bch441-work-abc-units/BIN-PPI-Analysis.R
2021-09-15 20:12:10 -04:00

324 lines
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R

# tocID <- "BIN-PPI-Analysis.R"
#
#
# Purpose: A Bioinformatics Course:
# R code accompanying the BIN-PPI-Analysis unit.
#
# Version: 1.4
#
# Date: 2017-08 - 2020-10
# Author: Boris Steipe (boris.steipe@utoronto.ca)
#
# Versions:
# 1.4 Update vector ID's for betweenness centrality.
# 1.3 Bugfix: called the wrong function on ENSPsel in l. 220
# 1.2 2020 Updates; Rewrite for new STRINg V11;
# Deprecate save()/load() for saveRDS()/readRDS()
# 1.1 Change from require() to requireNamespace(),
# use <package>::<function>() idiom throughout,
# use Biocmanager:: not biocLite()
# 1.0 First live version
# 0.1 First code copied from 2016 material.
#
# TODO:
#
#
# == DO NOT SIMPLY source() THIS FILE! =======================================
#
# If there are portions you don't understand, use R's help system, Google for an
# answer, or ask your instructor. Don't continue if you don't understand what's
# going on. That's not how it works ...
#
# ==============================================================================
#TOC> ==========================================================================
#TOC>
#TOC> Section Title Line
#TOC> ---------------------------------------------------------------
#TOC> 1 Setup and data 50
#TOC> 2 Functional Edges in the Human Proteome 86
#TOC> 2.1 Cliques 129
#TOC> 2.2 Communities 170
#TOC> 2.3 Betweenness Centrality 184
#TOC> 3 biomaRt 231
#TOC> 4 Task for submission 302
#TOC>
#TOC> ==========================================================================
# = 1 Setup and data ======================================================
# Not surprisingly, the analysis of PPI networks needs iGraph:
if (! requireNamespace("igraph", quietly = TRUE)) {
install.packages("igraph")
}
# Package information:
# library(help = igraph) # basic information
# browseVignettes("igraph") # available vignettes
# data(package = "igraph") # available datasets
# In order for you to explore some real, biological networks, I give you a
# dataframe of functional relationships of human proteins that I have downloaded
# from the STRING database. The full table has 8.5 million records, here is a
# subset of records with combined confidence scores > 980
# The selected set of edges with a confidence of > 964 is a dataframe with about
# 50,000 edges and 8,400 unique proteins. Incidentaly, that's about the size of
# a fungal proteome. You can load the saved dataframe here (To read more about
# what the scores mean, see http://www.ncbi.nlm.nih.gov/pubmed/15608232 ).
STRINGedges <- readRDS("./data/STRINGedges.rds")
head(STRINGedges)
# Note that STRING has appended the tax-ID for Homo sapiens - 9606 - to the
# Ensemble transcript identifiers that start with ENSP. We'll remove them:
STRINGedges$a <- gsub("^9606\\.", "", STRINGedges$a)
STRINGedges$b <- gsub("^9606\\.", "", STRINGedges$b)
head(STRINGedges)
# = 2 Functional Edges in the Human Proteome ==============================
# There are many possibilities to explore interesting aspects of biological
# networks, we will keep with some very simple procedures here but you have
# to be aware that this is barely scratching the surface of possibilities.
# However, once the network exists in your computer, it is comparatively
# easy to find information online about the many, many options to analyze.
# Make a graph from this dataframe
?igraph::graph_from_data_frame
gSTR <- igraph::graph_from_data_frame(STRINGedges, directed = FALSE)
# CAUTION you DON'T want to plot a graph with 8,000 nodes and 50,000 edges -
# layout of such large graphs is possible, but requires specialized code. Google
# for <layout large graphs> if you are curious. Also, consider what one can
# really learn from plotting such a graph ...
# Of course simple computations on this graph are reasonably fast:
compSTR <- igraph::components(gSTR)
summary(compSTR) # our graph is fully connected!
hist(log(igraph::degree(gSTR)), col="#FEE0AF")
# this actually does look rather scale-free
(freqRank <- table(igraph::degree(gSTR)))
plot(log10(as.numeric(names(freqRank)) + 1),
log10(as.numeric(freqRank)), type = "b",
pch = 21, bg = "#FEE0AF",
xlab = "log(Rank)", ylab = "log(frequency)",
main = "8,400 nodes from the human functional interaction network")
# This looks very scale-free indeed.
(regressionLine <- lm(log10(as.numeric(freqRank)) ~
log10(as.numeric(names(freqRank)) + 1)))
abline(regressionLine, col = "firebrick")
# Now explore some more:
# == 2.1 Cliques ===========================================================
# Let's find the largest cliques. Remember: a clique is a fully connected
# subgraph, i.e. a subgraph in which every node is connected to every other.
# Biological complexes often appear as cliques in interaction graphs.
igraph::clique_num(gSTR)
# The largest clique has 81 members.
(C <- igraph::largest_cliques(gSTR)[[1]])
