This Vignette accompagnies the CoRegNet package. It can be used either to get some additional information about the methods or to get examples of the use of the functions. Feel free to ask any question to the package maintainer (remy.c.nicolle at gmail dot com).

Introduction

The CoRegNet package aims at inferred a large scale transcription co-regulatory network from transcriptomic data, integrate external data on gene regulation to infer and analyse transcriptional programs. The particularity of the network inference algorithm proposed in the package is to learn co-regulation netwok in which the regulation is modeled by transcription factors which act in a cooperative manner to synergistically regulate target genes.

The package was used in a study of Bladder Cancer to identify the driver transcriptional programs from a set of 183 samples. Throughout this Vignette, a smaller version of the transcriptomic dataset is used to illustrate the use of the package.

        library(CoRegNet)
        data(CIT_BLCA_EXP,HumanTF)
        dim(CIT_BLCA_EXP)
        #showing 6 first TF in the gene expression dataset
        head(intersect(rownames(CIT_BLCA_EXP),HumanTF))

Construction of a large scale co-regulatory network from gene expression data

The inference algorithm implemented in the package is a hybrid version of the LICORN algorithm which is both based on a discrete and continuous version of the gene expression data. The reconstruction of the network involves 4 steps. First, the gene expression data is discretized. Second, all the potential sets of cooperative regulators are extracted using the apriori algorithm of frequent itemset mining. Third, the best combinations of co-activators and co-inhibitors are identified for each genes. Finally, a continuous model of regulation using a linear regression method with interaction terms is used to score the local gene regulatory network for each gene.

The minimal input datasets is : * a gene expression data.frame or matrix with unique column and row names containing sample and gene names respectively * a list of genes to be considered as Transcription factor (TF). The package contains a default list of TF either in the form of official gene symbol or EntrezGene IDs.

    # An example of how to infer a co-regulation network
    grn =hLICORN(CIT_BLCA_EXP, TFlist=HumanTF)
    print(grn)

The transcriptomic dataset is by default discretized using the discretizeExpressionData. The two main use of these function is either with or without a set of reference samples from the difference to the mean is used to set an expression value to -1, 0 or 1 using a predefined threshold. See the help for more details. A user defined method can be used to discretize the data using for instance a mixture of gaussian to identify samples in which a given gene is over-expressed, under-expressed or does not change.

    #default discretization. Uses the standard deviation of the whole dataset to set a threshold.
    disc1=discretizeExpressionData(CIT_BLCA_EXP)
    table(disc1)
    boxplot(as.matrix(CIT_BLCA_EXP)~disc1)

    #Discretization with a hard threshold
    disc2=discretizeExpressionData(CIT_BLCA_EXP, threshold=1)
    table(disc2)
    boxplot(as.matrix(CIT_BLCA_EXP)~disc2)

    # more examples here
    help(discretizeExpressionData)

The overall inference process is highly parallelizable since it can be indepedently launched on each target gene and therefore can be divided in as many threads as there are genes to infer regulators on. By default the hLICORN function uses the mclapply function of the parallel package (default in R >= 3.0), which itself uses 2 cores by default.

# running only on the 200 first gene in the matrix for fast analysis
    # Choosing to divide in 4 threads whenever possible
    options("mc.cores"=4)
    grn =hLICORN(head(CIT_BLCA_EXP,200), TFlist=HumanTF)
    print(grn)
    options("mc.cores"=2)
    grn =hLICORN(head(CIT_BLCA_EXP,200), TFlist=HumanTF)
    print(grn)

Although H-LICORN is an inference algorithm which is particularly efficient in identifying co-regulators, that is cooperative transcription factor, the package allows to input a regulatory network inferred by other methods or even experimentally defined.

Refining the inferred regulatory networks

The second step of the analysis uses external knowledge to enrich the inferred regulatory network. Two types of external data can be use : regulatory information such as Transcription Factor Binding Sites (TFBS) or ChIP data to support TF to gene interaction and co-regulatory information such as protein-protein interaction to support cooperative TF. These datasets can be easily integrated in a coregnet object using two functions : addEvidences} and addCooperativeEvidences.

