Big Data Flashcards
What is big data?
It is often hypothesis generating rather than hypothesis testing.
What types of big data are there?
- ‘OMICS’- genomics, transcriptomics, epigenomics
- Microscopy - fluorescent tagging in cells, automated image analysis. cell type, differentiation, contractility, migration, response to drugs
- Human physiology health- activity tracking, health records, questionnaires, blood samples.
Why is big data used?
To generate knowledge about:
- development
- physiology
- drug safety
- epidemiology
What is cDNA?
Reverse transcriptase generates synthetic DNA from RNA
How is transcriptomics carried out?
mRNA is extracted from a sample and converted to cDNA.
It is then sequenced on illumination next gen sequencing.
Make statistical comparisons.
Identify genes exhibiting differential expression.
What is normoxia and hypoxia?
Normoxia = 21% O2
Hypoxia = 1% O2
What is fold change?
How much gene expression increases or decreases by treatment.
What is significance?
The statistical significance of the difference in gene expression.
What do the colours of a volcano plot dictate?
Red = downregulated genes
Green = upregulated genes
What do gene ontology and biological pathway algorithms interpret?
The consequence of gene expression changes.
How is single cell RNA sequencing performed?
Tissue is dissected and treated with enzymes.
Single cell suspension.
Transcriptome is sequenced.
How is single cell RNA sequencing data plotted?
Using a UMAP plot.
- Each dot is a cell
- Close dots = similar
- Similar cells are clusters of same colour
How are risk genes identified?
GWAS.
Identifies SNPs found more frequently in cases than controls.
How are GWAS results presented?
Manhattan plots, where high scoring SNPs are identified as risk alleles.
What is an SNP?
Single nucleotide variant.
