65 Questions
What is the focus of functional analysis in genetics?
Understanding the different functional roles of genetic factors
Why is it important to look at coding genes in genetic studies?
Protein coding genes are well described and closer to the phenotype
What is the primary goal of studying genetic variation and GWAS?
To identify alleles associated with specific phenotypic traits
What is the key factor in determining whether a gene is driving a particular phenotype?
Understanding when and where the gene is expressed, its function, and its impact on pathways
What does differential expression analysis primarily focus on?
Analyzing the expression of coding genes
How does genetic variation contribute to functional analysis?
By providing insight into the different functional roles of genetic factors
What is the role of SPI-1 in the upregulation of IL1B?
SPI-1 is part of the transcription factor complex necessary for upregulation of IL1B
Which protein binds to LDL cholesterol receptors and can be blocked to reduce cholesterol levels?
PCSK9
What is the function of IL1B?
Causes inflammation
What is the effect of L-Arginine on the transcription of the IL1B gene and recruitment of C/EBP to SPI-1 at the IL1B promoter?
Inhibits both transcription of the IL1B gene and recruitment of C/EBP to SPI-1
How many drugs are mentioned in the text that target IL1B?
3 (anakinra, rilonacept, and canakinumab)
What is the role of bioinformatics software in drug discovery mentioned in the text?
Model the interactions between molecules to predict binding to active sites
What is the main difference between microarrays and RNA sequencing (RNAseq) for gene expression analysis?
Microarrays measure mRNA from select genes, while RNAseq provides a genome-wide measurement of all RNA transcripts.
What is essential for meaningful gene expression analysis using microarrays?
Well-annotated genomes and resources for probe design and manufacturing.
What is a key factor that regulates gene expression?
Region, developmental stage, and response to environmental signals.
What is the purpose of extracting RNA and converting it to cDNA for gene expression analysis?
To facilitate analysis using microarrays or RNA sequencing (RNAseq).
What is a requirement for experimental design in microarray studies to ensure meaningful results?
Balanced, randomized groups with biological replicates.
What aids in understanding the functional aspects of cells and identifying genes linked to specific phenotypes?
Gene expression analysis techniques like microarrays and RNAseq.
Which step is crucial in RNA sequencing?
Isolating RNA and converting to cDNA
What is important in microarray data analysis?
Structural analysis and biological confirmation
What is essential for interpreting gene expression analysis?
Considering p-values, fold change, and the magnitude of expression difference
What is crucial in RNA studies?
Complex study design including technical and biological replicates
What is necessary for RNA extraction and cDNA preparation?
Using fresh samples to avoid degradation
What is involved in gene expression data analysis?
Preprocessing to remove systematic bias and preserve biologically relevant changes
What is the purpose of False Discovery Rate (FDR) in gene expression analysis?
To account for multiple testing and give the probability of false positives among significant differences
What is a potential drawback of the Bonferroni method in gene expression analysis?
It may miss true positives
How does clustering heat maps aid in gene expression analysis?
Visualizing gene expression profiles and sample similarities
What does gene ontology categorize gene functions into?
Cellular component, biological process, and molecular function
How does enrichment analysis using gene ontology contribute to gene expression analysis?
Helps understand the pathways/processes affecting a phenotype
What role do transcription factors like Spi1 and C/EBP play in gene regulation?
Critical roles in gene regulation and inflammatory responses
In a GWAS result, when a TAG-SNP is significantly associated with the disease phenotype this indicates that:
It is in linkage with the disease-causing allele
Genetic drift is strongest in:
Small populations
In GWAS studies, the problem with using a standard P-value is that there would be many false positive results because of multiple testing. One approach to reduce this problem is:
Bonferroni correction
A ___________ block is a set of SNPs that are associated together.
Haplotype
The measure of effect size, or the strength of association, is represented by:
Odds ratio
Around 45% of the human genome is derived from repetitive elements. One of the most common types of these are ______________.
L1 retrotransposons
The __________ is the number of reads that map to a sequence at a specific position.
Coverage
One of the most effective in solution targeted enrichment strategies that enable construction of a DNA library with same specific regions of a whole genome from different samples uses ____________ to capture the desired sequences.
RNA baits
What is the dominant system used today in next generation sequencing?
