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Friday, 6 January 2017

Visualizing the kinome in R - a 'simple' tree...

A paper by Manning et al in Science in 2002 showed an phylogenetic tree of the kinases in the human genome. With the help of a beautiful poster and web resources by Cell Signaling Technologies, this visualisation has become a classic among researchers working on protein kinases.

It has been used in many ways and the paper itself has be very extensively cited.
Examples include:
This blog post uses the sequences available on the protein kinase website (kinase.com) to create a tree using R. My hope is that this will be the first of few posts that will develop into being able to reproduce the visualisation from the Science and to render a similar image to that created by Cell Signaling Technology. This is really a key objective for me as I want to use this visualisation for my teaching.

If you are interested, please test the code and make comments. This is an ongoing project and I welcome feedback.

So here is the first version of the kinome phylogenetic tree:

I have made a more simple phylogenetic tree of the human proteins with the rel homology domain here which talks about the complexity of making trees.

Here is the script that makes this:


# first version of generating a the kinome visualisation in R
# data is here: http://kinase.com/kinbase/FastaFiles/Human_kinase_domain.fasta
# in fasta format...
# need to extract the data into R... 
# need Biostrings package - downloaded as part of seqinr package

file <- c("http://kinase.com/kinbase/FastaFiles/Human_kinase_domain.fasta")

# step 1 is read in the FASTA files. 
kinases <- readAAStringSet(file, format = "fasta")
# that seems to work. 
# 516 sequences. 
# good.  

# step 2 do the multiple sequence alignment
kinaseAlign <- msa(kinases)  
# takes a bit of time!  - about 3.5 min on my computer...
# currently using default substitution matrix and CLUSTALW 
# creates an object with Formal class 'MsaAAMultipleAlignment' [package "msa"] with 6 slots

# step 3: convert Msa Alignment object into alignment for seqinr 
kinaseAlign2 <- msaConvert(kinaseAlign, type="seqinr::alignment")
class(kinaseAlign2) # it's an alignment
# worked 
# List of 4

# step 4: compute distance matrix - dist.alignment() function from the seqinr package:
d <- dist.alignment(kinaseAlign2, "identity")
# Class 'dist'

kinaseTree <- nj(d)  # from ape package, I think...
# class "phylo"
# List of 4

# good idea to save the tree locally... remove comment symbol
# write.tree(kinaseTree, file = "kinaseTree")
# to read back in:
# kinaseTree <- read.tree(file = "kinaseTree")

     main="Phylogenetic Tree of kinases")
# too difficult to read so remove the tip.labels which are the kinase names.

     main= "Phylogenetic Tree of kinases", 
     show.tip.label = FALSE)

     type = "unrooted", 
     main= "Phylogenetic Tree of kinases", 
     show.tip.label = FALSE)

# looks quite stylish a a little similar to visualisation in the Science paper
plot(kinaseTree, "u", 
     use.edge.length = FALSE,
     show.tip.label = FALSE)

# need to add colour
# argument is edge.color
plot(kinaseTree, "u", 
     use.edge.length = FALSE,
     show.tip.label = FALSE,
     edge.color = "red")

# want to add selected labels to give some orientation 
# extract tip.labels
tipLabels <- kinaseTree$tip.label

# add some labels we like to orient ourselves:
kinaseLabels <- c("IKKa","JAK3","ErbB2", 
                  "NEK11", "MLK1", "PKCb", 
                  "CDK9", "FRAP")

# find these in the alignment - they will be tip labels
labelNo <- NULL
for(i in 1:length(kinaseLabels)){
  labelNo <- c(labelNo, grep(kinaseLabels[i], kinaseTree$tip.label))
# generates a vector of 9 numbers. Some labels in two names. 

# make a vector of blank tiplabels
tipLabels_2 <-  rep('', length(kinaseTree$tip.label))

# add the labels we want to the vector...
for(i in 1:length(labelNo)){
  tipLabels_2[labelNo[i]] <- tipLabels[labelNo[i]]

# make a new tree
kinaseTree_fewLabels <- kinaseTree

# replace the tip labels with the shorter list.
kinaseTree_fewLabels$tip.label <- tipLabels_2

# make the plot with these
plot(kinaseTree_fewLabels, "u", 
     use.edge.length = FALSE,
     show.tip.label = TRUE,
     edge.color = "red",
     cex = 0.7)

# remove "Hsap" using gsub() function 
tipLabels_2 <- gsub("Hsap", "", tipLabels_2)
kinaseTree_fewLabels$tip.label <- tipLabels_2
plot(kinaseTree_fewLabels, "u", 
     use.edge.length = FALSE,
     show.tip.label = TRUE,
     edge.color = "red",
     cex = 0.7)

# add a title and source and you have the image at the top...
plot(kinaseTree_fewLabels, "u",
     main="Phylogenetic tree of human kinase domains",
     sub="source: www.kinase.com & Manning et al Science (2002) 398:1912-1934",
     use.edge.length = FALSE,
     show.tip.label = TRUE,
     edge.color = "red",
     cex = 0.7)

# this looks quite good and is enough for today. 

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