About:
Here you will find a description of the organization and functionality of the different components
of the main SKMATLAS homepage.
Anatomy of the homepage:
The SKMATLAS homepage consists mainly of 3 sections that warrant descriptions.
The other one sections are self-explanatory. Figure 1 shows the different sections of the TCDB
homepage with their respective components.
Figure 1. Components of the SKMATLAS homepage. The page is organized in 3
main sections: A. Top menu bar. B.Global search box. C. Quick access to Multi-omics data for each
species.
Each section is described separately below.
A:The top menu bar section
This section (Figure 1A) covers the top menu bar, which includes the following eight tabs:
The Home tab
This tab provides a quick shortcut link to the main SKMATLAS homepage.
The Statistics tab
This tab links to a page show statistics for different dimensions of all data
including fourteen species and six omics. All data were counted by number of samples, number of
reads, developmental stage, number of breed, muscle type, number of peaks groupings, respectively.
Figure 2. Statistics for different dimensions of all data
The Browse tab
By choosing specie, this tab returns the a statistic of biosample and list
of sample of this specie grouped by omics.
Figure 2. Browsing sample of one specie grouped by omics.
The Genome Browser tab
By choosing specie, this tab links to genome browser which for exploring the data of Epidermomics of one specie.
Figure 3. Genome browser
The Search tab
This tab links to a page for advance search function. The details of advance search to see Search page.
The Analysis tab
This tab needs choose analysis function: DoHeatmap and Network.The details of analysis to see Analysis function.
The Tools tab
This tab returns the table of software used in our standard analysis process and every software name can links to its’ official website.
Figure 4. list of software used in the standard analysis process
The Help tab
This tab links to the main SKMATLAShelp page, which provides a number of tutorials designed to maximize the benefit you get from SKATLAS.
B: Global search box.
This section (Figure 1B) is a global search box. User can find a bioproject, biosample, gene,GO term,KEGG pathway by using this search box.
Search a bioproject or biosample
Using bioproject ID or biosample ID to find a bioproject or biosample.
Figure 5. Global search by biosample ID. This result links to detail information of this biosample.
The result of global search by bioproject ID is same to biosample.
Search a gene
Figure 6. Global search by gene ID. The page is organized in 2 main sections:A. This Gene ID links to GenePage. B. Block section show the list of genes of List of homologous from Biomart.
Figure 7.Global search by symbol. This page shows genes in all species named this symbol.
Search a GO term or a KEGG pathway ID
Figure 8.Global search by GO term ID. This page shows a list of genes in this term. The result of global search by KEGG pathway ID is same to GO term ID.
C: Quick access to Multi-omics data for each species.
Figure 9. Cards of 14 species with simple statistic.
In this section, when the mouse hovers over a card, the card drawer structure opens to see a simple count of the number of various omics samples of the species, clicking to jump to BrowsePage.