Illumina
How do Illumina sequencing instruments work?
ligating adapters to DNA fragments that are bound to a dense lawn of oligonucleotides on a flow cell and undergo bridge amplification and then are sequenced in parallel
What is the quality indicator provided in the fasaq file from an Illumina sequencer?
Phred score
What are the advantages of GWAS studies to identify genes that affect phenotypes?
Can be applied to quantitative and complex traits
What is a quantitative trait?
Result of cumulative action of many genes.
What does linkage disequilibrium refer to?
nonrandom association of two or more alleles at two or more different loci
What metric provides information on the quality of an assembly?
N50
What does inbreeding reduce the frequency of?
heterozygotes
What is the metric used to measure the divergence of allele frequencies in subpopulations?
Fixation Index (Fst)
What does the Common Dominant Model of inheritance state?
Either 1 or 2 copies of allele A are required for gamma-fold increase in disease risk.
What is a cytokine that causes inflammation?
IL1B
Identify the protein that binds to LDL cholesterol receptors (LDLR). When it binds, it is blocked, and more LDLR is presented thus removing more cholesterol.
PCSK9
There are >30 genes that increase the risk of what?
Coronary Disease
What is the monoclonal antibody that blocks the protein PCSK9, which prevents PCSK9 from binding those target cholesterol receptors? This helps reduce cholestrol.
alirocumab
Identify the following term:
Provides insight into the pathways/processes that are affecting the phenotype.
enrichment analysis
Many websites are available for the analysis of individual proteins. Name 2 excellent resources:
ExPASy and ISREC
A protein's secondary structure is determined by the amino acids what?
side chain
What is the role of bioinformatics software in drug discovery, as mentioned in the text?
Modeling protein interactions to predict molecules that may bind to active sites
What is the primary function of IL1B, as mentioned in the text?
Causing inflammation and associated with Auto-Inflammatory Diseases (AID)
What is the potential effect of L-Arginine on the transcription of the IL1B gene and recruitment of C/EBP to SPI-1 at the IL1B promoter?
Inhibits both transcription of the IL1B gene and recruitment of C/EBP to SPI-1
What is the main focus of functional analysis in genetics, as mentioned in the text?
Understanding the impact of genetic variation on cellular processes
What is the number of additional genes mentioned in the text that increase the risk of coronary artery disease, aside from PCSK9?
More than 30
Which software platform integrates visualization, modeling, simulations, and methodology development for drug discovery?
MOE (Molecular Operating Environment)
Which protein is part of the transcription factor complex necessary for upregulation of IL1B?
Spi-1
What is the primary role of IL1B in the body?
Causing inflammation
Which amino acid can theoretically dock to the Spi-1 DBD pocket, blocking C/EBPβ binding?
Arginine
What is the name of the monoclonal antibody that targets the PCSK9 protein?
Alirocumab
Study Notes
Key Concepts in Gene Expression Analysis
- Trivial ratio differences may not be significant due to variation, despite large values.
- P-value of 0.05% results in 5% false positives in all tests, leading to significant but non-existent differences.
- False Discovery Rate (FDR) is used for multiple testing in gene expression, giving the probability of false positives among significant differences.
- Bonferroni method is stringent and may miss true positives in gene expression analysis.
- Clustering heat maps visualize gene expression profiles and sample similarities, aiding in identifying regulatory networks or pathways.
- Successful gene expression analysis involves understanding phenotypic effects, protein families, physical properties, and gene ontology.
- Gene expression is dynamic and affected by lifestyle; positive changes can be achieved through learning, exercise, diet, fasting, and specific breathing techniques.
- Gene ontology categorizes gene functions into cellular component, biological process, and molecular function, providing insight into biological systems and pathways.
- Enrichment analysis using gene ontology helps understand the pathways/processes affecting a phenotype.
- Protein structure changes, such as amino acid substitutions, can have dramatic effects, leading to diseases like cystic fibrosis and sickle cell disease.
- Protein analysis involves determining secondary and tertiary structures using algorithms, prediction, and databases like the Protein Data Bank.
- Transcription factors like Spi1 and C/EBP, and cytokines like IL-1B, play critical roles in gene regulation and inflammatory responses.
Test your knowledge of key concepts in gene expression analysis with this quiz. Explore topics such as P-values, false discovery rate, clustering heat maps, gene ontology, protein structure analysis, and the impact of lifestyle on gene expression. Sharpen your understanding of gene regulation and inflammatory responses with this insightful quiz.
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