Genomics Flashcards
how big is the nuclear genome
3.2 gb
what is the gene classification of molecular function and what is an example
what a gene product can do without specifying where or when. An example is an enzyme
what do you need to do to generate a hypothesis in functional genomics
increased gene expression
decreased gene expression
-removal of gene or insertion
mutate the gene
what is the gene classification of biological process and what is an example
classifies the 1 or. more distinct steps, time, transformation an example is signal transduction
how much of DNA is fucntional
80.4
what is integrative
involves one or two omes
what is dynamic
evaluates the impact of change
what is mukltifactoral
delivers global analysis of ones
what is gene ontology
explains what a gene or transcriptional unit does, offers new targets ad biomarkers of disease
what does gene ontology exclude
structures, domains, expression level and binding partners
what is GO classification
classifies genes into a hierarchy, placing products with similar functions together
what is MF
molecular function - what a gene product can do with out specificying where or when
what is BP
biological process - 1 or more distinct step
what is CC
cellular comment - part of larger object
what is enrichment for GO
more than 5% chance
what is functional genomics
-satrt with genome
-identofy things that change
-generate hypothesis
-evaluate gene hypothesis by increased gene expression for example
-define function
what is comapartive genomics
looking at genomes, gene set, or genes as a whole
how they operate across large groupings e.g. speicies within a genus
-biological function
-unique gene set functions
what is comparative genomics at gene level
DNA, RNA or protein
aligns sequence for comparison
calauclatyes common anscetros based on known mutation rate model
describe phyloegenetic relationships
what does comparative genomics at gene level identify
common regions
functional domains
unique features
what is multi locus sequence typing
can have a look at genetic epidemiology
what is a homologue gene
largely comparable sequences
descendants of a common ancestor
sequence divergence
what are orthologues
homologous caused by speciation
usually similar function
what is a paralogue
duplicate event within a genome
divergent sequence
different function
what is a xenologue
homologous transferred within species
what are analogues
same function
unrelated sequence
not from common ancestor
what is forward genetics
phenotype to gene
know phenotype of interest
induce mutations
- find infdividuals with knock outs
-find responsible gene
-confirm function by complementqatiojn
what is reverse genomics
gene to phenotype
inhibit genes
homologous recombination
test for phenotype biomarker
find gene reponsible
reverse the effect
when would you get hemizgous bacteria in homologous recombination
when homozygous is non viable
how do you do gene targeting in mice
take embryonic stem cells and transfected cell with an antibiotic resonance and homologue
all the cells with transfection will survive and proliferate
then inject cells into blastocytes of fertilised eggs of other mice
establish in the walls of blast ocytes making chimeras
where do you put phenotypes and biomarkers for mice
mouse genome informatic database
what are the two enzyme systems used in bacterial recombination
lamba red and recET
what 3 proteins does lamb red use
-gam protein
-exo protein
-beta protein
how does invivo cloning work for recombineering DNA
gap repair or
linear fragment joining
how does ssDNA recombination take place
uses beta protein and a high conc of single straded DNA which correspond to lagging strand. it is highly effecient
what does an enhancer trap do
see what enhancer does by making a trap with its own promoter which prevents trancriptiojn
what does a promoter trap do
stops the expression of down stream exons
what does a poly A trap do
eliminates exons
what is knock down
when there is a reduction of an expression of the gene
what does siRNA librbay screening do
4-10 siRNA per gene and try and bring down RNA which should bring down protein level
screen phenotypic biomarkers
what is CISPR-CAS9
like SIRNA as cell trys to repair DNA it adds mutation to the genes
what is used for foward genetics
CRISP-CAS9 and siRNA
what is forward genetics
-identofying phyla in with lost trait
lost trait causes genetic erosion
matching patter of loss and mutation accusation suggests functional relationship
what is transcriptional analysis
Quanitfying the amount of a specific RNA in a sample
what does transcriptional analysis require
purification of RNA
elimartion of DNA
requires labelling
require quantification approach
what’s the most common RNA
ribosomal
what are caveats of transcriptional anaylsis
mutations impact assay performance
splice varnats
rna is not a protein
rna can be edited
how to do transcrioitnal analysis
-nanapore
-reverse transcriptase
RNA to DNA (cDNA)
with cDNA can clone, ligate adapters or ice
what are sources if error om ct
experimental
biological
assay
target/total RNA ratio isn’t fixed
what is an endogenous control
take a known RNA and spike it and bring through to quantification and use the delta ct
how can you analyse the results
DAVID - most popular, cut and paste
IPA- very expensive but very informative
what does DAVID do
it allows you to identify enriched biological themes and discover enriched functional related gene groups
what maps does DAVID make
biocarta and KEGG pathways
when do you use GSEA
to test significance of a group of genes
you rank gens from most to least expressed in one group and then calculates a peak enrichment score
what do you need to do after characterisation of gene list
set off a cutoff value and fold change and integrate the gene list
