20240722_184901

• ◆ Proteins have different functional regions called domains.
• ■ Post-translational modifications
• ■ Two methods used to analyze the proteome
  • ◆ Two-dimensional gel electrophoresis (PAGE) : charge & size
  • ◆ Mass spectrometry : use electromagnets to identify proteins by the masses of their atoms and displays them as peaks on a graph
• ● Epistasis
  • ■ Gene-gene interaction, = modifier genes
• ● Peptides
  • ■ Definition
    • ◆ <50 amino acid chains
• ● Metabolomics
  • ■ Emergence : both gene function & protein function are affected by internal & external environment of the cell
  • ■ Metabolome : the quantitative description of all of the small molecules in a cell or organism
  • ■ Methods to separate molecules
    • ◆ Gas chromatography, high-performance liquid chromatography (HPLC)
  • ■ Methods to identify molecules
    • ◆ Mass spectrometry, nuclear magnetic resonance spectroscopy
• ● Two methods to block translation
  • ■ Antisense RNA: 원래 short, single stranded RNA molecule, no translation 유발
  • ■ SiRNA: 원래 short, double stranded RNA molecule, fragmented translation 유발, 더 stable
• ● HAIRPIN LOOP
  • ■ an unpaired loop of messenger RNA (mRNA) that is created when an mRNA strand folds and forms base pairs with another section of the same strand. The resulting structure looks like a loop or a U-shape.
  • ■ hairpin loops can also form in DNA molecules, but are most commonly observed in mRNA.
  • ■ Function
    • ◆ it can direct RNA folding, protect structural stability for messenger RNA (mRNA), provide recognition sites for RNA binding proteins, and serve as a substrate for enzymatic reactions.[1]
• ● A short hairpin RNA or small hairpin RNA (shRNA/Hairpin Vector)
  • ■ an artificial RNA molecule with a tight hairpin turn that can be used to silence target gene expression via RNA interference (RNAi).[1][2]
• ● Transomics
  • ■ Collection of single omic layers
  • ■ (Yugi et al. 2016, PMID) Good resource!
• ● Mendellian randomization
  • a- 장점:
    • i) can see causality, not just correlation
    • ii) 병발생 이외에 progression도 볼 수 있겠다?
  • b- 단점: quantification 정도? 보통은 risk factor 임을 밝힘?
  • c- Mendelian randomization (MR) uses either individual genetic variants, or polygenic risk scores comprised of multiple genetic variants,
  • d- Assumption
    • i) the genotype must only affect the disease status indirectly via its effect on the exposure of interest.[5]
    • ii) There are no common causes (i.e. confounders) of the genetic variant(s) and the outcome of interest. This is known as the “independence” or “exchangeability” assumption.

	도구변수 (instrument variable) (교란요인으로부터 자유로운 장점, 대개 SNP사용)		독립변수 exposure	종속변수 outcome
	Genetic variation (SNPs)
Example	FTO SNP		BMI	DM
	rs1805313(ALAD 유전자) SNP	혈중 납 농도와 강한 연관성이 존재하는	혈중납	ADHD
	혈중 철분 수치와 연관이 있는 유전자 변이(SNP)		혈중 철	수명
	test

test

• ● Clustering
  • a- K means clustering
    • i) K-means clustering은 데이터를 입력받아 이를 소수의 그룹으로 묶는 알고리즘이다. 이 알고리즘은 아래의 [그림 1]처럼 label이 없는 데이터를 입력받아 각 데이터에 label을 할당함으로써 k개로의 군집화를 수행한다.
    • ii) 각 클러스터와 거리 차이의 분산을 최소화하는 방식으로 동작한다.
• eRA commons
  • b- https://era.nih.gov/erahelp/Commons/default.htm#Commons/1_Admin/mgacct_create.htm%3FTocPath%3DAdmin%2520Module%7CAccounts%7C____2
  • c- https://era.nih.gov/register-accounts?q=registration_accounts.cfm
  • d- Account
    • i) Only individuals with legal signing authority at the university or organization (e.g., CEO, Dean)—known as signing officials (SOs)—can register their organizations. → Once the organization is registered, the SO can register or affiliate the principal investigator (PI) in Commons.
    • ii) SO, AO, AA, BO 들이 PD/PI를 위해 만들어주ㄹ수 있음.
    • iii) Users cannot create their own accounts

Logarithm

Base (밑)	example	Exponent (지수)= "log"	"inverse log"			synonym	written
2	23 = 8 3 = log2 ?   2-3 = 0.125   -3 = log2 0.125 Exponent = log2 Inverse Log	3	8	"log of 8 is 3 (to the base 2)"	"the inverse log is 8 (to the base 2)"
	2NPX=Original value 3을 알고, ? (inverse log)를 구할때는 https://www.rapidtables.com/calc/math/Log_Calculator.html 에서 'exponent calculator'를 선택 NPX 값을 알고, Original value (inverse log)를 구할때는 https://www.rapidtables.com/calc/math/Log_Calculator.html 에서 'exponent calculator'를 선택 → "Enter base"에 "2", "Enter Exponent"에 NPX값/beta값 등 입력 → 결과가 원래의 fold change			NPX is in a log2 scale, a 1 NPX difference means a doubling of protein concentration	1 = log2 2 2 = log2 4 3 = log2 8 Ie Original value: 2→4→8 일때, NPX: 1→2→3
	NPX = log2 Original value Original value 를 알고, NPX value 를 구할때는 https://www.rapidtables.com/calc/math/Log_Calculator.html 에서 'logarithm calculator'를 선택
10	102 = 100	2	100	2 is the logarithm of 100 to base 10	The base 10 logarithm of 100 is 2	Common, Briggsian	log n
e ≅ 2.718	(ex) = x e0.008 = 1.008	0.008	1.008		The base e logarithm of x	Natural logarithm	ln n
	0.008 = loge 1.008

• ■ 매년 같은 비율(예를 들어 x%)로 성장하면 그 크기가 두배가 되기 위해서는 70/x years 가 소요 된다.
• ■ 매년 5% 씩 성장하면 그 크기가 두배가 되는데 14년이 소요되고, 70년 후에는 32배가 된다.
• ■ 매년 7% 씩 성장하면 그 크기가 두배가 되는데 10년이 소요된다. 70년 후에는 128배가 된다.

Uncertain Spans

location	transcription	uncertainty
Mendelian randomization Example table, second row middle column	혈중 납 농도와 강한 연관성이 존재하는	The cell is rendered in red and the trailing copy spans the cell edge; whether 존재하는 is the full ending or whether further qualifier text continues is at the resolution edge of the photo.
eRA commons URL b-	https://era.nih.gov/erahelp/Commons/default.htm#Commons/1_Admin/mgacct_create.htm%3FTocPath%3DAdmin%2520Module%7CAccounts%7C____2	The URL fragment ____2 near the end is read as four underscores then 2; whether this reflects the original encoded path or an OCR artefact of the underline that hyperlinks usually carry is uncertain from the photo.
Logarithm table, eRA-style URL inside cells	https://www.rapidtables.com/calc/math/Log_Calculator.html	The inline calculator URL is read by combining a partly underlined hyperlink fragment with the surrounding text; the exact pathname after /calc/math/ matches Log_Calculator.html but is at the small-font edge of the photo.