Obtaining an account

In order to upload and analyze a dataset, you MUST have an account in the system. To obtain a new account, fill out the registration form accordingly. A confirmation email will then immediately be sent to the email address provided. To complete the registration process, the user must activate the account by clicking on the link provided in the confirmation email. Once the account is activated, the user can login to upload your dataset.

Accessing the Upload Form

1. For existing users who have datasets stored in the system:
   While signed into a user account, mouse over the "Data Manage" tab in the menu bar to access the drop down menu. Click on the "Upload data" option.
2. For new users and users with no datasets loaded in the system:
   Upon signing into a user account, there will be a prompt asking the user to upload a dataset. Or the user can use the same process as described above to access the upload form.

Data uploading



Each field of the upload form is explained below in detail:

1. Project information

1. Project title - Title of the project. Cannot exceed 15 characters.
2. Project description - Description of the project. There is no limit to the number of characters in the description.

1. Organism - Choose the organism from which the dataset was generated. The options currently include Arabidopsis, rice and tomato.
2. ID type - Choose the identification format used in the gene expression dataset. The options for this parameter are dependent on which organism is chosen. Options for Arabidopsis include: ATH1 genome array and TAIR locus number (e.g., AT1G01040). Options for rice include: Affymetrix genome array and the genome locus number (e.g., LOC_Os10g33000). Options for tomato include: TOM1 cDNA array (e.g., 1-1-7.4.19.9), TOM2 oligo array (e.g., LE3D02), Affymetrix genome array and SGN unigene (version: Tomato_200607_build_1; e.g., SGN-U314663).
   
   Note to tomato TOM2 oligo array users: Due to the multiple printing formats of TOM2 arrays, the system has stopped supporting the previous probe ID system for TOM2 arrays and started to use the original Plate IDs. Please contact us if there are any questions.

1. Expression data file - Enter the path and file name of the expression data file to be uploaded. The file must be in the correct format as indicated above.
2. Up-regulation cutoff - Sets minimum value that characterizes a gene as significantly up-regulated. Default value is 2.
3. Down-regulation cutoff - Sets maximum value that characterizes a gene as significantly down-regulated. Default value is 0.5. If the values in the dataset are fold changes or log2 transformed ratios, a negative value is needed as a cutoff.
4. Whether the data contains p values - Indicates whether or not the dataset contains p values. For datasets without p values, leave the check box blank.
5. p value cutoff - Sets value as maximum for significance. Default value is 0.05.

• This part is largely identical to the above section - "Upload gene expression data".

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: