1 Setup

library(BioPlex)
library(AnnotationDbi)
library(AnnotationHub)
library(graph)

Connect to AnnotationHub:

ah <- AnnotationHub::AnnotationHub()

Connect to ExperimentHub:

eh <- ExperimentHub::ExperimentHub()

OrgDb package for human:

orgdb <- AnnotationHub::query(ah, c("orgDb", "Homo sapiens"))
orgdb <- orgdb[[1]]
orgdb
#> OrgDb object:
#> | DBSCHEMAVERSION: 2.1
#> | Db type: OrgDb
#> | Supporting package: AnnotationDbi
#> | DBSCHEMA: HUMAN_DB
#> | ORGANISM: Homo sapiens
#> | SPECIES: Human
#> | EGSOURCEDATE: 2021-Sep13
#> | EGSOURCENAME: Entrez Gene
#> | EGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
#> | CENTRALID: EG
#> | TAXID: 9606
#> | GOSOURCENAME: Gene Ontology
#> | GOSOURCEURL: http://current.geneontology.org/ontology/go-basic.obo
#> | GOSOURCEDATE: 2021-09-01
#> | GOEGSOURCEDATE: 2021-Sep13
#> | GOEGSOURCENAME: Entrez Gene
#> | GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
#> | KEGGSOURCENAME: KEGG GENOME
#> | KEGGSOURCEURL: ftp://ftp.genome.jp/pub/kegg/genomes
#> | KEGGSOURCEDATE: 2011-Mar15
#> | GPSOURCENAME: UCSC Genome Bioinformatics (Homo sapiens)
#> | GPSOURCEURL: 
#> | GPSOURCEDATE: 2021-Jul20
#> | ENSOURCEDATE: 2021-Apr13
#> | ENSOURCENAME: Ensembl
#> | ENSOURCEURL: ftp://ftp.ensembl.org/pub/current_fasta
#> | UPSOURCENAME: Uniprot
#> | UPSOURCEURL: http://www.UniProt.org/
#> | UPSOURCEDATE: Wed Sep 15 18:21:59 2021
keytypes(orgdb)
#>  [1] "ACCNUM"       "ALIAS"        "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS"
#>  [6] "ENTREZID"     "ENZYME"       "EVIDENCE"     "EVIDENCEALL"  "GENENAME"    
#> [11] "GENETYPE"     "GO"           "GOALL"        "IPI"          "MAP"         
#> [16] "OMIM"         "ONTOLOGY"     "ONTOLOGYALL"  "PATH"         "PFAM"        
#> [21] "PMID"         "PROSITE"      "REFSEQ"       "SYMBOL"       "UCSCKG"      
#> [26] "UNIPROT"

2 Check: identify CORUM complexes that have a subunit of interest

Get core set of complexes:

core <- getCorum(set = "core", organism = "Human")

Turn the CORUM complexes into a list of graph instances, where all nodes of a complex are connected to all other nodes of that complex with undirected edges.

core.glist <- corum2graphlist(core, subunit.id.type = "UNIPROT")

Identify complexes that have a subunit of interest:

has.cdk2 <- hasSubunit(core.glist, 
                       subunit = "CDK2",
                       id.type = "SYMBOL")

Check the answer:

table(has.cdk2)
#> has.cdk2
#> FALSE  TRUE 
#>  2408     9
cdk2.glist <- core.glist[has.cdk2]
lapply(cdk2.glist, function(g) unlist(graph::nodeData(g, attr = "SYMBOL")))
#> $CORUM311_Cell_cycle_kinase_complex_CDK2
#>   P12004   P24385   P24941   P38936 
#>   "PCNA"  "CCND1"   "CDK2" "CDKN1A" 
#> 
#> $`CORUM1003_RC_complex_(Replication_competent_complex)`
#>  P09884  P20248  P24941  P35249  P35250  P35251  P40937  P40938  Q14181 
#> "POLA1" "CCNA2"  "CDK2"  "RFC4"  "RFC2"  "RFC1"  "RFC5"  "RFC3" "POLA2" 
#> 
#> $`CORUM1004_RC_complex_during_S-phase_of_cell_cycle`
#>  P09874  P09884  P11387  P15927  P18858  P20248  P24941  P27694  P28340  P35244 
#> "PARP1" "POLA1"  "TOP1"  "RPA2"  "LIG1" "CCNA2"  "CDK2"  "RPA1" "POLD1"  "RPA3" 
#>  P35250  P35251  Q07864 
#>  "RFC2"  "RFC1"  "POLE" 
#> 
#> $`CORUM1656_p27-cyclinE-CDK2_complex`
#>   P24864   P24941   P46527 
#>  "CCNE1"   "CDK2" "CDKN1B" 
#> 
#> $`CORUM3015_p27-cyclinE-Cdk2_-_Ubiquitin_E3_ligase_(SKP1A,_SKP2,_CUL1,_CKS1B,_RBX1)_complex`
#>   P24864   P24941   P46527   P61024   P62877   P63208   Q13309   Q13616 
#>  "CCNE1"   "CDK2" "CDKN1B"  "CKS1B"   "RBX1"   "SKP1"   "SKP2"   "CUL1" 
#> 
#> $`CORUM5556_CDK2-CCNA2_complex`
#>  P20248  P24941 
#> "CCNA2"  "CDK2" 
#> 
#> $`CORUM5559_CDC2-CCNA2-CDK2_complex`
#>  P06493  P20248  P24941 
#>  "CDK1" "CCNA2"  "CDK2" 
#> 
#> $`CORUM5560_CDK2-CCNE1_complex`
#>  P24864  P24941 
#> "CCNE1"  "CDK2" 
#> 
#> $`CORUM6589_E2F-1-DP-1-cyclinA-CDK2_complex`
#>  P24941  P78396  Q01094  Q14186 
#>  "CDK2" "CCNA1"  "E2F1" "TFDP1"

