Home Manager

The Home section is accessible by clicking the “Home” icon from the Welcome page. In the Home Page you can create, load and modify an Experiment Package with a more intuitive approach.

Creating an Experiment Package

Adding a new Experiment Package

To create an Experiment Package from scratch the first thing to do is to click the “Add New” button.

Uploading a new Experiment Package

To upload an Experiment Package the first thing to do is to click the “Upload” button.

Editing an Experiment Package

To edit the configuration of an Experiment Package, click on the “Edit Pack” button on the package’s blue box in the Home section. You will be redirected to the configuration page.

The configuration articulates in three sections, explained in detail in the following sections:

  1. General information editing and reference organism assigning

  2. Dataset configuration

  3. Ontologies selection

After the editing is complete you can save the configuration by clicking the “Save” button.

Edit Experiment’s General Information

By editing the first section in the configuration page you can perform the following:

  1. Assign a title to the package

  2. Assign a reference organism to the package by selecting it from the “Organism” selector.

  3. Write a comment

Configure a Dataset

The configuration of a dataset requires the following general steps:

  1. Select what -omic science is representative of the dataset by using the “Select omic” selector

  2. Select what kind of ID is being adopted in your dataset

  3. Select which column is holding the IDs

  4. Select which column is holding an Effect Size Static value (e.g. logFC), if any

  5. Select which column is holding a p-value, if any

  6. Upload your dataset in a tab-separated text format by either copy and paste it in the coloured text area, or by uploading it using the “Upload {omic} pack” button below

Gene Ontologies

Your Home Page also provides a list of cellular compartments that are nothing less than Gene Ontologies. Each one of the entries represents a gene list of Entrez Gene IDs and you can select the ones you are more interested in by clicking the “+” button located on the right side of each box. A search box is also provided to filter the ones you are most interested in. Gene Ontologies of interest will be added to the other list alongside the preselected ones: Nucleus, Cytoplasm, Mitochondrion, Lysosome, Endoplasmic Reticulum, Golgi Apparatus, Cytoskeleton, Membrane. You can of course remove them by clicking the “-” button in the selected boxes. Cellular compartments selected will be found in a dropdown menu after PathLay has completed the analysis and it’s ready to show the results on functional pathways. Once a cellular compartment is chosen, only genes and proteins localized in that compartment will remain displayed on the pathways (see more “Pathway Explorer”).

Downloading an Experiment Package

The “Download” button allows you to package the currently loaded datasets and configurations in a zip archive and export it from PathLay for other uses, for instance, this archive can be uploaded as a new Experiment Package into another PathLay account.