The package KEGGlincs and the functions contained within it are designed such that users can explore KEGG pathways in a more meaningful and informative manner both visually and analytically. This method of pathway analysis is approached via functions that handle the following (related) objectives:
The idea of 'expanded' nodes and edges should become very clear after reviewing
the following example KEGGlincs workflows. Please keep in mind, the individual
functions detailed in the following workflows are incorporated into the
KEGG_lincs 'master function'; these workflows are designed to provide users a
with a better understanding of how this function works, how pathway topology is
represented in KGML files, and how this package could be used with
non-LINCS edge data (see Workflow 2).
This workflow is intended to give users insight into the 'expansion' of KEGG pathway mapping via manipulation of the source KGML file. The only input required is the KEGG pathway ID for your pathway of choice. The primary goal for this method of pathway re-generation is to give users insight into the complexity that underlies many KEGG pathways but is in a sense 'hidden', yet hard-coded, in the curated KGML files. Users can also see the exact pathway topology that is used for input in analyses such as SPIA (Signaling Pathway Impact Analysis).
FoxO_KGML <- get_KGML("hsa04068") #Information from KGML can be accessed using the following syntax: slot(FoxO_KGML, "pathwayInfo")
#Get address for pathway with active links: slot(slot(FoxO_KGML, "pathwayInfo"), "image")
#Download a static pathway image (png file) to working directory: image_link <- slot(slot(FoxO_KGML, "pathwayInfo"), "image") download.file(image_link, basename(image_link), mode = "wb")
Note that KEGG IDs are converted to gene/compound symbols; this conversion
accounts for the majority of computing time behind the
function. For quicker map generation, users may chose to change the argument
FALSE; this will result in edges being identified by
pairs of accession numbers instead of symbols in the final pathway map (example
at end of this workflow using
KEGG_lincs master function).
FoxO_KEGG_mappings <- expand_KEGG_mappings(FoxO_KGML, convert_KEGG_IDs = FALSE)
FoxO_KEGG_mappings <- expand_KEGG_mappings(FoxO_KGML)
FoxO_edges <- expand_KEGG_edges(FoxO_KGML, FoxO_KEGG_mappings)
length(graph::nodes(FoxO_KGML)) # 'Un-expanded' nodes nrow(FoxO_KEGG_mappings) # 'Expanded' nodes length(graph::edges(FoxO_KGML)) # 'Un-expanded' edges nrow(FoxO_edges) # 'Expanded' edges
Note: While the
node_mapping_info function is rather trivial, the
edge_mapping_info functions differently when data is added.
#Modify existing data sets; specify as nodes and edges FoxO_node_mapping_info <- node_mapping_info(FoxO_KEGG_mappings) FoxO_edge_mapping_info <- edge_mapping_info(FoxO_edges) #Create an igraph object GO <- get_graph_object(FoxO_node_mapping_info, FoxO_edge_mapping_info) class(GO)
cyto_vis(GO, "FoxO Pathway with Expanded Edges[no data added]")
Edge Color Key:
Red: Activation or Expression *
Orange: Activating PTM **
Green: PTM (no activation/inhibition activity defined)
Purple: Inhibiting PTM
Black(dashed): Indirect effect (no activation/inhibition activity defined)
*Any dashed colored line indicates that the effect is indirect
**PTM = post-translational modification or, as KEGG defines them, 'molecular events'.
Notice that the original KEGG pathway image includes visual elements such as cellular-component-demarcations and certain edges (especially those 'connecting' genes to other pathways) that are not rendered in Cytoscape. These are features that are either not explicitly part of the pathway topology (i.e. not nodes or edges connecting nodes) or have not been hard-coded in the KGML file. The node labels may also differ between maps (KEGGlincs labels nodes as the first 'alias' in the respective KGML slot as there is no corresponding 'label' slot).
*Note: to have the pathway maps automatically formatted for convenient viewing
and proper node size, please use the function
This function requires systems to have the R package RCy3 installed, which is
not yet available for all systems.
Otherwise please follow the steps under
CytoscapeSettings.Rmd to reproduce
the maps generated in this vignette.
The steps above may be avoided if the user does not wish to generate
intermediary files/objects by making use of the function
If users would like the Cytoscape-rendered map along with the detailed list of
expanded edges (as an R object),
KEGG_lincs can be invoked as follows:
FoxO_edges <- KEGG_lincs("hsa04068")
To speed up the mapping process (at the expense of having edges labelled with
pairs of gene accession numbers as opposed to symbols) users may change the
convert_KEGG_IDs argumet to
KEGG_lincs("hsa04068", convert_KEGG_IDs = FALSE)
*Note: As with
cyto_vis, please use the function
cyto_vis_auto) available from :
While the functions described in Workflow 1 are certainly useful for any users wishing to gain deeper insight into KEGG pathway topology and 'hard-coded' KGML information, the drving force motivating the KEGGlincs package development is the association of experimental data with pathway edges.
The companion data package KOdata provides data for the edges rendered by the
KEGG_lincs. This data package includes two unique data sets;
one contains lists of significantly up- and down-regulated genes corresponding
to knocked-out genes (within individual experiments, genes are 'turned off' via
shRNA) across a variety of cell-lines measured at specific times and
the other is a binary record of baseline gene expression (gene is either
expressed or not expressed) for most cell-lines from the knock-out data set.
While this package was developed primarily as a way to compare pathway topology between cell-lines or within cell-lines [across time] using LINCS L1000 data, this workflow will demonstrate the package's flexibility for users incorporating edge data from any source.
As a hypothetical scenario, our goal will be to compare pathway topology between cell-lines for an important cancer-related pathway: the p53 Signaling Pathway.
