[BioC] Measuring shifts in intronic expression independently of exons

Fri Aug 30 15:35:55 CEST 2013

Dear Jim, Martin & list

Martin's proposal of using splice graphs is definitely the way to go, it is conceptually appealing, would have more power, and results are potentially more readily interpretable. That said, the current state of what we have in DEXSeq does the testing exon-by-exon, and lack of power does not seem to be James' problem. Regarding James' questions:

1. It is fine, and to be expected, that the sum of per-exon counts is larger than the per-gene count. This is OK because a read that covers multiple exons is counted multiple times, for each of the overlaps. This makes sense for the testing setup of DEXSeq. It tests, marginally, exon by exon, whether its relative usage among all transcripts from the locus is condition-dependent. Since the tests are marginal, correlations between counts of neighbouring exons are not a problem. Each overlap of a read is a postiive piece of evidence for it being expressed. 

2. Regarding your high number of results, here are some considerations:
- the fact that swapping sample labels leads to greatly reduced sets of hits is reassuring 
- definitely do go ahead with visualising the results to see what is going on and whether this large number of calls is justified by the data (please keep us in the loop)
- did you see the "plotDEXSeq" function
- an effect size (fold-change) cutoff might help focus the results on the most interesting instances. How does the volcano plot look like?

	Hope this helps
	Wolfgang

On 29 Aug 2013, at 21:27, James Perkins <jimrperkins at gmail.com> wrote:

