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analytical exam 2 > Genomics > Flashcards

Genomics Flashcards

1
Q

how big is the nuclear genome

A

3.2 gb

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2
Q

what is the gene classification of molecular function and what is an example

A

what a gene product can do without specifying where or when. An example is an enzyme

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3
Q

what do you need to do to generate a hypothesis in functional genomics

A

increased gene expression
decreased gene expression
-removal of gene or insertion
mutate the gene

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4
Q

what is the gene classification of biological process and what is an example

A

classifies the 1 or. more distinct steps, time, transformation an example is signal transduction

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5
Q

how much of DNA is fucntional

A

80.4

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6
Q

what is integrative

A

involves one or two omes

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7
Q

what is dynamic

A

evaluates the impact of change

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8
Q

what is mukltifactoral

A

delivers global analysis of ones

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9
Q

what is gene ontology

A

explains what a gene or transcriptional unit does, offers new targets ad biomarkers of disease

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10
Q

what does gene ontology exclude

A

structures, domains, expression level and binding partners

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11
Q

what is GO classification

A

classifies genes into a hierarchy, placing products with similar functions together

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12
Q

what is MF

A

molecular function - what a gene product can do with out specificying where or when

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13
Q

what is BP

A

biological process - 1 or more distinct step

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14
Q

what is CC

A

cellular comment - part of larger object

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15
Q

what is enrichment for GO

A

more than 5% chance

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16
Q

what is functional genomics

A

-satrt with genome
-identofy things that change
-generate hypothesis
-evaluate gene hypothesis by increased gene expression for example
-define function

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17
Q

what is comapartive genomics

A

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

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18
Q

what is comparative genomics at gene level

A

DNA, RNA or protein
aligns sequence for comparison
calauclatyes common anscetros based on known mutation rate model
describe phyloegenetic relationships

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19
Q

what does comparative genomics at gene level identify

A

common regions
functional domains
unique features

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20
Q

what is multi locus sequence typing

A

can have a look at genetic epidemiology

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21
Q

what is a homologue gene

A

largely comparable sequences
descendants of a common ancestor
sequence divergence

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22
Q

what are orthologues

A

homologous caused by speciation
usually similar function

23
Q

what is a paralogue

A

duplicate event within a genome
divergent sequence
different function

24
Q

what is a xenologue

A

homologous transferred within species

25
what are analogues
same function unrelated sequence not from common ancestor
26
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
27
what is reverse genomics
gene to phenotype inhibit genes homologous recombination test for phenotype biomarker find gene reponsible reverse the effect
28
when would you get hemizgous bacteria in homologous recombination
when homozygous is non viable
29
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
30
where do you put phenotypes and biomarkers for mice
mouse genome informatic database
31
what are the two enzyme systems used in bacterial recombination
lamba red and recET
32
what 3 proteins does lamb red use
-gam protein -exo protein -beta protein
33
how does invivo cloning work for recombineering DNA
gap repair or linear fragment joining
34
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
35
what does an enhancer trap do
see what enhancer does by making a trap with its own promoter which prevents trancriptiojn
36
what does a promoter trap do
stops the expression of down stream exons
37
what does a poly A trap do
eliminates exons
38
what is knock down
when there is a reduction of an expression of the gene
39
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
40
what is CISPR-CAS9
like SIRNA as cell trys to repair DNA it adds mutation to the genes
41
what is used for foward genetics
CRISP-CAS9 and siRNA
42
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
43
what is transcriptional analysis
Quanitfying the amount of a specific RNA in a sample
44
what does transcriptional analysis require
purification of RNA elimartion of DNA requires labelling require quantification approach
45
what's the most common RNA
ribosomal
46
what are caveats of transcriptional anaylsis
mutations impact assay performance splice varnats rna is not a protein rna can be edited
47
how to do transcrioitnal analysis
-nanapore -reverse transcriptase RNA to DNA (cDNA) with cDNA can clone, ligate adapters or ice
48
what are sources if error om ct
experimental biological assay target/total RNA ratio isn't fixed
49
what is an endogenous control
take a known RNA and spike it and bring through to quantification and use the delta ct
50
how can you analyse the results
DAVID - most popular, cut and paste IPA- very expensive but very informative
51
what does DAVID do
it allows you to identify enriched biological themes and discover enriched functional related gene groups
52
what maps does DAVID make
biocarta and KEGG pathways
53
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
54
what do you need to do after characterisation of gene list
set off a cutoff value and fold change and integrate the gene list

analytical exam 2 (6 decks)

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