We can then also inspect the graph with plotting utilities from the Rgraphviz package:

plot(cdk2.glist[[1]], main = names(cdk2.glist)[1])

3 Check: extract BioPlex PPIs for a CORUM complex

Get the latest version of the 293T PPI network:

bp.293t <- getBioPlex(cell.line = "293T", version = "3.0")

Turn the BioPlex PPI network into one big graph where bait and prey relationship are represented by directed edges from bait to prey.

bp.gr <- bioplex2graph(bp.293t)

Now we can also easily pull out a BioPlex subnetwork for a CORUM complex of interest:

n <- graph::nodes(cdk2.glist[[1]])
bp.sgr <- graph::subGraph(n, bp.gr)
bp.sgr
#> A graphNEL graph with directed edges
#> Number of Nodes = 4 
#> Number of Edges = 5

4 Check: identify interacting domains for a PFAM domain of interest

Add PFAM domain annotations to the node metadata:

bp.gr <- BioPlex::annotatePFAM(bp.gr, orgdb)

Create a map from PFAM to UNIPROT:

unip2pfam <- graph::nodeData(bp.gr, graph::nodes(bp.gr), "PFAM")
pfam2unip <- stack(unip2pfam)
pfam2unip <- split(as.character(pfam2unip$ind), pfam2unip$values)
head(pfam2unip, 2)
#> $PF00001
#>  [1] "P28566" "P25106" "P23945" "Q9HBX9" "P16473" "P04201" "Q9HC97" "P30968"
#>  [9] "Q9Y2T6" "Q14330" "P46089" "Q15391" "Q9BXA5" "Q13304" "P61073" "P21462"
#> [17] "P25090" "Q99679" "P21730" "P30556" "P43088" "P32246" "P32249" "Q9Y2T5"
#> [25] "Q7Z602" "P43657" "O00398" "Q9H244" "Q86VZ1" "Q9NPB9" "Q99788" "P51684"
#> [33] "P35414" "O00590" "Q9H1Y3" "P55085" "O15218" "Q9GZQ4" "P25101" "Q9NS66"
#> [41] "Q9NQS5" "P21453" "P14416" "P24530" "P32239" "Q16581" "O00421" "Q9UHM6"
#> [49] "Q8N6U8" "P20309" "O15354" "Q9BXC0" "P47775" "P30550" "P49146" "P47900"
#> [57] "Q8TDU9" "P25103" "P35372" "P41597" "Q9P296" "P28335" "O95136" "P08173"
#> [65] "P29371" "P41146" "P43119" "O95977" "Q9HBW0" "Q99677" "Q9BXB1" "Q8WXD0"
#> [73] "O43193" "P30989" "Q8NGU9" "P47901" "P22888" "Q9GZN0" "P21917" "O60755"
#> [81] "Q8TDV0" "O43614" "Q9NS67" "P08912" "Q9UPC5" "Q8TDV2" "Q92633" "Q9NQ55"
#> [89] "Q13585" "Q9UBY5" "Q9H228" "P28222"
#> 
#> $PF00002
#>  [1] "Q8IZP9" "P41587" "Q8IZF4" "P49190" "P32241" "P47871" "P48960" "Q8IZF5"
#>  [9] "O14514" "Q03431" "Q9NYQ6" "Q9HCU4" "Q8WXG9" "Q9NYQ7" "O60242" "O60241"
#> [17] "Q9HAR2" "O94910" "Q8IWK6" "O95490" "Q96PE1" "Q86SQ4"

