■ About Mouse Circadian Proteome Atlas

The Mouse Circadian Proteome Atlas is an interactive visualization platform designed to explore circadian and developmental dynamics of gene and protein expression across multiple mouse tissues. It integrates transcriptomic and proteomic data—including total protein, nuclear protein, and their phosphorylated peptides—measured at six circadian time points (CT2, CT6, CT10, CT14, CT18, and CT22) and across key developmental stages.

Users can select from five major data categories:

• "32 tissues":
  Line graphs display temporal profiles of protein amount for the target gene at the six time points across 32 tissues.
• "Liver":
  Line graphs display temporal profiles for the target gene at the six time points in the liver:
  mRNA, total protein (whole-cell), nuclear protein (Nuc-sup and Nuc-ppt), and phosphorylated peptide in whole-cell and Nuc-sup.
• "SCN":
  Line graphs display temporal profiles for the target gene at the six time points in the SCN:
  total protein (whole-cell) and phosphorylated peptide in whole-cell.
• "FASPS liver":
  Line graphs display temporal profiles for the target gene in the liver from WT and FASP (PER2-S662G) mice as shown in category 2 “Liver"
• "Development":
  An upper bar graph displays expression changes of protein amount for the target gene at different developmental stages (E9.5, E13.5, E17.5 and P1.5).
  Lower line graphs display the expression levels of the target gene at the six time points on E17.5 in four tissues (Forebrain, Liver, Lung, and Heart).

If the target gene has multiple isoforms, each isoform is plotted on a separate line graph using distinct colors.

■ Result Display Screen

The following result shows the temporal profiles of the target gene "Aldh1l1" across 32 tissues.

■ How to Use

• Select one data category from "32 tissues", "Liver", "SCN", "FASPS liver", or "Development".
• When you start typing the gene name, a list of suggested results will appear.
• If you select "32tissues" and click the "Search" button,
  32 temporal profiles for the target gene at the six time points in the 32 tissues will be shown.
  If the target gene has multiple isoforms, each isoform is plotted on a separate line graph using distinct colors.
• Numerical data and graphs can be downloaded using the "Save as CSV" and "Save as HTML" buttons.
• By clicking the menu icon, you can toggle the "Normalize," "Scaling," and "Axis" options On/Off. For more information, please refer to the section below, "Graph Display Options"

Graph Display Options

Normalize On:
Each graph will be normalized to have a maximum value of 1.
The absolute values of the original data will be lost.

Scaling On:
The y-axis scale for all graphs will be unified from 0 to the maximum value of the entire dataset.
Scaling On is recommended to compare the expression levels across 32 tissues, while Scaling Off is recommended to compare the phase of circadian rhythms across 32 tissues.

Scaling Off:
Each graph will be automatically adjusted to the optimal range individually.

Axis Off:
The ticks on the x-axis and y-axis will be hidden.

*When Normalize is On, the y-axis range will be 0–1 regardless of the Scaling On/Off status.

Glossary

Term	Description
Target gene	The gene selected by the user for visualization of temporal profiles.
Isoform	A variant of a gene resulting from alternative splicing or transcription.