and compare mutations and copy number variants between the two groups
  • Compare genome from your patient’s tumor to the known genomes
  • Why is this beneficial?
7
Q

Selected techniques used in genomics:

A
  1. Whole genome sequencing
  2. Bioinformatics
  3. Transcriptomics
    • RNAseq
8
Q

Combines biology and computer science.

A

Bioinformatics

9
Q

Bioinformatics examples

A
  • Find DNA with a sequence of interest.
  • Align sequences for similarities.
  • Predict structure, therefore function of RNA and protein
  • Describe gene interactions (interacto maps)
  • Map phylogenetic relationships
10
Q

Part of the promoter region; transcription factors will bind to for transcription to proceed.

A

Response element

11
Q

Compare the sequence of a gene product with unknown function to a similar gene product with known function.

  • Analyze a region of sequence that might encode a particular protein function.
  • Goal: to assign a predictive function for a gene (or a set of genes) of interest.
A

Sequence Similarity Searches

12
Q

The study of the complete set transcripts that are produced by a genome under a specific condition.
-Uses RNAseq

A

Transcriptomics

13
Q

Method provides the sequences of all transcripts in a sample.
-Transcriptome= all transcripts

A

RNAseq

14
Q

Method of RNAseq

A
  1. extract RNA
  2. Make cDNA
  3. Sequence cDNA using Next Gen. sequencing technology
15
Q

What can RNAseq tell you?

A

The relative amounts of each transcript and different splice variants.