CausalPath

causal interactions from molecular profiles

CausalPath works on a set of molecular profiles and predicts the causal mechanisms that act on the data. It integrates prior knowledge from biological pathway databases, and uses them to explain new observations. While the main focus is phosphoproteomics, CausalPath can also work on global proteomic, transcriptomic, acetylomic and methylomic profiles, and combinations of them.

Causalpath mechanism

> Load input files for analysis

Please prepare your input files following this guide               , and bundle them in a zip file without a folder structure. A sample input is available here.

> View results from a previous analysis

Select the root folder of your analysis results to upload.

CausalPath is described in detail in the following publications.

Babur, Ö., et al. (2021). Causal interactions from proteomic profiles: Molecular data meet pathway knowledge. Patterns, 2(6), 100257.

Luna, A., et al. (2021). Analyzing causal relationships in proteomic profiles using CausalPath. STAR protocols, 2(4), 100955.

Source code is also available!

This is a collaborative project with contributions from the below institutions.

Please reach out to causalpath@cs.umb.edu for questions and comments.

General

Name
Description
Type
Additional Compound Padding
Edge Arrow Size
Allow Compound Resize
Infer Nesting on Load
Enable Ports
Enable Topology Grouping of SIF Nodes
Highlight Style
Display Labels for Named Complexes
Adjust Node Label Font Size Automatically
Label Size
Fit Labels to Nodes
Fit Labels to Information Boxes
Recalculate Layout on Complexity Management
Rearrange on Complexity Management
Animate on Drawing Changes
Open...
Style

Process Description

Validation Results