Lesson 3 Flashcards
In what 2 ways can you compare expression profiles in a heat map?
By comparing rows (usually y-axis is genes) in the expression matrix and by comparing columns (usually c-axis is different tissues)
What 2 methods are utilized to perform clustering?
Hierarchical clustering and partitioning methods
What is the most used clustering method?
Hierarchical clustering
Describe hierarchical clustering:
Represented by a tree in which the length of the branches reflects the degree of similarity between objects → can be used to order genes in the original data table so that genes or groups of genes with similar expression are adjacent
What is different about the partitioning method of clustering?
The number of groups is pre- determined
Why is cluster analysis not the preferred organization method?
There are many ways of measuring distances among gene expression profiles→ very subjective
What is the easiest way to analyze the diversity of expression between 2 genes?
Fold-change method
What partitioning software was originally used for facial recognition but has been utilized for the study of genomic data?
Genomic nonnegative matrix factorization (gNMF)
What is the most brutal method to adjust a p-value?
Bonferroni adjustment → divide each p-value obtained by the number of genes tested = often get zero
What is the most used p-value for the t-test? What if the results need to be more strict?
0.05 / 0.01
What are the 5 steps in the standard gene-centered analysis?
- Collect gene sets
- Order genes by expression difference
- Measure enrichment score (Es) for each gene set
- Record MES for actual data
- Permute class labels
What are the 3 sources of gene sets?
Gene ontology annotation (GOA), pathway databases, and gene set collections
Name the 3 components of gene ontology annotation:
Cellular components, biological processes, and molecular functions
What is the meaning of an enrichment score?
Reflects the degree to which a set is overrepresented at the extremes of the entire ranked list