    # ChIP data from the CHEA database
    data(CHEA_sub)

    #ChIP data from the ENCODE project
    data(ENCODE_sub)

    # Protein protein interactions between TF from the HIPPIE database
    data(HIPPIE_sub)

    # Protein protein interactions between TF from the STRING database
    data(STRING_sub)

    enrichedGRN = addEvidences(grn,CHEA_sub,ENCODE_sub)
    enrichedGRN = addCooperativeEvidences(enrichedGRN,HIPPIE_sub,STRING_sub)

The coregnet object with added evidences contains a statistical analysis of the enrichment of the inferred interactions in the validated external evidences using a fisher exact test as exemplified below.

    print(enrichedGRN)

The added evidences can also be used to refine the inferred network and select local gene regulatory network based on the added external knowledge. This is done based on the work of the modEncode consortium which proposed a method to integrate orthogonal datasets (Transcriptome, Epigenetic marks, binding sites, ..) to learn a global network. Briefly, the method assigns one scores for each dataset to all possible interactions to assign a final score using a weighted mean. This final merged score is used to select the best regulatory interactions. Here, instead of scoring and selecting single edges, the methods is extended to work with local regulatory network (sets of co-activators and co-inhibitors of a given gene). For each dataset, a score is assigned to each local network by counting the number of validated interactions found in the local network normalised by the total number of possible interactions. The score given by the network inference method, an adjusted R2 in the case of hLICORN, and each of the score given by the external datasets are then merged. Two methods are proposed to do so. The default is the unsupervised method, a simple unweighted mean, and was shown by the modENCODE consortium to give the best results. The supervised method uses a user defined reference dataset as a reference set of interactions. A Generalized Linear Model is then used to predict the presence of a reference interaction based on the score of the other datasets including the network inference score.

        # Default unsupervised refinement method
    refinedGRN = refine(enrichedGRN)
    print(refinedGRN)
    # Example of supervised refinement with the CHEA chip data
    refinedGRN = refine(enrichedGRN, integration="supervised",
            referenceEvidence="CHEA_sub")
    print(refinedGRN)

N.B. : It is possible to integrate regulatory evidences to coregnet networks inferred using other methods than hLICORN. However, integrating co-regulatory evidences and refining the network is only relevant on networks encoding local regulatory network originally containing cooperative regulators instead of simple TF to gene interaction pairs.

Identification of active transcriptional programs

The goal of the CoRegNet package is to identify the sets of active cooperative TF in a given sample or set of samples. A measure of transcriptional activity was developed to estimate the level of activity of given transcription regulator in a given sample. This measure, termed the influence, is the comparison the expression of the activated and repressed genes of a TF in a transcriptional network. It is based on a measure of divergence (welch’s t statistics) of these two sets of genes in one sample. Basically, if the genes activated by a TF are highly expressed while the repressed genes are under-expressed, the TF has a high influence. Using a coregulatory network encoded in a coregnet
object and a matrix of gene expression, wether it is the data use for the inference or another one (cell lines transcriptomes for instance). The output is a matrix with the same number of columns (samples) and as many rows (TF) as TF with a sufficient number of targets (min 10 activated and 10 repressed) in the transcriptional network.

    CITinf =regulatorInfluence(grn,CIT_BLCA_EXP)
This new dataset of transcriptional influence can be used as a condensed

view of the whole transcriptome dataset. Data mining and machine learning can be applied to it to identify clusters, predict sample classes or extracting relevant features. More interestingly, it can be used to visualize the entire dataset with a much smaller number of feature making heatmaps a sufficient tools to evualuate all samples. The package proposes a visualization tool based on an interactive shiny webpage. The objective of the embeded visualization tool is to navigate the transcriptional programs through the network of cooperative transcription factors and identify the specific transcriptional program of a sample or a set of samples defined by a clinical subgroup.

