WEIRAUCH

Question 1

The control of gene production is referred to as _____________.

Answer 1

gene regulation

Question 2

Gene regulation has two broad categories: _________ and _________ regulation.

Answer 2

Transcriptional, post-transcriptional

Question 3

___________ is the process by which DNA is transcribed into RNA.

Answer 3

Transcription

Question 4

Transcription factors are proteins that ________ and _________ the synthesis of genes in response to specific cues.

Answer 4

turn on, turn off

Question 5

Humans have approximately ________ transcription factors.

Answer 5

1639

Question 6

Transcription factors interact with the genome by __________ to short sequences.

Answer 6

binding

Question 7

Each transcription factor recognizes a specific _______ motif in the genome.

Answer 7

DNA

Question 8

TF regulatory elements are usually located near the genes they ___________.

Answer 8

control

Question 9

Humans have approximately ________ genes, all of which are controlled by multiple regulatory elements.

Answer 9

20000

Question 10

The _________ of these elements in the genome determines how when and why genes are turned on and off.

Answer 10

regulatory logic

Question 11

________ are expressed only in specific cells or conditions.

Answer 11

Many TFs

Question 12

The anatomy of a typical TF includes the ________ domain.

Answer 12

POU

Question 13

The anatomy of a typical TF includes the ________ domain.

Answer 13

Homeo

Question 14

A SELEX experiment uses a library of random ________ and multiple rounds of selection/amplification to determine which oligos the TF can bind.

Answer 14

oligos

Question 15

PFM stands for ________.

Answer 15

Position Frequency Matrix

Question 16

________ interactions can affect TF binding specificity.

Answer 16

Co-factor

Question 17

It is largely ________ how prevalent co factor interaction that affects TF binding specificity is.

Answer 17

unknown

Question 18

_________ affinity influences TF binding and function in vivo.

Answer 18

DNA sequence

Question 19

Interactions with _________ influence TF binding and function in vivo.

Answer 19

co-factors

Question 20

Relative concentrations of TFs and co factors (aka _________) influence TF binding and function.

Answer 20

competition

Question 21

____________ modifications also influence TF binding and function in vivo.

Answer 21

TF post translational

Question 22

________ accessibility, which includes nucleosome positioning, influences TF binding and function in vivo.

Answer 22

Chromatin

Question 23

_________ status influences TF binding and function in vivo.

Answer 23

DNA methylation

Question 24

DNA _______ topology influences TF binding and function in vivo.

Answer 24

local

Question 25

DNA _______ topology, which includes looping, influences TF binding and function in vivo.

Answer 25

long range

Question 26

_________ footprinting is a technique for increasing precision and sensitivity in computational TF analyses.

Answer 26

Phylogenetic

Question 27

TFBS __________ in sets of sequences is a technique for increasing precision and sensitivity in computational TF analyses.

Answer 27

over representation

Question 28

Leverage of genome wide _________ data is a technique for increasing precision and sensitivity in computational TF analyses.

Answer 28

functional

Question 29

Phylogenetic footprinting is also called sequence _________.

Answer 29

conservation

Question 30

Phylogenetic footprinting is great for increasing __________.

Answer 30

specificity

Question 31

Phylogenetic footprinting is bad for ___________.

Answer 31

sensitivity

Question 32

TFBS over representation uses the ______ in numbers to find TF binding sites.

Answer 32

power

Question 33

Identifying TF binding sites in individual sequences is ____________.

Answer 33

challenging

Question 34

If a set of genes is thought to be __________, statistics can be used to find TF binding sites they share.

Answer 34

co-regulated

Question 35

________ motifs is one of the two basic categories for TFBS over representation which scans a library of PWMs to see if any are statistically over represented in the set.

Answer 35

Known

Question 36

_________ is one of the two basic categories for TFBS over representation which searches for common patterns in the set.

Answer 36

De novo

Question 37

____________ data can be leveraged to determine TF binding, like ENCODE.

Answer 37

Functional