AtlaZ is a toolkit designed for the analysis and visualization of zebrafish gene expression data across developmental stages and tissues. This package facilitates the integration of anatomical data, gene expression profiles, and ontological information, enabling researchers to explore the assortment of gene expression across developmental stages in zebrafish.
The package uses the E-ERAD-475 dataset available from the Expression Atlas which contains the expression values of all genes found in zebrafish across all developmental stages.
It was built as an R package, and was developed as a part of a course project for BCB410H1: Applied Bioinformatics during the Fall 2023 semester at the University of Toronto. The development environment used was:
| Software | Version |
|---|---|
| R | 4.3.1 |
| Platform | arch64-apple-darwin20 (64-bit) |
| OS | macOS Sonoma 14.1.2 |
To install the latest development version of AtlaZ, run the following code in R:
install.packages("devtools")
library("devtools")
devtools::install_github("ashenafee/AtlaZ", build_vignettes = TRUE)
library("AtlaZ")To run the Shiny app:
runAtlaZ()To get an overview of AtlaZ in your R session, run the following code:
ls("package:AtlaZ")
data(package = "AtlaZ")
browseVignettes("AtlaZ")AtlaZ has one major class, Gene, which is used to store information
about a gene. It has the following attributes:
| Attribute | Description |
|---|---|
geneSymbol |
The gene symbol of the gene. |
ensemblID |
The Ensembl ID of the gene. |
zfinID |
The ZFIN ID of the gene. |
anatomy |
An AnatomyList object containing information on the different possible areas where this gene is expressed. |
ontology |
An OntologyList object containing information on the different possible GO groups this gene falls into. |
The AnatomyList class stores many Anatomy objects which contain
information on a specific area where a gene is expressed. In a similar
fashion, the OntologyList class stores many Ontology objects which
contain information on a specific GO group a gene falls into. These
classes are a new addition as prior there was lots of wrangling with
nested lists to get this information. By using these classes, it is much
easier to access the information from one single Gene object.
Data Visualization
plotGeneExpression is a function that creates a line plot of gene
expression values for a specific gene over different developmental
stages. The line plot is an effective way to visualize how the
expression of a particular gene changes across different stages of
development. Each point on the line corresponds to a gene expression
value at a particular developmental stage, and the line’s progression
shows the trend of these values over time. This can help researchers
identify patterns or anomalies in gene expression, which can be critical
in understanding gene function and its role in development.
plotMultipleGeneExpression does the same thing as
plotGeneExpression, but for multiple genes. This is useful for
comparing the expression of multiple genes across different
developmental stages.
Fetching from ZFIN
getZfinBackgroundInfo(zfinId: str) is a function that fetches
background information about a gene from ZFIN. This function was
initially used to obtain the anatomical and ontological information, but
getGeneInfo() is now favoured.
Fetching from Ensembl
getGeneInfo(geneSymbols: str[]) is a function that fetches information
on one or more genes from Ensembl. This function is used to populate the
Gene object with information about the gene. This function is also
used to populate the AnatomyList and OntologyList objects with
information about the different areas where the gene is expressed and
the different GO groups the gene falls into, respectively.
Figure 1. An overview
of the AtlaZ workflow and how it works on a high level.
AtlaZ mainly uses the data from the E-ERAD-475 dataset, and that’s where most functionality is unlocked/tested.
If data is provided as input (i.e., it’s from the user and not from ZFIN), it must be cleaned up and formatted first before it can be used by AtlaZ. This data must be formatted with the following headings: Gene ID, Gene Name, zygote, cleavage 2-cell, blastula 128-cell, blastula 1k-cell, blastula dome, gastrula 50%-epiboly, gastrula shield, gastrula 75%-epiboly, segmentation 1-4 somites, segmentation 14-19 somites, segmentation 20-25 somites, pharyngula prim-5, pharyngula prim-15, pharyngula prim-25, hatching long-pec, larval protruding mouth larval day 4, larval day 5.
A valid Ensembl identifier must be under Gene ID with a valid gene
symbol under Gene Name. The rest of the columns can consist of
numerical values as those represent expression values across each
development stage.
My name is Ashenafee Mandefro, and I am the author of this package. I’ve worked with large databases similar to ZFIN in the past (i.e., GenBank, Ensembl) and I want to adapt my skills to a zebrafish context, given that fits into the context of my current thesis project at the Lin Lab. You can see more of my projects here.
Expression Atlas is used as the primary data source in AtlaZ, with the primary dataset being E-ERAD-475 dataset. Aside from Expression Atlas, more datasets are available for download from ZFIN from their website which is available here. The data provided by ZFIN is licensed under the Creative Commons Attribution 4.0 International License.
Generative AI was used to help with creating the initial documentation for each function. Specifically, GitHub Copilot was prompted with the contents of the function and an initial docstring, and it generated a final docstring that was then edited by the author. More information on GitHub Copilot is available here.
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This package was developed as part of an assessment for 2023 BCB410H: Applied Bioinformat- ics course at the University of Toronto, Toronto, CANADA. AtlaZ welcomes issues, enhancement requests, and other contributions. To submit an issue, use the GitHub issues.