Functional genomics Flashcards
What is the updated central dogma?
DNA>mRNA>proteins>phenotype
What does functional genomics do?
Tells us what genes do and discovers biomarkers for pathology.
What is comparative genomics?
Looks at genomes, gene sets, or genes to determine the number of CHROMOSOMES, the total number of GENES PER CHROMOSOME, their LOCATIONS, and their SEQUENCE DIVERGENCE. This identifies any common characters.
What are forward and reverse
genetics?
FORWARD: Phenotype to gene
REVERSE: Gene to phenotype
This is to find the responsible gene and confirm its function.
What are the methods for transcriptional analysis?
RT-PCR, cDNA microarrays, RNA-SEQ, DAVID, GSEA, IPA.
What does RNA-SEQ report?
DIFFERENTIAL EXPRESSIONS per gene, splice variants, SNPs, insertions deletions, chromosomal rearrangements.
What is the Database for Annotation, Visualisation and Integrated Discovery (DAVID) for?
To discover enriched biological themes, GO terms, and enriched functional-related gene groups. To cluster redundant annotations. To visualize genes on pathway maps.
What is the Gene Set Enrichment Analysis (GSEA) for?
Tests the significance of a group of genes that might belong to a KNOWN PATHWAY.
What is the Ingenuity Pathway Analysis for?
It is a list of molecular and gene interactions to reveal any relationship between genes. More powerful than Gene set enrichment analyses.
What are the drawbacks of siRNA and CRISPR screens?
Both systems assume that it works to bring the protein of interest down within the timeframe of the experiment. Both systems cannot identify splice variants unless explicitly designed to do so. Both systems assume there are no off-target effects (epigenetic effects, effects on other genes).
