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Flashcards in Genomics Deck (15):

The study of an entire genome or genomes



Two major subfields of genomics:

1. Functional Genomics
2. Comparative Genomics


The global analysis of the function of sequences in a genome.
-Understand genome and phenotype of an organism
-Useful when considering complex traits.

Functional genomics


Comparison of entire genomes from different species, individuals, or groups.
-Studies genetic variation, evolutionary relatedness
-Asks "what sequences are different and what are similar?"

Comparative Genomics


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

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)


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

-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?


Selected techniques used in genomics:

1. Whole genome sequencing
2. Bioinformatics
3. Transcriptomics


Combines biology and computer science.



Bioinformatics examples

-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


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

Response element


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.

Sequence Similarity Searches


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



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



Method of RNAseq

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


What can RNAseq tell you?

The relative amounts of each transcript and different splice variants.