Cellnetr by pcahan1

CellNet is a network biology-based computational platform that more accurately assesses the fidelity of cellular engineering than existing methodologies and generates hypotheses for improving cell derivations. CellNet is based on the reconstruction of cell type specific gene regulatory networks (GRNs), which we performed using publicly available microarray data on 21 cell and tissue types from both human and mouse samples. Code to run CellNet locally is available for download on this site. You can also analyze your data through our our servers, where you can also explore predicted transcriptional targets of over 1,200 mouse or human transcriptional regulators.

CellNet was written by Patrick Cahan with input from Hu Li, Samantha Morris, and Edroaldo Lummertz da Rocha.

It is provided under the OSI-approved Artistic License (version 2.0).

Release 0.1 -- 08-14-2014

The first version of CellNet is now available. This software a beta release, meaning that it is a work in progress, and new features will be added in the near future. To report a bugs or to discuss this software (but not the web application, please), go to the CellNet user group.

Requirements

CellNet was written in R. The following R packages, available through CRAN, are required:

ggplot2
gplots
randomForest
igraph

You can install them packages from within an R session by typing:

> install.packages(c("ggplot2", "gplots", "randomForest", "igraph"))

You will also need to install the affy package from Bioconductor. You can install it from within an R session by typing:

> source("http://bioconductor.org/biocLite.R") 
> biocLite("affy")

You will also need to install the following Bioconductor annotation packages. Please note that you must download these particular versions in order for CellNet to run properly:

We recommend that you install these packages to directory where they will not be overwritten. For example, we install these in the directory ~/sample_packages/install_dir. After you have downloaded these files, you can install them by typing at the shell:

R CMD INSTALL -l ~/sample_packages/install_dir package name

Installation

To install CellNet, download the compressed package, then at the shell type:

R CMD INSTALL -l ~/sample_packages/install_dir cellnetr.0.1.tar.gz

Finally, you need to download CellNet Objects, one per platform, which contain the training data, classifiers, and gene regulatory networks

The directory where you place these files will be referred to as 'path_CN_obj' in the code snippets below.

Setting up R environment for CellNet

# Set your library path so that it points to the correct platform and annotation libraries:
.libPaths("~/sample_packages/install_dir")

# load cellnet
library("cellnetr")

# load appropriate gene annotation sources
# mouse
library("org.Mm.eg.db")
# if human 
# library("org.Hs.eg.db")

# load platform annotation
# mouse4302
library("mouse4302cdf");
library("mouse4302.db");

# mogene10
# library("mogene10sttranscriptcluster.db");
# library("mogene10stv1cdf");

# hgu133plus2
# library("hgu133plus2.db");
# library("hgu133plus2cdf");

# hugene10
# library("hugene10sttranscriptcluster.db");
# library("hugene10stv1cdf");

# set up path the CellNet objects containing the classifiers, GRNs, etc
# Edit this so that it points to the path where you saved the CellNet objects 
path_CN_obj<-"~/CellNet/CN_Objects/"; 
# change to reflect your platform
myPlatform<-"mouse4302" 

# name of the column in the sample data table that indicates experimental groups or replicates
# set to "", or "sample_name" if there are no replicates
cName<-"description1"

# target tissue or cell type.
targetCT<-"hspc"

Load data and run CellNet

# Load sample table and fix the data file names 
# replace 'sampleTab.csv' with your sample table name. See [Step 2 here](http://dev.cellnet.hms.harvard.edu/run/) for a description of the sample table format and an example table.
stQuery<-expr_readSampTab("sampleTab.csv");
stQuery<-geo_fixNames(stQuery);

# load and normalize expression data
expQuery<-Norm_cleanPropRaw(stQuery, "mouse4302");

# load right CellNet object
cnObjName<-switch(myPlatform,
                  mouse4302 = paste(path_CN_obj, "cnProc_mouse4302_062414.R",sep=''),
                  mogene10stv1 = paste(path_CN_obj, "cnProc_mogene_062414.R",sep=''),
                  hgu133plus2 = paste(path_CN_obj, "cnProc_Hg1332_062414.R",sep=''),
                  hugene10stv1 = paste(path_CN_obj, "cnProc_Hugene_062414.R",sep=''));

cnProc<-utils_loadObject(cnObjName);

# Run CellNet
tmpAns<-cn_apply(expQuery, stQuery, cnProc, dLevelQuery=cName);

# Score transcription factors
tfScores<-cn_nis_all(tmpAns, cnProc, targetCT);

Visualize the results

# Classification heatmap
cn_hmClass(tmpAns);

classification heatmap

# Gene regulatory network status of starting cell type (esc) GRN
cn_barplot_grnSing(tmpAns, cnProc, "esc", c("esc"), bOrder=NULL, norm=T);

grn status esc

# Gene regulatory network status of target cell type (hspc) GRN
cn_barplot_grnSing(tmpAns, cnProc, "hspc", c("hspc"), bOrder=NULL, norm=T);

grn status hspc

# Network influence score of HSPC GRN transcriptional regulators.
# factor heatmap
cn_plotnis(tfScores, limit=15);

tr nis scores

# Gene expression in the training data set
mp_rainbowPlot(cnProc[['expTrain']],cnProc[['stTrain']],"Meis1", dLevel="description1")

gexp

Features to be added in the near future

Adding a cell or tissue type
Adding a new platform
Adding a new species
Reconstructing GRNs de novo
Identifying cell and tissue specific sub-networks