# Pick one of the proteins and find out what this fully connected cluster of 81
# proteins is (you can simply Google for any of the IDs). Is this expected?
# Plot this ...
R <- igraph::induced_subgraph(gSTR, C) # a graph from a selected set of vertices
# color the vertices along a color spectrum
vCol <- rainbow(igraph::gorder(R)) # "order" of a graph == number of nodes
# color the edges to have the same color as the originating node
eCol <- character()
for (i in seq_along(vCol)) {
eCol <- c(eCol, rep(vCol[i], igraph::gorder(R)))
}
oPar <- par(mar= rep(0,4)) # Turn margins off
plot(R,
layout = igraph::layout_in_circle(R),
vertex.size = 3,
vertex.color = vCol,
edge.color = eCol,
edge.width = 0.1,
vertex.label = NA)
par(oPar)
# ... well: remember: a clique means every node is connected to every other
# node. We have 81 * 81 = 6,561 edges. This is what a matrix model of PPI
# networks looks like for large complexes.
# == 2.2 Communities =======================================================
set.seed(112358) # set RNG seed for repeatable randomness
gSTRclusters <- igraph::cluster_infomap(gSTR)
set.seed(NULL) # reset the RNG
igraph::modularity(gSTRclusters) # ... measures how separated the different
# membership types are from each other
tMem <- table(igraph::membership(gSTRclusters))
length(tMem) # About 700 communities identified
hist(tMem, breaks = 50, col = "skyblue") # most clusters are small ...
range(tMem) # ... but one has > 200 members
# == 2.3 Betweenness Centrality ============================================
# Let's find the nodes with the 10 - highest betweenness centralities.
#
BC <- igraph::centr_betw(gSTR)
# remember: BC$res contains the results
head(BC$res)
BC$res[1] # betweenness centrality of node 1 in the graph ...
# ... which one is node 1?
igraph::V(gSTR)[1]
# to get the ten-highest nodes, we simply label the elements of BC with their
# index ...
names(BC$res) <- as.character(1:length(BC$res))
# ... and then we sort:
sBC <- sort(BC$res, decreasing = TRUE)
head(sBC)
# This ordered vector means: node 3 has the highest betweenness centrality,
# node 721 has the second highest, etc.
(BCsel <- as.numeric(names(sBC)[1:10]))
# We can use the first ten labels to subset the nodes in gSTR and fetch the
# IDs...
(ENSPsel <- names(igraph::V(gSTR)[BCsel]))
# Task:
# =====
# IMPORTANT, IF YOU INTEND TO SUBMIT YOUR ANALYSIS FOR CREDIT
# We are going to use these IDs to produce some output for a submitted task:
# therefore I need you to execute the following line, note the "seal" that this
# returns, and not change myENSPsel later:
myENSPsel <- selectENSP(ENSPsel)
# Next, to find what these proteins are...
# We could now Google for all of these IDs to learn more about them. But really,
# googling for IDs one after the other, that would be lame. Let's instead use
# the very, very useful biomaRt package to translate these Ensemble IDs into
# gene symbols.
# = 3 biomaRt =============================================================
# IDs are just labels, but for _bio_informatics we need to learn more about the
# biological function of the genes or proteins that we retrieve via graph data
# mining. biomaRt is the tool of choice. It's a package distributed by the
# bioconductor project. This here is not a biomaRt tutorial (that's for another
# day), simply a few lines of sample code to get you started on the specific use
# case of retrieving descriptions for ensembl protein IDs.
if (! requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
if (! requireNamespace("biomaRt", quietly = TRUE)) {
BiocManager::install("biomaRt")
}
# Package information:
# library(help = biomaRt) # basic information
# browseVignettes("biomaRt") # available vignettes
# data(package = "biomaRt") # available datasets
# define which dataset to use ... this takes a while for download
myMart <- biomaRt::useMart("ensembl", dataset="hsapiens_gene_ensembl")
# what filters are defined?
( filters <- biomaRt::listFilters(myMart) )
# and what attributes can we filter for?
( attributes <- biomaRt::listAttributes(myMart) )
# Soooo many options - let's look for the correct name of filters that are
# useful for ENSP IDs ...
filters[grep("ENSP", filters$description), ]
# ... and the correct attribute names for gene symbols and descriptions ...
attributes[grep("symbol", attributes$description, ignore.case = TRUE), ]
attributes[grep("description", attributes$description, ignore.case = TRUE), ]
# ... so we can put this together: here is a syntax example:
biomaRt::getBM(filters = "ensembl_peptide_id",
attributes = c("hgnc_symbol",
"wikigene_description",
"interpro_description",
"phenotype_description"),
values = "ENSP00000000442",
mart = myMart)
# A simple loop will now get us the information for our 10 most central genes
# from the human subset of STRING.
CPdefs <- list() # Since we don't know how many matches one of our queries
# will return, we'll put the result dataframes into a list.
for (ID in myENSPsel) {
CPdefs[[ID]] <- biomaRt::getBM(filters = "ensembl_peptide_id",
attributes = c("hgnc_symbol",
"wikigene_description",
"interpro_description",
"phenotype_description"),
values = ID,
mart = myMart)
}
# So what are the proteins with the ten highest betweenness centralities?
# ... are you surprised? (I am! Really.)
# = 4 Task for submission =================================================
# Write a loop that will go through your personalized list of Ensemble IDs and
# for each ID:
# -- print the ID,
# -- print the first row's HGNC symbol,
# -- print the first row's wikigene description.
# -- print the first row's phenotype.
#
# Write your thoughts about this group of genes.
#
# (Hint, you can structure your loop in the same way as the loop that
# created CPdefs. )
# Submit the "seal" for your ENSP vector, the ENSP vector itself, the R code
# for this loop and its output into your report if you are submitting
# anything for credit for this unit. Please read the requirements carefully.
# [END]