Data Upload

The Upload Data menu at the top of the tranSMART window lets you upload analysis data for a study. It also lets you define information about the analysis (the analysis metadata), such as analysis name, description, data type, sample size, tissue, phenotype, and so on.

Data that you upload through the two-page data upload form is fully integrated with the studies and analyses that have already been loaded in the tranSMART data warehouse. The data is immediately searchable via tranSMART Browse.

Analysis data is uploaded from a tab-separated text file. To ensure that this file is in the proper format for uploading, use one of the provided templates. For information, see File Templates on page 133.

Uploading Analysis Data

Before you begin to upload analysis data, you must have a properly formatted file containing the data in a directory on your local computer or on a network server that is accessible from your computer.

To ensure that the data is in a properly formatted file, use one of the file templates provided. For information, see File Templates.

To upload analysis data:

  1. At the top of the tranSMART window, click the Upload Data menu.

  2. The first Upload Data page appears. On this page, the fields Study, Analysis Type to Upload, and Analysis Name are required.

  3. In Study, select the name of the study associated with the analysis. To do so, do either of the following:

    • Type part of the study name in the text box. tranSMART lists all study names that contain those characters in a contiguous string anywhere in the name (not case sensitive). When you see the name you want, click it. If you do not see the name, type more characters.
    • Click the Browse button to browse the list of study names. Select the one you want and click Select.

    The study metadata appears under the study name. If the selected study is not the one you want, click Change to select a different name.

    Note

    If you do not see the study you want, click the Email administrator button at the upper right corner of the page to inquire about the study.

  4. In Analysis Type to Upload, select the data type of the analysis data.

  5. In Analysis Name, type a name for the analysis.

    This is the name that will appear in the list of analyses for the study.

  6. In Analysis Description, type a description of the analysis.

    The description should contain enough information to help a researcher who is scanning the analyses find the ones that are of interest.

  7. Click Enter metadata.

    The second page of the data upload form appears. The page name will reference the data type you selected on the previous page.

  8. In File, click the Browse button to navigate to the tab-delimited text file that contains the analysis data.

    Optionally, click Download Template to open or save the template for the data type that you are uploading.

  9. Complete the upload data form by providing information for the remaining fields on the form, as described in the table below:

    Analysis Metadata Data Type Description
    Disease or Phenotype All

    Type one or more characters in the name of a disease or observation that is relevant to the analysis. tranSMART lists the names that contain the characters in a contiguous string anywhere in the name.

    Click the name of the relevant disease or observation. If you do not see the name you want, type more characters.

    To add another disease or observation, click Add new.

    Population All Specify the population of individuals to whom the analysis applies.
    Sample Size All Specify the number of subjects who were included in the study.
    Tissue All The type of tissue on which testing was performed.
    Cell Type All The type of cell on which testing was performed.
    (Genotype) Platform: Vendor All

    The genotype platform vendor.

    To add another vendor and platform, click Add new.

    (Genotype) Platform All The specific genotype platform involved in the study. Platform names will vary with the vendor you select.
    Genome Version All The human genome version on which the analysis data is based.
    Expression Platform: Vendor eQTL

    The gene expression platform vendor.

    To add another vendor and platform, click Add new.

    Expression Platform eQTL The specific gene expression platform involved in the study. Platform names will vary with the vendor you select.
    Model Name All The name of the model that was used to perform the analysis.
    Model Description All The description of the model.
    Statistical Test All The statistical test that was used to analyze the data.
    P-value cutoff <= All The p-value threshold applied to the data being uploaded. The uploaded data contains records with a p-value that is equal to or less than the specified p-value cutoff.
    Research Unit All The research unit that performed the analysis or to whom the analysis is relevant..
  10. Click Upload to upload the analysis data and metadata.

File Templates

Analysis data must be contained in a properly formatted, tab-separated text file.

tranSMART includes templates for the supported analysis data types (GWAS, Metabolic GWAS, eQTL). Be sure to use these templates for the analysis data to upload.

The data must contain values in the rsid and p-value columns.

You can download the templates from the data upload form in tranSMART. To do so:

  1. At the top of the tranSMART window, click the Upload Data tab.

    The first page of the upload data form appears. The templates are available from the second page, so you must provide information on the required fields of this page to proceed to the next.

  2. In Study, select any study name.

  3. In Analysis Type to Upload, select the data type for the analysis data that you will upload.

  4. In Analysis Name, type any name.

  5. Click Enter metadata.

    The second page of the data upload form appears.

  6. Click Download Template to the right of the File field:

    image236

    You will be prompted to open or save the template for the data type you specified in step 3.

  7. Click Save, specify a location for the file to be saved, and click Save.

  8. Close the Download dialog box.

  9. Click the Cancel button on the upload data form.