Week 14 (Single Cell) Flashcards
what are the 4 major downstream analyses of single cell transcriptomic data
- differential expression
- gene set enrichment
- cell-cell communication
- trajectory inference
define DEG process
the sample view aggregates counts per sample-label combination to create pseudobulks
what is the underlying concept of differential gene expression?
single cell data sets are negative binomial distributed that is defines as a discrete probability distribution that models the number of failures in a sequence of independent and identically distributed trials before a specified number of successes occurs
what can you interpret from this data that has one set of cells from someone with a virus vs the control?
there is a higher expression when the virus is present (you can tell by the intensity of color of the slashes because they represent expression level)
define ontology
a set of concepts and categories in a subject area or domain that shows their properties and the relations between them
gene function classification involves grouping genes based on what three roles?
- biological processes
- molecular activities
- cellular locations
define enrichment analysis
a computational method that identifies biological pathways that are overrepresented in a group of genes
what is enrichment analysis useful?
it helps researchers gain insight into gene lists from genome-scale experiments
ligands must bind to a highly ________ receptor
specific
do we know how cells communicate?
we can interpret how cells communicate and make an inference, but it is difficult to know for sure
what is the goal of cell to cell communication analysis?
to infer putative cell to cell communication among various cell types in an organ system using the level of individual genes that are expressed in each
by knowing what ligand one cell produces and knowing that a cell near it has a specific receptor for that ligand what can we interpret?
we can infer how the cells communicate
can single cell generate a lot of hypothesis?
yes! lots of hypothesis
how can cell cell communication be helpful in cancer research?
you can learn how cancer evades the immune cells so that the cel is not killed and cancer continues to grow
why is it important to use multiple tools to run analysis?
being able to take multiple different sets of data and compare them to create a multifunctional way to look at data
what is the purpose of cell trajectory analysis?
allocation of cells to lineages and then ordering them based on pseudo time values within the lineages
define trajectory
the curve that a body describes in space; a path, progression, or line of development resembling a physical trajectory
pseudotime
the distance along the trajectory from its position back to the beginning
why doe we do trajectory analysis, in your own words?
to understand the origin and the end of the cells development
single cell trajectory have a _______ relationship that can help describe the trajectory
graphical
trajectory analysis goal
to study the underlying dynamics of a biological process of interest
trajectory analyses outcomes
- discover unique cell ineages
- estimate differences between differentially expressed genes between lineages
- determine which genes are potentially driving cell fate
transcription factors
a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence
what is the goal of gene regulatory networks?
to test for the unexpected enrichment or transcription factor binding sites in a cell type specific manner to estimate the interplay between chromatin, transcription factors and genes