Let’s focus on PF02023, corresponding to the zinc finger-associated SCAN domain. For each protein containing the SCAN domain, we now extract PFAM domains connected to the SCAN domain by an edge in the BioPlex network.

scan.unip <- pfam2unip[["PF02023"]]
getIAPfams <- function(n) graph::nodeData(bp.gr, graph::edges(bp.gr)[[n]], "PFAM")
unip2iapfams <- lapply(scan.unip, getIAPfams)
unip2iapfams <- lapply(unip2iapfams, unlist)
names(unip2iapfams) <- scan.unip

Looking at the top 5 PFAM domains most frequently connected to the SCAN domain by an edge in the BioPlex network …

pfam2iapfams <- unlist(unip2iapfams)
sort(table(pfam2iapfams), decreasing = TRUE)[1:5]
#> pfam2iapfams
#> PF02023 PF00096 PF01352 PF06467 PF00249 
#>     208     169      99      14       8

… we find PF02023, the SCAN domain itself, and PF00096, a C2H2 type zinc finger domain. This finding is consistent with results reported in the BioPlex 3.0 publication.

See also the PFAM domain-domain association analysis vignette for a more comprehensive analysis of PFAM domain associations in the BioPlex network.

5 Check: expressed genes are showing up as prey (293T cells)

Get RNA-seq data for HEK293 cells from GEO: GSE122425

se <- getGSE122425()
se
#> class: SummarizedExperiment 
#> dim: 57905 6 
#> metadata(0):
#> assays(2): raw rpkm
#> rownames(57905): ENSG00000223972 ENSG00000227232 ... ENSG00000231514
#>   ENSG00000235857
#> rowData names(4): SYMBOL KO GO length
#> colnames(6): GSM3466389 GSM3466390 ... GSM3466393 GSM3466394
#> colData names(41): title geo_accession ... passages.ch1 strain.ch1

Inspect expression of prey genes:

bait <- unique(bp.293t$SymbolA)
length(bait)
#> [1] 8995
prey <- unique(bp.293t$SymbolB)
length(prey)
#> [1] 10419
ind <- match(prey, rowData(se)$SYMBOL)
par(las = 2)
boxplot(log2(assay(se, "rpkm") + 0.5)[ind,], 
        names = se$title, 
        ylab = "log2 RPKM")

How many prey genes are expressed (raw read count > 0) in all 3 WT reps:

# background: how many genes in total are expressed in all three WT reps
gr0 <- rowSums(assay(se)[,1:3] > 0)
table(gr0 == 3)
#> 
#> FALSE  TRUE 
#> 33842 24063
# prey: expressed in all three WT reps
table(gr0[ind] == 3)
#> 
#> FALSE  TRUE 
#>   599  9346
# prey: expressed in at least one WT rep
table(gr0[ind] > 0)
#> 
#> FALSE  TRUE 
#>   305  9640

Are prey genes overrepresented in the expressed genes?

exprTable <-
     matrix(c(9346, 1076, 14717, 32766),
            nrow = 2,
            dimnames = list(c("Expressed", "Not.expressed"),
                            c("In.prey.set", "Not.in.prey.set")))
exprTable
#>               In.prey.set Not.in.prey.set
#> Expressed            9346           14717
#> Not.expressed        1076           32766

Test using hypergeometric test (i.e. one-sided Fisher’s exact test):

fisher.test(exprTable, alternative = "greater")
#> 
#>  Fisher's Exact Test for Count Data
#> 
#> data:  exprTable
#> p-value < 2.2e-16
#> alternative hypothesis: true odds ratio is greater than 1
#> 95 percent confidence interval:
#>  18.29105      Inf
#> sample estimates:
#> odds ratio 
#>   19.34726

Alternatively: permutation test, i.e. repeatedly sample number of prey genes from the background, and assess how often we have as many or more than 9346 genes expressed:

permgr0 <- function(gr0, nr.genes = length(prey)) 
{
    ind <- sample(seq_along(gr0), nr.genes)
    sum(gr0[ind] == 3)
}
perms <- replicate(permgr0(gr0), 1000)
summary(perms)
#>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
#>    1000    1000    1000    1000    1000    1000
(sum(perms >= 9346) + 1) / 1001
#> [1] 0.000999001

6 Check: is there a relationship between prey frequency and prey expression level?

Check which genes turn up most frequently as prey:

prey.freq <- sort(table(bp.293t$SymbolB), decreasing = TRUE)
preys <- names(prey.freq)
prey.freq <- as.vector(prey.freq)
names(prey.freq) <- preys
head(prey.freq)
#> HSPA5 HSPA8 TUBB8   UBB  YBX1 YWHAH 
#>   199   192   176   173   139   132
summary(prey.freq)
#>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
#>    1.00    2.00    6.00   11.34   16.00  199.00
hist(prey.freq, breaks = 50, main = "", xlab = "Number of PPIs", ylab = "Number of genes")

Prey genes are involved 11 PPIs on average.

