New developments in high-throughput biological studies mean that the genes that are active in just a single cell can now be determined. However, analyzing the complex datasets that result can be challenging. Now, a research team has developed CAPITAL, a new computational tool for comparing complex datasets from single cells.
RNA sequencing provides information on the subset of the entire population of genes that are actively being expressed, or are “switched on”. As technology has advanced, it has become possible to sequence the RNA population of just a single cell. This can provide a great deal of information on the specific changes in gene expression involved when a large population of mixed cells undergoes dynamic, transitional processes, such as differentiation or cell death, because each individual cell can be specifically analyzed rather than all the different cell types being pooled.
CAPITAL is specifically designed to compare complex datasets from single cells undergoing transitional processes. These analyses are carried out by defining a “pseudotime trajectory”, which places the cells along a hypothetical path that reflects their progress through the transitional process. These trajectories are not always straightforward and linear; they can become very complex and branching. In the past, only linear trajectories could be aligned for comparison, but the team’s innovation means that complex branching trajectories can now be accurately and automatically aligned and compared.
After developing the algorithm used for CAPITAL, which implements a method known as tree alignment, they tested it on both synthetic datasets and authentic datasets from bone marrow cells. The results demonstrated that CAPITAL is statistically more accurate and robust than the computational algorithms that existed previously, showing major advances over these methods.
Trajectory comparison is a powerful analysis that can, as an example, identify the gene expression dynamics between different species to provide information on evolutionary processes. “We showed in this study that CAPITAL can reveal the existence of different molecular patterns between humans and mice even when the expression patterns are similar and appear to be conserved,” says the lead author. “This will allow the identification of novel regulators that determine cell fates.” This technology is not limited to just this type of data, as the senior author explains: “Our novel computational tool can be applied to a wide range of high-throughput datasets, including pseudotemporal, spatial, and epigenetic data.”
This powerful new technique will allow the global comparison of single-cell trajectories, which may lead to the identification of novel disease-associated genes that could not be identified by earlier comparative methods. Thus, CAPITAL represents a significant advance in the field of single-cell biology.
https://www.nature.com/articles/s41467-022-33681-3
http://sciencemission.com/site/index.php?page=news&type=view&id=publications%2Falignment-of-single&filter=25
CAPITAL to advance single-cell RNA data analysis
- 765 views
- Added
Edited
Latest News
Metabolic rewiring promotes…
By newseditor
Posted 18 Apr
A drug to prevent flu-induc…
By newseditor
Posted 18 Apr
New origin of deep brain waves
By newseditor
Posted 17 Apr
Starving cells hijack prote…
By newseditor
Posted 17 Apr
Miniature battery-free epid…
By newseditor
Posted 17 Apr
Other Top Stories
Frequent alterations in cytoskeleton remodelling genes in lung cancer
Read more
New role for a long noncoding RNA in tumor growth via altered glyco…
Read more
Identifying kinases that drive metastasis
Read more
Drug provides another treatment option for an early form of breast…
Read more
Role of epigenome on TGF-β/SMAD mediated Cancer
Read more
Protocols
MemPrep, a new technology f…
By newseditor
Posted 08 Apr
A tangible method to assess…
By newseditor
Posted 08 Apr
Stem cell-derived vessels-o…
By newseditor
Posted 06 Apr
Single-cell biclustering fo…
By newseditor
Posted 01 Apr
Modular dual-color BiAD sen…
By newseditor
Posted 31 Mar
Publications
How does the microbiota con…
By newseditor
Posted 18 Apr
The integrated stress respo…
By newseditor
Posted 18 Apr
The immunobiology of herpes…
By newseditor
Posted 17 Apr
Circulating microbiome DNA…
By newseditor
Posted 17 Apr
Spindle oscillations in com…
By newseditor
Posted 17 Apr
Presentations
Hydrogels in Drug Delivery
By newseditor
Posted 12 Apr
Lipids
By newseditor
Posted 31 Dec
Cell biology of carbohydrat…
By newseditor
Posted 29 Nov
RNA interference (RNAi)
By newseditor
Posted 23 Oct
RNA structure and functions
By newseditor
Posted 19 Oct
Posters
A chemical biology/modular…
By newseditor
Posted 22 Aug
Single-molecule covalent ma…
By newseditor
Posted 04 Jul
ASCO-2020-HEALTH SERVICES R…
By newseditor
Posted 23 Mar
ASCO-2020-HEAD AND NECK CANCER
By newseditor
Posted 23 Mar
ASCO-2020-GENITOURINARY CAN…
By newseditor
Posted 23 Mar