How to upload your own experimental data?

Created by Arie Baak, Modified on Fri, 28 Apr, 2023 at 3:03 PM by Arie Baak

OVERVIEW

You can upload your own experimental data for analysis in the platform (for example, a file containing differentially expressed genes with corresponding log2 fold change and p-value). This is recognized as a complex set by the platform.

STEPS

Note	A user action, such as click or enter, is italicized. A visible item on the platform, such as a [link] or a [button], is in square brackets. A link to another article or external source is underlined.

1. Save your set in csv format.

!	Important: The set you want to upload must be saved in csv format and contain multiple columns of data including at least one with measurement data.

2. Click the [+ Create] button on the [Sets] page: this opens up the [Add set] page where you can upload the set.

3. Enter the name, tag, and description for the set.

4. Proceed to the [Upload] file section and select the appropriate [Type] and [Taxonomy] options based on the types and taxonomy of concepts in your file:

Select one of the options under [Type] (default is gene)
Select one of the options under [Taxonomy] (default is Homo sapiens). This is only required for gene and protein set. Click on the drop down menu for other taxonomy options.
Click on the [Choose File] button. A pop-up window opens for you to locate your csv file. Double click on the file to upload.

5. Annotate the uploaded file in the pop-up window. The window automatically pops up if the file to be uploaded contains multiple columns.

Note

The content of each column in the file needs to be annotated:

From the [Column content type] drop down list, select whether the column contains [Text] or [Number].

From the [Sets contents of column] drop down list, select a content identifier. Different options are available depending on the content type selected:

If [Text] is selected as the content type, then these options are available for selection:

If [Number] is selected as the content type, then these options are available for

[Gene Identifier]

[Protein Identifier]

[Compound Identifier]

[Other]

[Ignore: When Selected, do not import this column]*

[RNA Expression: FPKM]

[RNA Expression: TPM]

[RNA Expression: RPKM]

[Differential Expression: Log2 Fold change]

[siRNA: Inhibition]

[Pharmacology: IC50]

[Pharmacology: EC50]

[Statistics: Z-score]

[Statistics: p-value]

[Other]

[Ignore: When selected, do not import this column]*

* If you don't want to import a column, select the [Ignore] option. If you decide to include a certain column later on, you can locate and open this complex set in the [Sets] folder and click the [pencil icon] next tot the set and then click the [Config set] button to change these settings.

6. Click the [Submit] button to save the annotations for the file.

7. Click the [Save] button to save the set. The set is now available in your [Sets] folder. The set type is [Complex] since it contains multiple columns.

How to upload your own experimental data?

OVERVIEW

STEPS

A user action, such as click or enter, is italicized.

A visible item on the platform, such as a [link] or a [button], is in square brackets.

A link to another article or external source is underlined.