MuscleAtlasExplorer

Welcome to the Muscle Atlas Explorer!

Are you interested in skeletal muscle transcriptomics? This webpage enables you to explore the data in E-MTAB-1788↗, a very large collection of microarray gene expression datasets.

For more background regarding this web application, click the About tab above.

Get started by searching for a gene of interest! Save CSV
This tab can be used to filter the samples based on phenotypes. To include a filter criterion, click the checkbox on the left side and change the values on the right side. If a subset of samples have been selected, all plots will be adjusted to only show these samples. A spreadsheet of the selected samples can be downloaded using the "Save CSV" button.
Save CSV
This table contains all the genes present in the dataset. Selecting a gene by clicking it will plot that gene in the "Gene plots" tab.
A plot of any phenotype versus the expression of a single gene can be made in this tab. A gene has to be selected in the "Gene table" tab.
This tab contains a selection of precalculated linear model analyses of genotypes versus gene expression. The "Sample" tab contains a table of the results, while the "Plot" tab shows a plot of the expression of a selected gene versus the relevant phenotype.

Welcome to the Muscle Atlas Explorer!

This webpage allows scientists to explore the data in E-MTAB-1788↗, a comprehensive and curated dataset of gene expression microarray data from human muscle.

Please take note that MuscleAtlasExplorer is under active development. Some functions may not work, and output may change in the future as the web application and underlying data are improved and curated.

With this application, you can:

  • filter and select samples by phenotype
  • visualize the selected samples in different ways
  • browse the genes with expression data, and
  • plot the relationship between gene expression and phenotype.

The MuscleAtlasExplorer web application is made by researchers at Lund University Diabetes Centre in collaboration with SciLifeLab.

Phenotype Phenotype ID key Description Type
Sample ID Sample_ID Unique sample ID. string
Sex Sex Sex of patient.
Values:
male , female
mixed : NA but source dataset has both males and females as described in publication.		 factor
Age category Age_category Average age of patient group derived from publication.
NA if exact age is known.		 factor
Age continuous Age_continuous Reported age in years. number
Age group
middle:
old:
Young:
YoungTomiddle: 		factor
BMI group average BMI_group_average Average BMI of patient group derived from publication.
NA if exact BMI is known.		 factor
BMI continuous BMI_continuous Reported patient BMI in kg/m2. number
Physical capacity group average Physical_capacity_group_average Average VO2max of patient group derived from publication in mL/kg/min. factor
Physical capacity continuous Physical_capacity_continuous VO2max of patient in mL/kg/min. number
Diabetes status Diabetes_status Diabetes status.
Values:
NGT: Normal glucose tolerance.
IGT: Impaired glucose tolerance.
T2D: Type 2 diabetes.
IGT or T2D: Either impaired glucose tolerance or type 2 diabetes.
NonT2D: 		factor
Diabetes family history Diabetes_family_history Family history of diabetes. factor
Supercontrol Supercontrol A supercontrol is defined as a sample from a patient with no reported diseases, BMI below 30 and no severe interventions. factor
Other disease Other_disease Reported diseases apart from diabetes status. factor
Study intervention Study_intervention Intervention in the study which the sample originates from. factor
Muscle type Muscle_type The sampled muscle coded as Latin names. factor
Microarray platform Microarray_platform Microarray platform. factor
Study ID Study_ID Study ID. factor

How to cite Muscle Atlas Explorer

We hope that the Muscle Atlas Explorer web application aids your research.

If data from this web application becomes part of one of your articles, please cite the article that accompanies this webpage:

[Articles to cite - TBA]

Alternatively, citation information can be imported directly to Zotero and EndNote using their respective browser extensions.