How to use.
Search public microarray experiments to analyze correlations to other data.
a) Search experiments of your interest by keyword or differentially expressed genes.
b) Select an experiment from the list. Click on an experiment name.
c) You will get the result.
The result is consist of a network graph and a list of correlated experiments. If you click an experiment name on the list, you can jump to new network graph that is centered at the clicked experiment.
How to read result.
a) Relation map of gene expression profiles
Node: Gene expression profiles
Edge: Relationship between nodes (Threshold)
Strong positive (one-way) correlation coefficient (≥ 0.7)
Strong negative (one-way) correlation coefficient (≤ -0.65)
Weak positive (both directions) correlation coefficient (≥ 0.5)
Weak negative (both directions) correlation coefficient (≤ -0.5)
Orange node indicates center experiment used as a query.
Gray edge and characters indicate experiment tags that are extracted as over-represented terms in experiment names.
b) A list of experiments correlated with a query experiment.
Score : The score indicates rank of correlation from the query experiment
Spearman's correlation between the center and the other experiment calculated by using module of the center (a query) experiment.
Spearman's correlation between the center and the other experiment calculated by using module of a experiment in each row.
c) Detail of correlation and trend of differentially expressed genes.
d) Basic statistics of the experiments and their replications.
e) Link from the main window.
*Link to original data
Link to sub-relationmap centered at the clicked experiment.
Link to information of microarray experiments.
You can get original Microarray data here.
Analysing your own data.
a) Data preparation
Format (Microarray data)
- Macroarray Chip: Affymetrix AG, ATH1, and Arabidopsis gene 1.1 ST array GeneChip
- Other macroarray data can be input using AGI code
- Number of Replicate Samples: more than 2 chips (Control data sets are required)
- See a sample of the data format.
Format (RNA-seq data)
b) File upload