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