Please note: Plots (Histogram) comparing the candidate genes with the other maize genes is generated using a randomly downsampled set of other maize genes. The size of the randomly downsampled genes is equal to the size of the user defined candidate genes.
Example Candidate gene list:
To demonstrate the potential use case of the user candidate gene analysis, we gathered a set of fifty stress genes that were differentially expressed between the control and salt stress samples and used them to identify unique characteristics common among salt stress genes .
Please go through the below explanation for details on table and plot interpretations
Table column interpretation:
MicroRNAs (miRNAs) are endogenous non-coding small RNAs that play essential regulatory roles in plant
development and environmental stress responses.
Therefore, for all miRNA's, counts were calculated
for three regions: one using the gene body,second inclusive of the upstream and downstream region,
defined as a 1KB region directly upstream of the gene start site, and
1 KB region directly downstream of the gene end site, third covering larger base pair inclusive of the upstream and
downstream region, defined as a 5KB region directly upstream of the gene start site, and
5 KB region directly downstream of the gene end site:
1. Within miRNA ( miRNA within the gene model)
2. 1kb miRNA ( miRNA within 1kb of the gene model)
3. 5kb miRNA ( miRNA within 5kb of the gene model)
4. Labels
The labels are the classes or the groups the genes are mapped into.The labels can act as both target variable or feature as per the need of the user for solving their specific problem
4.1 No Label
This selection is provided to enable users to view the properties of all genes without labeling them into different gene categories or annotations. This is to let users examine the features of multiple genes and identify common patterns among them. As it involves the inspection of all the genes therefore they work only for "Submit for analysis" button .
4.2 Classical Genes
Classical genes can be defined as the most well-studied genes mainly for their visible mutant phenotype (for example: liguleless3).
4.3 Pan-genome Genes
A gene in a given taxonomic group is either present in every individual (core), or absent in at least a single individual (dispensable).
4.4 Origin Genes
Gene duplication is an important evolutionary mechanism allowing new genetic material and thus opportunities to acquire new gene functions for an organism. There are different origins of duplications such as whole-genome duplications, tandems, etc.
Graph interpretations:
To the top right corner of the plots/graphs, there are options to download plot,
zoom-out/zoom in, reset axes, autoscale, toggle spike lines, show closest data on
hover, compare data on hover, box select, pan and lasso. Users can also select
specific legends to view data only for the selected legends. Details on the interactive
plot options are available here:
Interactive graph features
1. Marginal Plot
The Marginal plots are histrogram plot showing the frequency distribution of the selected gene features alonghwith higlighting the candidate genes. This plot will enable the user to easily identify where thier candidate gene lie among the other maize genes for the selected feature.
2. Histogram
The Histogram shows the frequency distribution of the selected insertion feature such as Within miRNA, 1kb miRNA and 5kb miRNA. The X-axis in the histogram represents the range of values present in the selected insertion. The Y-axis represents the frequency of values. In addition to the graph,to increase the interpretability of the data, We have also included P-values, mean and standard deviations of the selected datasets.
For further details on these features please go through the below tool :https://jbrowse.maizegdb.org/