README.rmd

# functional enrichment for GTEx paper

### Guangchuang Yu
#### 07/15, 2015



Refer to the [issue](https://github.com/GuangchuangYu/DOSE/issues/6), this document will reproduce functional analysis using [DOSE](http://www.bioconductor/packages/DOSE) and [clusterProfiler](http://www.bioconductor.org/packages/clusterProfiler) packages.


The paper and supplemental files are located at [paper folder](paper).

In page 63 of [supplemental file](paper/Mele.SM.pdf), the authors mentioned that *genes with high contribution of individuals to splicing variation* were used in GO enrichment analysis.

![](figures/Screenshot 2015-07-15 20.03.05.png)

The **Individual and Tissue contribution to variation of splicing** was stored in [supplemental table 17](paper/LargeSupplementTABLES_May1st_2015.xlsx), which was exported as a [csv file](tableS17.csv).


```{r}
require(magrittr)
require(DOSE)
require(RDAVIDWebService)
require(clusterProfiler)

table17 <- read.csv("paper/tableS17.csv")

gene <- with(table17, gene_id[ Individuals > quantile(Individuals, 0.98)])
gene %<>% as.character %>% gsub("\\.\\d+", "", .)

head(gene)
length(gene)
save(gene, file="cache/gene.rda")
```

The authors did not mention how they define __*high contribution*__, here I use the top 2% of genes and get `r length(gene)` genes with 168 genes that could be mapped in the DAVID database. Slightly large than the number (139) reported in [supplemental file](paper/Mele.SM.pdf).

The GO enrichment result reported in [supplemental table 18](paper/LargeSupplementTABLES_May1st_2015.xlsx) is:

![](figures/Screenshot 2015-07-15 19.49.01.png)


I pasted the genes into DAVID and got similar results.

![](figures/Screenshot 2015-07-15 21.10.11.png)
![](figures/Screenshot 2015-07-15 21.10.28.png)

Although the gene list I selected here is slighly different from the one author selected (which we don't know), it can reproduce the results reported in the paper.


Here, I use these genes to perform enrichment analyses and compare results from DAVID and clusterProfiler.

+ [GO (BP) enrichment analysis](GO_BP.md)
+ [KEGG enrichment analysis](KEGG.md)
+ [DO enrichment analysis](DO.md)
+ [Reactome enrichment analysis](Reactome.md)