Data View

The DataView module provides information and visualisations of the dataset to quickly lookup a gene, check the counts, or view the data tables. It has five panels, which are briefly explained below, followed by more detailed information for each panel.

The Gene Overview panel displays figures related to the expression level of the selected gene, correlation, and average expression ranking within the dataset. In the Sample QC panel, the total number of counts (abundance) per sample and their distribution among the samples are displayed. This is most useful to check the technical quality of the dataset, such as total read counts or abundance of ribosomal genes. In Counts table panel, the exact expression values across the samples can be looked up, where genes are ordered by the correlation with respect to the first gene. Gene-wise average expression of a phenotype sample grouping is also presented in this table. In the Sample information panel, more complete information about samples can be found. Finally, the Contrasts panel, shows information about the phenotype comparisons.

Settings panel

Users can find the settings panel on the right hand side. The panel contains the main settings for the analysis. The analysis can be started by selecting a gene of interest from the Gene settings. Users can filter and select samples in the Filter samples settings, or collapse the samples by predetermined groups in the Group by settings. Under Options, it is possible to visualize the information on a raw count level or logarithmic expression level (logCPM).

Gene Overview

The Gene Overview panel displays figures related to the expression level of the selected gene, correlation to other genes, and average expression ranking within the dataset. To find out more information from the literature, hyperlinks are provide to connect the selected gene to OMIM, KEGG, and GO databases. It also shows the correlation of the gene in other datasets such as ImmProt and HPA, and plots the cumulative correlation. Furthermore, it displays the tissue expression for a selected gene using the genotype-tissue expression GTEx dataset. For each chart of the panel (left to right, top to bottom), a detailed explanation is provided below.

Gene info:

To find out more information from the literature, hyperlinks are provide to connect the selected gene to public databases, including OMIM, KEGG, and GO.

Gene Expression:

Expression barplot of grouped samples (or cells) for the selected gene. Samples (or cells) in the barplot can be ungrouped by setting the Group by under the main Options.

Average Rank:

Ranking of the average expression of the selected gene.

t-SNE clustering:

T-SNE clustering of samples (or cells) colored by an expression of the gene selected in the Search gene dropdown menu. The red color represents an over-expression of the selected gene across samples (or cells).

Top correlated genes:

Barplot of the top positively and negatively correlated genes with the selected gene. Absolute expression levels of genes are colored in the barplot, where the low and high expressions range between the light blue and dark blue colors, respectively.

Tissue expression (GTEX):

Tissue expression for the selected gene in the tissue expression GTEx database. Colors corresponds to “tissue clusters” as computed by unsupervised clustering.

Sample QC

In the Sample QC panel, the total number of counts (abundance) per sample and their distribution among the samples are displayed. For each sample, users can also see the percentage of counts in terms of major gene types such as ribosomal genes, heatshock proteins, or kinases. Abnormal abundance of certain genes may indicate technical problems. A detailed explanation is provided below for every chart of the panel (left to right, top to bottom).

Total counts:

A barplot of the total number of counts (abundance) for each group. The samples (or cells) can be grouped/ungrouped in the Group by setting uder the main Options.

Median counts distribution:

A boxplot of the total number of counts (abundance) for each group.

Density distribution of counts:

A plot showing the density distribution of counts for each group.

Dataset abundance of major gene types:

A barplot showing the percentage of counts in terms of major gene types such as CD molecules, kinanses or RNA binding motifs for each group.

Abundance of major gene types per group:

A barplot showing the average count levels of major gene types such as CD molecules, kinanses or RNA binding motifs for each group.

Counts Table

Under the Counts table panel, the exact expression values across the samples can be read, where genes are ordered by the correlation with respect to the first gene. Gene-wise average expression of a phenotype sample grouping is also presented in this table.

The samples (or cells) in the table can be ungrouped by setting the Group by under the main Options to see the exact expression values per sample (or cell). The genes in the table are ordered by the correlation (rho column) with respect to the selected gene. SD column reports the standard deviation of expression across all samples (or cells).

Sample Information

In the Sample information panel, users can check information about samples and their phenotype grouping through three outputs (left to right, top to bottom):

Phenotype clustering:

A plot showing phenotype clustering. Phenotypes can be unclustered via the Settings icon

Phenotype association:

A phenotype association matrix showing correlation between phenotypes.

Sample information:

A table with sample information.

Contrasts

In the Contrasts panel, more complete information about contrasts can be found. It summarizes the contrasts of all comparisons. Here, users can check which samples belong to which groups for the different comparisons. Non-zero entries ‘+1’ and ‘-1’ correspond to the group of interest and control group, respectively. Zero or empty entries denote samples not use for that comparison.

Through the settings icon on top of the plot, users can display samples individually or in groups.