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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
Q

what are analogues

A

same function
unrelated sequence
not from common ancestor

26
Q

what is forward genetics

A

phenotype to gene
know phenotype of interest
induce mutations
- find infdividuals with knock outs
-find responsible gene
-confirm function by complementqatiojn

27
Q

what is reverse genomics

A

gene to phenotype
inhibit genes
homologous recombination
test for phenotype biomarker
find gene reponsible
reverse the effect

28
Q

when would you get hemizgous bacteria in homologous recombination

A

when homozygous is non viable

29
Q

how do you do gene targeting in mice

A

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
Q

where do you put phenotypes and biomarkers for mice

A

mouse genome informatic database

31
Q

what are the two enzyme systems used in bacterial recombination

A

lamba red and recET

32
Q

what 3 proteins does lamb red use

A

-gam protein
-exo protein
-beta protein

33
Q

how does invivo cloning work for recombineering DNA

A

gap repair or
linear fragment joining

34
Q

how does ssDNA recombination take place

A

uses beta protein and a high conc of single straded DNA which correspond to lagging strand. it is highly effecient

35
Q

what does an enhancer trap do

A

see what enhancer does by making a trap with its own promoter which prevents trancriptiojn

36
Q

what does a promoter trap do

A

stops the expression of down stream exons

37
Q

what does a poly A trap do

A

eliminates exons

38
Q

what is knock down

A

when there is a reduction of an expression of the gene

39
Q

what does siRNA librbay screening do

A

4-10 siRNA per gene and try and bring down RNA which should bring down protein level
screen phenotypic biomarkers

40
Q

what is CISPR-CAS9

A

like SIRNA as cell trys to repair DNA it adds mutation to the genes

41
Q

what is used for foward genetics

A

CRISP-CAS9 and siRNA

42
Q

what is forward genetics

A

-identofying phyla in with lost trait
lost trait causes genetic erosion
matching patter of loss and mutation accusation suggests functional relationship

43
Q

what is transcriptional analysis

A

Quanitfying the amount of a specific RNA in a sample

44
Q

what does transcriptional analysis require

A

purification of RNA
elimartion of DNA
requires labelling
require quantification approach

45
Q

what’s the most common RNA

A

ribosomal

46
Q

what are caveats of transcriptional anaylsis

A

mutations impact assay performance
splice varnats
rna is not a protein
rna can be edited

47
Q

how to do transcrioitnal analysis

A

-nanapore
-reverse transcriptase
RNA to DNA (cDNA)
with cDNA can clone, ligate adapters or ice

48
Q

what are sources if error om ct

A

experimental
biological
assay
target/total RNA ratio isn’t fixed

49
Q

what is an endogenous control

A

take a known RNA and spike it and bring through to quantification and use the delta ct

50
Q

how can you analyse the results

A

DAVID - most popular, cut and paste
IPA- very expensive but very informative

51
Q

what does DAVID do

A

it allows you to identify enriched biological themes and discover enriched functional related gene groups

52
Q

what maps does DAVID make

A

biocarta and KEGG pathways

53
Q

when do you use GSEA

A

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
Q

what do you need to do after characterisation of gene list

A

set off a cutoff value and fold change and integrate the gene list

analytical exam 2 (6 decks)

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