How to use.
Search and select a query experiment.
a) Search experiments or view a list of all experiments.
b) Select an experiment from the list. Click on an experiment name.
c) You will get the result.
If you click a node on the network or experiment name on a table, you can jump to new network 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)
Pink node indicates center experiment used as a query.
square: stress or stimulation treatment
pentagon: tissue specific profiles
octagon: chemical treatment
b) A list of experiments correlated with a query experiment.
Score : The score indicates rank of correlation from the query experiment
Control Experiment : A biological control for each experiment
upper value :
Spearman's correlation between the center and the other experiment calculated by using module of the center (a query) experiment.
lower value :
Spearman's correlation between the center and the other experiment calculated by using module of a experiment in each row.
c) Basic statistics of the experiments.
d) Detail of correlation.
The upper arrow is a link to detail page on the correlation that is calculated using the module of the center experiment.
The lower arrow is a link to detail page on the correlation that is calculated using the module of the experiment in each low.
e) Link from the main window.
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
- Macroarray Chip: Affymetrix ATH1 GeneChip
- Format: microarray suite 5, tab-deliminated text format
- Number of Replicate Samples: more than 2 chips (Control data sets are required)
b) File upload