Which of the following best describes a limitation of one-to-one ortholog approaches in plants?

They ignore gene duplications common in plants

How does OMG determine if two clusters are related?

By statistically testing overlap of their orthologous marker gene groups

Which type of gene data does the OMG method rely on?

Top-ranked cluster marker genes

If plant cell types were music genres, what would OMG do?

Find common instruments across genres and build a playlist

Why does OMG use Fisher’s exact test?

To evaluate the statistical significance of shared OMGs between clusters

What is the primary goal of the OMG method?

To identify and compare plant cell types across species

What is a key advantage of OMG over other methods?

It does not need integration, making it faster and more scalable

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OMG paper

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Answers

1
Which statistical test does OMG use to assess significance of overlap between clusters?
Chi-squared test
t-test
Fisher’s exact test
Wilcoxon test
2
Which of the following best describes a limitation of one-to-one ortholog approaches in plants?
Plants lack enough marker genes
Most orthologs are pseudogenes
They ignore gene duplications common in plants
They require animal reference genomes
3
How does OMG determine if two clusters are related?
By statistically testing overlap of their orthologous marker gene groups
By calculating cosine similarity between their PCA embeddings
By their expression magnitude
By the percentage of mitochondrial reads
4
Which type of gene data does the OMG method rely on?
Promoter sequences
Top-ranked cluster marker genes
Whole-genome alignments
Protein interaction networks
5
What does OMG stand for in this study?
Organismal Marker Gene clusters
Orthogonal Marker Genes
Orthologous Marker Gene Groups
Orthologous Molecular Groups
6
If plant cell types were music genres, what would OMG do?
Find common instruments across genres and build a playlist
Play every song at once and hope for harmony
Use random noise as a soundtrack
Only play Arabidopsis hits from the '90s
7
Why does OMG use Fisher’s exact test?
To normalize expression counts
To find nearest neighbors in UMAP space
To check for overrepresented GO terms
To evaluate the statistical significance of shared OMGs between clusters
8
What is the primary goal of the OMG method?
To visualize RNA-seq reads in 3D
To create new plant species using single-cell sequencing
To identify and compare plant cell types across species
To compare raw gene expression data between animal tissues
9
Which tool is used to generate orthologous gene groups in the OMG pipeline?
OrthoFinder
DESeq2
CellRanger
BLASTn
10
What is a key advantage of OMG over other methods?
It always uses the newest data
It doesn’t require any statistics
It relies on single-copy genes only
It does not need integration, making it faster and more scalable

OMG paper Flashcards | StudBud