> Hi Wolfgang, list
> 
> Thank you very much for the helpful tip.
> 
> I did exactly as you suggested, the code is below. I wanted to do it using the pasilla package in order to create an instructive example, and so that you could potentially recreate the analysis, but strangely sometimes the gene read counts from pasillaGenes are lower than the summed exon counts from the pasillaExon object. Or at least that's the case according to my code!
> 
> If you (or anyone else who is reading this) can think of a good public data set for this please let me know, ideally one that is already in bioconductor and fairly easy to manipulate. Otherwise I am happy to submit my current dataset to bioc or make available some other way once its corresponding paper has been published
> 
> So, code below. Any comments or suggestions would be appreciated, if you think there are ways I could tune DEXSeq for this purpose:
> 
> To start with I loaded in all the necessary files and made a counts object with Gend ID:E001 for intronic and GeneID:E002 for exonic.
> 
> # c50tx - table of counts using reads mapping to anywhere in gene c50ex - reads mapping to exons only
> intMat <- as.data.frame(c50tx) - as.data.frame(c50ex)
> exMat <- as.data.frame(c50ex)
> 
> # Remove genes for which intron count is below 100
> intMat.2 <- intMat[! apply(intMat, 1, function(x) sum(x < 100)) > 3, ]
> exMat <- exMat[! apply(intMat, 1, function(x) sum(x < 100)) > 3, ]
> intMat <- intMat.2 
> 
> row.names(intMat) <- paste(row.names(intMat), ":E001", sep="")
> row.names(exMat) <- paste(row.names(exMat), ":E002", sep="")
> # Now I combine the different tables in order to get a combined table as so:
> both <- rbind(intMat, exMat)
> both <- both[order(row.names(both)), ]
> head(both)
> 
> # Now I turn this into an exon count set
> gIDs <- matrix(unlist(strsplit(row.names(both), ":")), ncol=2, byrow=TRUE)[,1]
> names(gIDs) <- row.names(both)
> gIDs <- as.factor(gIDs)
> eIDs <- matrix(unlist(strsplit(row.names(both), ":")), ncol=2, byrow=TRUE)[,2] 
> names(eIDs) <- row.names(both)
> des <- data.frame(condition=c(rep("case",3), rep("control", 3)))
> row.names(des) <- colnames(both)
> ecS <- newExonCountSet(
>   countData = both,
>   design = des,
>   geneIDs=gIDs,
>   exonIDs=eIDs)
> 
> Once I had this I ran normalisation etc. and looked for genes with 'differential exon/intron usage':
> 
> ecS <- estimateSizeFactors(ecS)
> ecS <- estimateDispersions(ecS)
> ecS <- fitDispersionFunction(ecS)
> head(fData(ecS)$dispBeforeSharing)
> 
> ecS <- testForDEU(ecS)
> head(fData(ecS)[, c("pvalue", "padjust")])
> ecS <- estimatelog2FoldChanges(ecS, averageOutExpression=FALSE)
> res2 <- DEUresultTable(ecS)
> sum(ecS$pad
> 
> 
> So - out of 29516 genes 'tested', ~7000 had > 100 intronic counts for at least 3 conditions and ~4000 of these were DEU (FDR<0.1). This seems quite a high number of genes, so I wonder if the method is being conservative enough.
> 
> That said, tried swapping the sample labels a few times, which lead to 0 genes being called as DEU, which is a good sign I think.
> 
> Interestingly, comparing intron:exon for case and controls for the significant DEU genes shows a 4:1 ratio of genes that with an increased intronic expression in case samples, suggesting the experimental intervention is leading to increased intronic expression.
> 
> So, does this approach seem valid? My main question is whether it is a little unconservative. I'm currently using ggbio to plot the read alignments for the significant genes and looking for interesting looking patterns of intronic expression that are consistent across replicates of the same class (and that differ between classes). I've found a few things that look interesting for follow up.
> 
> Thanks a lot for your help,
> 
> Jim
> 
> On 9 August 2013 16:02, Wolfgang Huber <whuber at embl.de> wrote:
> Dear James
> have you already checked the DEXSeq package and the paper http://genome.cshlp.org/content/22/10/2008.long
> This does not apply 1:1 to what you are asking for, but afaIcs the main modification would be for you to define "counting bins" (on which the input to DEXSeq is computed by read overlap counting) that represent (i) exons and (ii) introns and then check for changes in relative intro usage (the 'ratios' you mention below).
> Let me know how it goes
>         Wolfgang.
> 
> On 9 Aug 2013, at 10:02, James Perkins <j.perkins at ucl.ac.uk> wrote:
> 
> > Dear list,
> >
> > I would like to know if an experimental treatment leads to a significant
> > shift in intronic expression for some genes.
> >
> > Imagine I have an experiment with 6 biological replicates of a given
> > tissue. I believe that the treatment might lead to an increased intronic
> > expression for some genes, unrelated to exonic expression.
> >
> > 3 of these receive no treament, they are used as control. The other 3
> > receive experimental treatment.
> >
> > I then sequence the mRNA from these samples (Illumina, single end reads,
> > ~40 million reads per sample), to obtain 6 fastq files, I align these to a
> > refernce genome and get bam files.
> >
> > I was thinking that a fairly easy way to see if some genes show a
> > consistent increased intronic expression following treatment would be to
> > count intronically aligning reads for each gene (e.g. using GenomicRanges)
> > and use something like DESeq to look for genes showing a significant change
> > in intronic "expression".
> >
> > However, the problem is that this might be due to exonic expression, due to
> > premature mRNAs etc., so I might end up finding genes that are
> > differentially expressed at the exon level, and as a result the increased
> > exon expression has caused increased intronic expression as a by product.
> > Obviously I am not so interested in these genes wrt this method, I can find
> > these using "traditional" DE methods.
> >
> > In addition, when I tried profiling intronic regions using reads mapping to
> > introns, (using DESeq) it led to dodgy MA plots, where the 0 FC line was
> > quite far above the minimum mean expression point, i.e. it didn't go
> > through the middle of the clump of data points (if that makes sense). I
> > wonder if this is due to the size factor calculation being based on
> > intronic "expression" (well, reads mapping to introns), which is generally
> > much lower than exon expression and therefore being somewhat unreliable.
> >
> > So  I would like to take this exon expression out of the equation, so to
> > speak.
> >
> > I thought that one way might be to compare the ratios of exonic to intronic
> > reads between samples, for each gene.
> >
> > For example one gene might have 30, 35 and 33 exonically mapping reads and
> > 10,11 and 12 intronically mapping reads for control samples
> >
> > For case samples it might have 33, 32 and 34 exonically mapping reads;
> > 20,21 and 19 intronically mapping reads.
> >
> > So we could compare 10/30, 11/35 and 12/33 for control to 20/33, 21/32  and
> > 19/34 for case.
> >
> > Does this methodology sound reasonable? It is necessarily based on the
> > assumption that intronic "expression" due to unspliced RNAs is correlated
> > with exon expression.
> >
> > If it sounds reasonable, is there a test that is recommended to compare the
> > ratios in such a way, that takes into account the biological replication of
> > samples? I could do a simple test (chi squared) to compare the relative
> > frequencies, but this wouldn't take into account the replicates.
> >
> > I realise this isn't really a specific bioconductor question, but hopefully
> > it might be of interest to some of the list subscribers.
> >
> > Many thanks,
> >
> > Jim
> >
> > --
> > James R Perkins, PhD
> >
> >       [[alternative HTML version deleted]]
> >
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> 
> 
> 
> 
> 
> 
> -- 
> James R Perkins PhD