Analysis Results and Visualization

Volcano Chart Gene

Components:

• Genes are grouped in up-regulated(red), down-regulated(green), and non-significant(gray).

  • If the gene is colored(not gray), it indicates that there is a significant difference in gene expression(fold change).

  • The higher the point, the more significant it is.

• Panel outlined with group color that shows gene ID, p-value, and log2FC when hovering a data point.

• Export.

How to:

• Show/hide a group: Click the group in the chart key.

Mean Average Expression Chart

• Genes are grouped in downregulated(blue), upregulated(red), and not significant(gray).

• Panel that shows the log2FC of a point when hovering.

• Export.

How to:

• Show/hide a group: Click the group in the chart key.

Circos Chart

• Result table.

How to:

• Select a specific pathway: Click the pathway's section on the circumference of the circle.

• Reset chart: Click inside the chart.

Pathway Volcano Chart

• Significant pathways are high and to the right of the chart.

• Panel that shows pathway name when hovering.

• Result table.

• Export.

How to:

• Use AI Interpretation: Click the information icon (i) beside significant pathways.

• Change threshold: Edit the threshold input.

• View specific values of Normalized score: Slide the toggles up/down in the top right corner of the chart.

Forest Chart

• Compare the score of different methods within a pathway.

  • If a method is to the right of the central vertical line, it is up-regulated. If it is to the left, it is down-regulated.

  • If the confidence interval intersects with the central vertical line, it is statistically insignificant.

• Panel detailing each method's score, CI start, and CI end when hovering by pathway.

• Result table.

• Export.

How to:

• Use AI Interpretation: Click the information icon(i) beside the pathway name.

• Sort the chart differently: Use the dropdown menu for Sorted by:.

• Change which methods are displayed: Click the method in the chart key or select/unselect.

• Change the amount of information seen at once: Slide the toggles up/down on the right-hand side.

Bar Chart

• Compare the score of each method in a pathway.

  • If a method is hashed, it is significant.

• Panel that shows the score of the methods in the pathway when hovering.

• Result table.

• Export.

How to:

• Use AI Interpretation: Click the information icon (i) beside the pathway name.

• Sort the chart differently: Use the dropdown menu for Sorted by:.

• Change which methods are displayed: Click the method in the chart key or select/unselect.

• Change the threshold: Change the value above the chart.

• Change the amount of information seen at once: Slide the toggles up/down on the right-hand side.

KEGG Pathway Map

• Significant genes are outlined.

  • Refer to legend for up-regulated and down-regulated.

• Panel that shows gene types when hovering over the outlined.

• Result table.

How to:

• Export chart: Press Save Canvas and it will download as a png.

• Show only significant genes: Select Show only significant genes?

  • Change threshold: Area to change shown only after selecting the above.

Pathway Network

• Each node represents a pathway in the analysis. The size of each node indicates how many genes it contains.

• Edges signify that there are common genes between pathways and indicates how many there are.

• Panel that shows the p-values of each method.

• Result table.

How to:

• Navigate chart: Click on node to drag it around, scroll up to zoom in, scroll down to zoom out, and drag in blank space to move entire chart.

• Choose which methods are shown: Select/unselect method.

• Change the amount of pathways shown: Input value into Select top ___ pathways.

• Sort the pathways differently: Use the dropdown menu beside Selected pathways sorted by:.

• Export chart: Press Export as PNG and it will download as a png.

Venn Diagram

• Shows the amount of genes and percentage for each applicable analysis/intersection.

• Panel that shows intersection name and percentage when hovering.

How to:

• Choose which analyses are used: Select/unselect analysis.

• View specific information for intersection: Click the intersection to view Gene ID, Symbol, and Description.

  • Search for specific Gene ID, Symbol, or Description: Click on the search icon in the headers.

Heatmap Gene

Components:

• Heatmaps of -log10 pFDR and log2FC by protein for each applicable analysis.

• Panel that shows protein name and -log10 pFDR or log2FC when hovering.

• Export.

How to:

• View specific values: Slide the toggles up/down for the corresponding heatmap.

• Change the amount of information seen at once: Slide the toggles up/down on the far right.

KEGG Map Multi Analysis

• The number of color rectangles in the bottom of a node corresponds to the number of analyses included in the session (refer to legend).

• Significant genes are outlined

  • Refer to legend for up-regulated and down-regulated.

• Panel that shows gene types when hovering over the outlined.

How to:

• Change which analyses are used: Select/unselect analysis.

• Export chart: Press Save Canvas and it will download as a png.

• Show only significant genes: Select Show only significant genes?

  • Change threshold: Area to change shown only after selecting the above.

Note: KEGG Map Multi Analysis does not produce a visualization until analyses are chosen.

Heatmap

• Panel that shows the enrichment score for method of pathway when hovering the big square and a path when hovering the circle.

• If the enrichment score is greater than 1, it is overrepresented.

• Export.

How to:

• Choose which methods are shown: Select/unselect method.

• Change the amount of information seen at once: Slide the toggles up/down on the right-hand side.

• View specific values of some value: Slide the toggles left/right in the bottom right corner of the chart.

Multi Analysis Forest Chart

• Compare the score of different methods within a pathway between analyses.

  • If a method is to the right of the central vertical line, it is up-regulated. If it is to the left, it is down-regulated.

  • If the confidence interval intersects with the central vertical line, it is statistically insignificant.

• Panel detailing each method's score.

• Export.

How to:

• Change which methods are displayed: Click the method in the chart key or select/unselect.

• Change the amount of information seen at once: Slide the toggles up/down on the right-hand side.

Multi Analysis Pathway Network

• Each node represents a pathway in the analysis. The size of each node indicates how many genes it contains.

• Edges signify that there are common genes between pathways and indicates how many there are.

• Panel that shows the p-values of each method.

• Result table.

How to:

• Navigate chart: Click on node to drag it around, scroll up to zoom in, scroll down to zoom out, and click on blank space to move entire chart.

• Choose which methods are shown: Select/unselect method.

• Change the amount of pathways shown: Input value into Select top ___ pathways.

• Sort the pathways differently: Use the dropdown menu beside Selected pathways sorted by:.

• Export chart: Press Export as PNG and it will automatically download.

Result table

• Highlight values: Change the thresholds for p-value and p-valueFDR.

• Select pathways to be shown in the visualization: Use the selectors.

• Sort and filter data: Click on the header for the desired column.

• Search for specific ID/Name: Click on the search icon in the header for ID/Name.

• Export to CSV: Click Export to CSV.

Export

• Generally appears in the top left corner of the chart.

• Export as PNG, JPEG, or SVG.

• Change width, height, and scale of export.

How to:

• Hide toolbox: Click the x.

• Un-hide toolbox: Refresh page.