Preliminary to the analysis of transcriptional program is the identification of the network of co-regulators underlying these programs. The definition of a pair of cooperative TF or co-regulator is dependent on the method used to construct the network, that is, wether it contains simple pairs of regulation (TF -> Gene, inferred using the ARACNE algorithm for instance) or sets of cooperative TF regulating each gene ({TF1,TF2,…} -> Gene, inferred using the LICORN algorithm). From the pair regulatory network, all combination of TF sharing at least one target gene is considered as a potential pair of co-regulator. From the cooperative network, these are defined by all pairs of TF which were inferred to be cooperative in the regulation of at least one target gene. Then, the significance of these pairs is tested using fisher’s exact test to assess wether these pairs of TF share more target genes than expected by chance (Benjamini-Hochberg multi test correction is applied). The final co-regulation network is defined by an edge between all pairs of significant TF (FDR 1%).

    # Coregulators of a hLICORN  inferred network
    head(coregulators(grn))
    #  Coregulators of an ARACNE inferred network
    head(coregulators(CITCoRTN))
In order to exemplify the use of the proposed analysis tool, additional

data are available through the package : the classification of our samples (based on the TCGA classification) and the copy number status of the transcription factor in the CIT cohort.

    data(CIT_BLCA_CNV)
    data(CIT_BLCA_Subgroup)

The minimum requirement to launch the visualization tool is a _coregnet} network object and a transcriptomic dataset. The influence dataset can also be added to accelerate the initialisation of the webpage but is otherwise recomputed and is therefore optional.

    display(grn,expressionData=CIT_BLCA_EXP,TFA=CITinf)

The top left part of the shiny application is used to change several parameters of the application.

The first selection input is usable only if a sample classification is available. When a particular subgroup is selected, the cytoscape network on the right, the nodes representing TF will adapt their color based on their mean activity level in the selected set of samples. If alteration data is available, the piechart inside each node will by modified to show the proportion of each copy number status in the selected set of samples.

The second input specifies an integer used as a threshold to select pairs of TF which share a minimum number of target genes (local regulatory network for hLICORN inferred network). This parameter controls the number of TFs and pairs of TFs displayed.

The third input can be used to search a TF in the network.

The layout button can be used to change the layout of the network. This can be a long process for larg networks.

The second panel is the cytoscape app to visualize and manipulate the network of coregulators.

The last panel is used to display specific plots. A heatmap of TF influence is displayed by default. If only a subset of TF are selected in the cytoscape panel, the heatmap will only display the influenceof the selected TF. Selecting a single TF will display data specific to that TF which is dependent on the data used as input. Each of the data is represented as an array of color ordered by the activity of the selected TF. The plotted data includes the expression of the TF, the activity of the TF and the expression of the activated and the repressed samples.

The visualization tool can also handle alteration data, sample classification and evidences of regulation or co-regulation. Several examples are shown below.

    # Visualizing additional regulatory or co-regulatory evidences in the network
    display(enrichedGRN,expressionData=CIT_BLCA_EXP,TFA=CITinf)

    # Visualizing alterations of the TF
    display(grn,expressionData=CIT_BLCA_EXP,TFA=CITinf,alterationData=CIT_BLCA_CNV )

    # Visualizing sample classification
    citclinical=split(CIT_BLCA_Subgroup$samples,CIT_BLCA_Subgroup$subgroup)
    display(grn,expressionData=CIT_BLCA_EXP,TFA=CITinf,clinicalData=citclinical)

    display(grn,expressionData=CIT_BLCA_EXP,TFA=CITinf,alterationData=CIT_BLCA_CNV,
            clinicalData=citclinical)

N.B. : the Cytoscape network snapshot is experimental and usually is one snapshot late. Usually going back and forth to the snapshot tab once or twice should do the trick to have the latest snapshot. Hopefully this will be corrected by the Cytoscape.JS team.


Snapshots and examples

The following contains snapshots of the shiny interactive user interface for the visualization of a co-regulatory network driving bladder cancer.

The Co-regulation page is divided in three parts (see figure 1). In the top left corner, a control panel lists the samples and samples subtype to analyze, the number of minimum GRN to select significant cooperative interactions and an input to search for a particular TF in the network. In the right part, an interactive Cytoscape javascript widget display the network of co-regulators. The color of the nodes reflects the activity of the TF in the selected subtype as shown in figure for two types of bladder cancers. The bottom part of the page contains a plot reactive to action performs on the network.

1. View of the shiny Web page

1. View of the shiny Web page

Subtype specific co-regulator network. The color of each TF/node is based on the mean influence in all samples of the subtype