Introduction
Input Data Format
Uploading and Processing
Obtaining an account
Upload Form
Data uploading
Processing Datasets
Project Management
Browsing Pathways
Promoter analysis
Analyzing Dataset
Changed Pathways
GO Enrichment
Functional classification
Searching
Adding New Platforms
Update Pathways and Genes
Contacts
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Processing Datasets
The uploaded datasets CANNOT be analyzed or explored until they are processed.
Immediately after the dataset is uploaded, the system will ask the user to process the
dataset. Processing can also be done at a later time at the "Project Management" page
which lists the uploaded datasets in the system under the current user (for more
information, see the "Project management" section). Datasets not yet processed have
an option to be processed under its list of actions.
The data processing step will assign a code to each gene under each condition to indicate
whether the expression of this gene is increased, decreased, or unchanged. The step will
also identify changed pathways under each condition and calculate the significance of the
change.
Significance of changed pathways
The significance of a changed pathway is determined using the hypergeometric distribution:
Where N is the total number of genes/metabolites in all the pathways, M is the total number
of genes/metabolites in a particular pathway, n is the total number of significantly changed
genes/metabolites in all the pathways, and x is the total number of significantly changed
genes/metabolites in that particular pathway.
The p value obtained above can be explained in the following way:
Suppose that we have a total of N genes in all the pathways, and M genes belong to a particular
pathway. Then the p value represents the possibility that, in a sample of n changed genes of
all the pathways, we observe x or more changed genes in that particular pathway.
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