WEIRAUCH Flashcards
The control of gene production is referred to as _____________.
gene regulation
Gene regulation has two broad categories: _________ and _________ regulation.
Transcriptional, post-transcriptional
___________ is the process by which DNA is transcribed into RNA.
Transcription
Transcription factors are proteins that ________ and _________ the synthesis of genes in response to specific cues.
turn on, turn off
Humans have approximately ________ transcription factors.
1639
Transcription factors interact with the genome by __________ to short sequences.
binding
Each transcription factor recognizes a specific _______ motif in the genome.
DNA
TF regulatory elements are usually located near the genes they ___________.
control
Humans have approximately ________ genes, all of which are controlled by multiple regulatory elements.
20000
The _________ of these elements in the genome determines how when and why genes are turned on and off.
regulatory logic
________ are expressed only in specific cells or conditions.
Many TFs
The anatomy of a typical TF includes the ________ domain.
POU
The anatomy of a typical TF includes the ________ domain.
Homeo
A SELEX experiment uses a library of random ________ and multiple rounds of selection/amplification to determine which oligos the TF can bind.
oligos
PFM stands for ________.
Position Frequency Matrix
________ interactions can affect TF binding specificity.
Co-factor
It is largely ________ how prevalent co factor interaction that affects TF binding specificity is.
unknown
_________ affinity influences TF binding and function in vivo.
DNA sequence
Interactions with _________ influence TF binding and function in vivo.
co-factors
Relative concentrations of TFs and co factors (aka _________) influence TF binding and function.
competition
____________ modifications also influence TF binding and function in vivo.
TF post translational
________ accessibility, which includes nucleosome positioning, influences TF binding and function in vivo.
Chromatin
_________ status influences TF binding and function in vivo.
DNA methylation
DNA _______ topology influences TF binding and function in vivo.
local
DNA _______ topology, which includes looping, influences TF binding and function in vivo.
long range
_________ footprinting is a technique for increasing precision and sensitivity in computational TF analyses.
Phylogenetic
TFBS __________ in sets of sequences is a technique for increasing precision and sensitivity in computational TF analyses.
over representation
Leverage of genome wide _________ data is a technique for increasing precision and sensitivity in computational TF analyses.
functional
Phylogenetic footprinting is also called sequence _________.
conservation
Phylogenetic footprinting is great for increasing __________.
specificity
Phylogenetic footprinting is bad for ___________.
sensitivity
TFBS over representation uses the ______ in numbers to find TF binding sites.
power
Identifying TF binding sites in individual sequences is ____________.
challenging
If a set of genes is thought to be __________, statistics can be used to find TF binding sites they share.
co-regulated
________ 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.
Known
_________ is one of the two basic categories for TFBS over representation which searches for common patterns in the set.
De novo
____________ data can be leveraged to determine TF binding, like ENCODE.
Functional
