Cancer
Define Angiogenesis
Angiogenesis --> formation of new blood vessels
What is the result of this code:
for i in range(1,13,2):
print(i)
Bonus 200 Points: What if instead it was:
for i in range(1,13,2):
print(i,end='')
1 3 5 7 9 11 (on separate lines)
Bonus Answer: 1357911
What is the result of this code:
string = " So Silly. "
string.strip()
"So Silly."
What is RNA-Seq?
Sequencing all of the RNA / transcripts of a cell (transcriptome).
Provides insight into what genes are expressed and different splicing variants.
This person was caught cheating in a Coldplay concert this year.
Who is Andy Byron, CEO of Astronomer?
What is the difference between benign and malignant?
Benign tumor cells don't move from their site of origin.
Malignant tumor cells invade other tissue.
What is the output of this code?
string = "FenleyBestTA"
result = ""
for char in string:
result = result + char * 2
print(result)
FFeennlleeyyBBeessttTTAA
What method can I use if I want to arrange a list in alphabetical order?
Bonus 200: How can I edit the method to arrange the list in reverse order?
.sort()
Bonus: .sort(reverse=True)
What p-value is considered significant?
What is p<0.05?
This popular movie released in 2006 is filming a sequel currently in NYC.
This protein class helps control the cell cycle by signaling cells to proceed past checkpoints like G1 and G2.
What is Cyclins
What is the result of this code:
list1 = [der, noa, fah]
list2 = [eva, sne, tim]
list1.append(list2)
print(list1)
[der, noa, fah, [eva,sne,tim]]
What is the similarity and difference between:
del list[index]
list.pop(index)
del list[index] simply just deletes the element at the specified index.
list.pop(index) ALSO deletes the element at the specified index, but it also RETURNS that element, and that element could be stored in a variable.
What does a volcano plot show?
A volcano plot is a type of scatter plot used to quickly visualize the results of differential expression analysis, such as in RNA-seq experiments.
It displays the log fold change in gene expression against the statistical significance (often represented by the negative logarithm of the p-value) for each gene.
This show had an episode where the plot was about "turning into pickles."
What is Rick and Morty?
What is the role of p53?
Is it an oncogene or tumor suppressor?
Bonus: What is its nickname?
p53 is a tumor suppressor that halts the cell cycle when DNA damage occurs, allowing time for repair or apoptosis if repair isn't possible.
Bonus: Its nickname is the "guardian of the genome".
Write code for this problem statement:
I have a list of 50 numbers. I want to take out only the numbers that are divisible by 3. Then I want to add 2 to each of those numbers.
new_list = []
for num in list:
if num % 3 == 0:
new_list.append(num+2)
What is the result of this code:
num = 2
while num % 2 == 0:
num += 2
Error: The while loop will continue forever.
Why / How was PCA used in the project?
Bonus 200: Why were the samples colored by type?
Bonus 100: What does PCA stand for?
PCA was used to reduce thousands of gene expression measurements per sample down to just two main axes (PC1 and PC2) that capture the biggest patterns of variation between samples.
Bonus: The samples were colored by type (primary, metastatic, normal) to see which samples group together based on similar expression profiles.
Bonus: Principal Component Analysis
This is the real name of Jay Z.
Who is Shawn Corey Carter?
[case] A patient has a BRCA1 mutation. Is BRCA1 a tumor suppressor or oncogene? How does this relate to breast cancer risk?
BRCA1 is a gene that produces a protein involved in repairing damaged DNA and is also known as a tumor suppressor gene.
A mutation increases the chance of cancer because damaged DNA builds up.
Write this for loop as a list comprehension.
new_list = []
old_list = [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16]
for num in old_list:
if num % 2 == 0:
new_list.append(num)
Hint: List comprehension Format:
[item for item in list if condition]
new_list = [num for num in old_list if num % 2 == 0]
What does "enumerate" do?
Hint: It's used as a way to loop through a list.
When used with a for loop, enumerate allows you to access both the index and value of the elements in a list.
What is normalization?
Bonus 500 Points: Explain why normalization was important for our project.
Normalization is the process of adjusting data measured in different scales to a common scale / convert a wide range of numbers to a smaller, more easily comparable range.
BONUS: Normalization REMOVES differences caused by different sequencing depths.
We start with raw read counts for each gene in each sample. But different samples might have different sequencing depths (some have more total reads just because the sequencer collected more data).
If we compared these raw numbers directly, it wouldn’t be fair — a sample with more reads overall would look like it has higher expression for every gene, even if biologically it’s the same.
This person famously said "I don't know her" when asked about Jennifer Lopez.
Who is Mariah Carey?