Lecture 2 FInal

Question 1

The goal of _________ is subdivided into a set of items (in our case, genes) in such a way that similar items fall not the same cluster, whereas dissimilar items fall into different clusters

Answer 1

clustering

Question 2

Why do we care about genes with similar expression?

Answer 2

genes with similar expression levels are often times regulated by similar mechanisms. An example of this transcription factor which regulate many genes

Question 3

How would clustering be used to restore clustering?

Answer 3

The painting is first muted in its colors and sliced into randomized rows. Computer clustering algorithms are able to reorder the rows by similarities off the intensities between the,. Rows with comparable intensities are arranged adjacent to one another, and the painting can be restored with reasonable precision

Question 4

What are 3 clustering algorithms

Answer 4

• k means or partitioning methods divided in a set of N objects into K clusters
• hierachical methods
• set organism feature maps

Question 5

_________ divides a set of N object into K clusters

Answer 5

K means or portioning methods

Question 6

____________ produces a set of nested clusters n which each pair of objects is progressively nested into a larger cluster until only one cluster set through iterative training

Answer 6

hierarchical methods

Question 7

__________ produces a cluster set through interactive “training”

Answer 7

set organizing feature MAP

Question 8

___________ aims to partition N observation into K clusters in which each observations belongs to the cluster with the

Answer 8

K means clustering

Question 9

________ are displayed in N dimensional space (n=2 if two samples)

Answer 9

Expression profiles

Question 10

first ________ is picked at random among all data points

Answer 10

cluster center

Question 11

other cluster centers are___________

Answer 11

picked as far away as possible

Question 12

Associate each data point to __________

Answer 12

the closest cluster center

Question 13

recompute cluster centers based on new clusters

Answer 13

*itterated until the clusters remain unchanged

Question 14

What are the downsides of K means

Answer 14

• if data is spare, clustering is not robust (releasing the procedure will likely give different clusters)
• The best # of closers is usually not know upfront- the data is forced into K clusters
• Outlirs throw off centroids

Question 15

__________ refers to the study of changes in the regulation of gene activity and expression that are not dependent on DNA sequence

Answer 15

Epigenetic

Question 16

While epigenetic often refers to the study of

Answer 16

single genes or sets of genes epigenomc refers to more global analysis of epigenetic changes across the entire genome

Question 17

____________ in addition to or above the genome

Answer 17

epigenome

Question 18

The concepts of Epigenetic:

Answer 18

-heritable but also reversible
-doesn’t involve changes to the DNA code
Can persist through or nine generations
-regulate gene expression
-main types: DNA methylation and histone modification

Question 19

DNA is not your destiny

Answer 19

epigenome changes are involved in the above phenomia

Question 20

Epigentic “marks” can tell your genes to switch on or off to speak loudly or whisper

Answer 20

it is through epigenetic marks that environmental factors like diet, stress, and prenatal nutrition can make an imprint on genes that is passed from one generation to the next

Question 21

__________ determines which genes are turned on or off in a cell type specific manner

Answer 21

epigenetics

Question 22

Maintenance of:

Answer 22

• gene repression/activation

- repeat silencing

Question 23

Epigentics can be used to study delevelopment and differentiation; whereas, clones and identical twins determined ____________

Answer 23

differences between individuals

Question 24

Genomic imprinting is a genetic phenomenon by which certain genes are ________________

Answer 24

expressed in a parent of origin specific manner

Question 25

_____________ 30 nm chromatin fiber

Answer 25

nucleosome

Question 26

_____________ allows large amounts of DNA to be compacted into a small space very efficiently

Answer 26

chromatin

Question 27

Histone modification includes ____________________

Answer 27

methylation, phosphorylation, and sumoylation

Question 28

___________ a process catalyzed by the addition of a methyl group to a cytosine reside modifying is to a 5 methyl cytosine residue modifying is to methyl cytosine 5

Answer 28

DNA methylation

Question 29

DNA methylation occurs largely in

Answer 29

CpG islands which is found in greater frequency upstream of the gene

Question 30

DNA methylation of the transcription factors thus ________________

Answer 30

suppress gene expression

Question 31

DNA methylation in vertebrates

Answer 31

1. DNA methylation occurs in 5th position of cytosine in CpG dinucleotides and is the major modification found vertebrate genomes 2. catalyzed by DA cytosine methyltransferases 3. Methylation patterns are established during development and differentiation heritable in somatic lineage cells 4. DNA methylation associates with gene repression in vitro and in vivo (imprinted genes, X chromosome inactivation, and silencing of tumor suppressing genes in cancer)

Question 32

__________ DNA methylation is powerful mechanism for the suppression of gene activity

Answer 32

gene silencing

Question 33

There is a reciprocal relationship between the

Answer 33

density of methylated cytosine residues and the transactional activity of a gene

Question 34

Technology for the study of DNA methylation

Answer 34

- Bisulfide DNA treatment, followed by PCR or direct hybridization to CPG island arrays - Methylated DNA immunoprecipitatiiion followed by array or deep sequencing - restricted enzyme digestion using mthylcytosine sensitive enzymes