The 'default' pathway (with no data added to edges) can be generated either by
following Workflow 1 or by using the
KEGG_lincs master function as follows:
From here, the first few lines of code are similar to those of Workflow 1:
p53_KGML <- get_KGML("hsa04115") p53_KEGG_mappings <- expand_KEGG_mappings(p53_KGML) p53_edges <- expand_KEGG_edges(p53_KGML, p53_KEGG_mappings)
An important aspect of the L1000 knock-out and expression data is that it is
incomplete; experimental data is not uniformly available for each cell-line.
Therefor (for this specific example with this specific data set) it is instructive to find out which cell-lines make sense to compare; intuitively, cell-lines with a similar percentage of pathway genes knocked out would be well suited for comparison. The following command accomplished this task in the form of an easily interpretable graphical output:
Another function (
refine_mappings) is automatically envoked when the
KEGG_lincs master function is called; this function 'prunes' edges from the
pathway that would not exist in the cell-line based on baseline expression data.
This is beyond the scope of this workflow and will be detailed elsewhere.
If users would like to access lists of specific gene knock-outs within the chosen pathway for each cell-line, the command can be invoked as follows:
p53_L1000_summary <- path_genes_by_cell_type(p53_KEGG_mappings, get_KOs = TRUE)
Resulting data frame:
p53_L1000_summary <- path_genes_by_cell_type(p53_KEGG_mappings, get_KOs = TRUE, generate_plot = FALSE) knitr::kable(tail(p53_L1000_summary))
The bar plot suggests that the group of cell lines colored in red have similar amounts of pathway information; for this example we will compare the PC3 (prostate cancer) and HA1E (immortalized normal kidney epithelial) cell-lines.
The following commands use the data objects generated above to generate cell-line specific edge attributes corresponding to specific pathway edges and the information from the L1000 knock-out data set:
p53_PC3_data <- overlap_info(p53_KGML, p53_KEGG_mappings, "PC3") p53_HA1E_data <- overlap_info(p53_KGML, p53_KEGG_mappings, "HA1E")
Example of edge data generated for the PC3 cell line (data columns generated after applying Fisher's exact test not shown):
overlap_info is by default set to
Users may be interested in follow-up analysis of the genes that are found to be
expressed in a concordant/discordant fashion between pairs of knock outs. This
information is easily accessible by changing the default as follows:
p53_PC3_data_with_gene_lists <- overlap_info(p53_KGML, p53_KEGG_mappings, "PC3", keep_counts_only = FALSE)
Example of edge data generated for the PC3 cell line that includes lists of concordant/discordant genes for knock out pairs (count data not shown):
By default, the function
overlap_info generates edges that are 'mapped', i.e.
the edge between any two nodes is hard-coded in the KGML file even though data
could be generated for all possible (think de novo) edges. A workflow that
describes how this can be achieved by simply changing a few default arguments
will be added shortly.
Notice the format of the data; in particular that the first two columns contain
gene symbols and act as a primary key (unique identifier) for an edge and the
rest of the columns are edge attributes. The following function
can be used with any dataset in this format and will append selected columns to
the edge dataset. Note that the data supplied does not need to be pre-arranged
in correct source -> target order as specified by the pathway topology; the
function automatically re-orients pairs correctly.
p53_PC3_edges <- add_edge_data(p53_edges, p53_KEGG_mappings, p53_PC3_data, only_mapped = TRUE, data_column_no = c(3,10,12)) p53_HA1E_edges <- add_edge_data(p53_edges, p53_KEGG_mappings, p53_HA1E_data, only_mapped = TRUE, data_column_no = c(3,10,12))
The following series of commands follow from workflow 1 (with minor adjustments
to arguments, notably ensuring that
data_added = TRUE is specified). The
edges in the resulting pathway maps are conditionally formatted to represent
both the significance and magnitude of the relationship between corresponding
nodes based on their concordance/discordance of up/down-regulated genes as
measured by Fisher's Exact Test.
p53_node_map <- node_mapping_info(p53_KEGG_mappings) p53_edge_map_PC3 <- edge_mapping_info(p53_PC3_edges, data_added = TRUE, significance_markup = TRUE) p53_edge_map_HA1E <- edge_mapping_info(p53_HA1E_edges, data_added = TRUE, significance_markup = TRUE) PC3_GO <- get_graph_object(p53_node_map, p53_edge_map_PC3) HA1E_GO <- get_graph_object(p53_node_map, p53_edge_map_HA1E) cyto_vis(PC3_GO, "Pathway = p53, Cell line = PC3") #Option: Save PC3 as .cys file and start a fresh session in Cytoscape cyto_vis(HA1E_GO, "Pathway = p53, Cell line = HA1E")
Edge colors represent the following possible combinations of direction of Fisher's Exact Test summary scores (a modified Odd's Ratio score; either positive(+) or negative (-)) and their corresponding [adjusted] p-values:
Red: OR(+), pval(sig)
Orange: OR(+), pval(non-sig)
Purple: OR(-), pval(non-sig)
Blue: OR(-), pval(sig)
Note that as with Workflow 1, the
KEGG_lincs master function can
automatically generate pathway maps identical to the final maps resulting
from Workflow 2 as follows:
KEGG_lincs("hsa04115", "PC3", refine_by_cell_line = FALSE) KEGG_lincs("hsa04115", "HA1E", refine_by_cell_line = FALSE)
The only differences are that the
KEGG_lincs function generates titles with a
slightly modified format and automatically 'refines' pathway edges for
cell-lines with baseline expression data.
```r knitr::include_graphics("image_files/p53_PC3.jpeg") knitr::include_graphics("image_files/p53_HA1E.jpeg")
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