INTERSPIA

Introduction

User submits input genes or proteins, target and other species, the STRING confidence score cutoff and interaction score cutoff.
INTERSPIA extends user's given proteins using the random walk with restart algorithm, and filters the extended proteins based on the given interaction score cutoff (optional).
INTERSPIA extracts orthologous proteins of other chosen species using the orthoDB database (v8), and collects protein-protein interactions in different species using the STRING DB (v10.5).
The collected protein-protein interactions among multiple species are visualized.

Please click on each of the following steps to see animations (also provided as a single PDF file ).

Configuring the analysis using user’s data
(1) Entering the list of proteins
(1-1) Selecting the type of the input genes or proteins

(1-2) Entering the list of genes or proteins manually
If user select the 'Ensembl' identifier, target species is automatically selected. If user select the others, target species is must be passively selected.
(1-3) Uploading a file with the list of genes of proteins
If user select the 'Ensembl' identifier, target species is automatically selected. If user select others, target species is must be passively selected.
(2) Additional parameters
(2-1) Protein extension process

(2-2) STRING confidence score cutoff

(3) Selecting a target species

(4) Selecting other species for comparison

(5) Clicking the “Submit” button to start the analysis

(6) An example data of the INTERSPIA analysis

(7) Refreshing the analysis page

Please click on each of the following steps to see animations (also provided as a single PDF file ).

1. Controlling options
(1) Searching a protein or an orthologous protein group

(2) Selecting layout
(2-1) Grouping by protein-protein interactions

(2-2) Grouping by orthologous protein IDs

(2-3) Hold button

(3) Handling interaction level

(4) Visualization setting of Protein-Protein Interactions (PPIs) type
(4-1) All interactions

(4-2) Only species-specific interactions

(4-3) Only conserved interactions

(5) Going back to the initial state

(6) Copying the URL of an analysis page

(7) Downloading figures and data
(7-1) Raw data

(7-2) Figures

2. Handling network
(1) Handling nodes
(1-1) Handling one of group of nodes

(1-2) Looking for information related to nodes

(2) Handling edges

3. Handling additional information
(1) Information of orthologous protein groups, proteins and interactions

(2) Handling selected edges

(3) Zoom-in and moving the network

(4) Handling the results of Gene Ontology enrichment analysis

(5) Handling the list of proteins