An R/Bioconductor package for cloud users for visualization and management of PPI networks
With the burgeoning development of cloud technology and services, there are an increasing number of users who prefer cloud to run their applications. All software and associated data are hosted on the cloud, allowing users to access them via a web browser from any computer, anywhere. This website presents cisPath, an R/Bioconductor package deployed on cloud servers for client users to visualize, manage, and share functional protein interaction networks.
Note: In the R source package, we selected only a small portion of the available protein-protein interaction (PPI) data as an example.
The file that contains the complete PPI information can be downloaded by the following links.
We have established an RStudio server using the free usage tier of the Amazon Elastic Compute Cloud (EC2) where several examples are presented for testing this package.
Users can run the examples by logging on via a web browser.
If the address changes for unforeseeable reasons and cannot be accessed, please refer to the following link and download the latest version of this document:
Note: As examples, we generated PPI data for several species from
Users can download the R scripts that we used to format the PPI data
The above PPI files will be accepted by this package. The interactions with confidence scores less than 700 have been filtered out (score < 700: low and medium confidence).
Users should cite these original database(s) if these files are used for publication.
Amazon Web Services
Amazon Web Services (AWS) has introduced a free usage tier for new customers of AWS, which can be used to test the cisPath package, and to build and share personal PPI databases.
Louis Aslett has provided various kinds of Amazon Machine Images (AMIs) which make deploying an RStudio Server very fast and easy. These AMIs are highly recommended, especially for free micro instance users.
The Bioconductor Team has also developed an Amazon Machine Image (AMI) optimized for running Bioconductor packages on the Amazon Elastic Compute Cloud. Instructions on how to launch the AMI can be found at here.
Other than cloud computing servers, users can choose to use cloud drivers as an alternative.
In this case, the user uploads the results to the cloud driver, which can then be visualized and shared with colleagues via browser.
Instructions on how to host webpages with Google Drive can be found at here.
Quick test (cisPath>=1.4.6)
How to use the formatted PPI data (cisPath>=1.4.6)
# Note: If R < 3.0 is used, please download the package from
Bioconductor and install manually. # To install this package, start R (>=3.0) and enter:
# Run the toy examples (~30 seconds)
infoFile <- system.file("extdata", "PPI_Info.txt", package="cisPath")
outputDir <- file.path(getwd(), "TP53_example")
# source protein: TP53 # Identify all shortest paths from TP53 to other proteins
results <- cisPath(infoFile, outputDir, "TP53")
# Note: If R < 3.0 is used, please download the package from Bioconductor and install manually.
# To install this package, start R (>=3.0) and enter:
# Download the sample PPI data that we have generated (may take several minutes)
dataDir <- file.path(getwd(), "PPIDATA")
dir.create(dataDir, showWarnings=FALSE, recursive=TRUE)
infoFile <- file.path(dataDir, "PPIdata.txt")
# (1)Display a list of given proteins in a PPI network (less than 1 minute)
outputDir <- file.path(getwd(), "networkView")
networkView(infoFile, c("TP53","GH1","MAGI1","IGF1","TFAP2A"), outputDir)
# (2)Identify the shortest path from TP53 to MAGI1 and GH1 (about 3 minutes)
outputDir <- file.path(getwd(), "MAGI1_GH1")
cisPath(infoFile, outputDir, "TP53", c("MAGI1", "GH1"))
# (3)Identify all shortest paths from TP53 to other proteins (about 10 minutes)
outputDir <- file.path(getwd(), "TP53_ALL")
cisPath(infoFile, outputDir, "TP53", byStep=TRUE)
# (4)Identify all shortest paths from PTEN to other proteins (about 10 minutes)
outputDir <- file.path(getwd(), "PTEN_ALL")
cisPath(infoFile, outputDir, "PTEN", byStep=FALSE)
# (5)Open the cisPath web page (about 1 minute)
outputDir <- file.path(getwd(), "cisPathWeb")
Potential users can click here (TP53 and PTEN)
to see typical results.
One of the following browser versions or higher is required to access RStudio: Firefox 3.5, Safari 4.0 or Google Chrome 5.0.
However, Opera and IE10 browsers will also properly display the results.
Please contact us if the paths do not display correctly.
UniProt database (version released 6/11/2014) Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res 2013, 41(Database issue):D43-47.
PINA database (version released 5/21/2014) Cowley MJ, Pinese M, Kassahn KS, Waddell N, Pearson JV, Grimmond SM, Biankin AV, Hautaniemi S, Wu J: PINA v2.0: mining interactome modules. Nucleic Acids Res 2012, 40(Database issue):D862-865.
iRefIndex database (v13.0 released 12/9/2013) Razick S, Magklaras G, Donaldson IM: iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics 2008, 9:405.
STRING database (v9.1) Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C et al: STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res 2013, 41(Database issue):D808-815.