There doesn’t seem to be a strong correlation between expression level and the frequency of gene to turn up as prey:

ind <- match(names(prey.freq), rowData(se)$SYMBOL)
rmeans <- rowMeans(assay(se, "rpkm")[ind, 1:3])
log.rmeans <- log2(rmeans + 0.5)
par(pch = 20)
plot( x = prey.freq,
      y = log.rmeans,
      xlab = "prey frequency",
      ylab = "log2 RPKM")

cor(prey.freq, 
    log.rmeans,
    use = "pairwise.complete.obs")
#> [1] 0.2035977

See also the BioNet maximum scoring subnetwork analysis vignette for a more comprehensive analysis of the 293T transcriptome data from GSE122425 when mapped onto BioPlex PPI network.

7 Check: differential protein expression (HEK293 vs. HCT116)

Get the relative protein expression data comparing 293T and HCT116 cells from Supplementary Table S4A of the BioPlex 3 paper:

bp.prot <- getBioplexProteome()
bp.prot
#> class: SummarizedExperiment 
#> dim: 9604 10 
#> metadata(0):
#> assays(1): exprs
#> rownames(9604): P0CG40 Q8IXZ3-4 ... Q9H3S5 Q8WYQ3
#> rowData names(5): ENTREZID SYMBOL nr.peptides log2ratio adj.pvalue
#> colnames(10): HCT1 HCT2 ... HEK4 HEK5
#> colData names(1): cell.line
rowData(bp.prot)
#> DataFrame with 9604 rows and 5 columns
#>             ENTREZID      SYMBOL nr.peptides log2ratio  adj.pvalue
#>          <character> <character>   <integer> <numeric>   <numeric>
#> P0CG40     100131390         SP9           1 -2.819071 6.66209e-08
#> Q8IXZ3-4      221833         SP8           3 -3.419888 6.94973e-07
#> P55011          6558     SLC12A2           4  0.612380 4.85602e-06
#> O60341         23028       KDM1A           7 -0.319695 5.08667e-04
#> O14654          8471        IRS4           4 -5.951096 1.45902e-06
#> ...              ...         ...         ...       ...         ...
#> Q9H6X4         80194     TMEM134           2 -0.379342 7.67195e-05
#> Q9BS91         55032     SLC35A5           1 -2.237634 8.75523e-05
#> Q9UKJ5         26511       CHIC2           1 -0.614932 1.78756e-03
#> Q9H3S5         93183        PIGM           1 -1.011397 8.91589e-06
#> Q8WYQ3        400916     CHCHD10           1  0.743852 1.17163e-03

A couple of quick sanity checks:

  1. The relative abundances are scaled to sum up to 100% for each protein:
rowSums(assay(bp.prot)[1:5,]) 
#>    P0CG40  Q8IXZ3-4    P55011    O60341    O14654 
#>  99.99994  99.99991  99.99996 100.00011 100.00006
  1. The rowData column log2ratio corresponds to the mean of the five HEK samples, divided by the mean of the five HCT samples (and then taking log2 of it):
ratio <- rowMeans(assay(bp.prot)[1:5, 1:5]) / rowMeans(assay(bp.prot)[1:5, 6:10])
log2(ratio)
#>     P0CG40   Q8IXZ3-4     P55011     O60341     O14654 
#> -2.8190710 -3.4198879  0.6123799 -0.3196953 -5.9510960
  1. The rowData column adj.pvalue stores Benjamini-Hochberg adjusted p-values from a t-test between the five HEK samples and the five HCT samples:
t.test(assay(bp.prot)[1, 1:5], assay(bp.prot)[1, 6:10])
#> 
#>  Welch Two Sample t-test
#> 
#> data:  assay(bp.prot)[1, 1:5] and assay(bp.prot)[1, 6:10]
#> t = -27.898, df = 7.5779, p-value = 6.482e-09
#> alternative hypothesis: true difference in means is not equal to 0
#> 95 percent confidence interval:
#>  -16.29035 -13.78047
#> sample estimates:
#> mean of x mean of y 
#>  2.482288 17.517700

The Transcriptome-Proteome analysis vignette also explores the agreement between differential gene expression and differential protein expression when comparing HEK293 against HCT116 cells.

8 SessionInfo

sessionInfo()
#> R version 4.1.1 (2021-08-10)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.3 LTS
#> 
#> Matrix products: default
#> BLAS:   /home/biocbuild/bbs-3.14-bioc/R/lib/libRblas.so
#> LAPACK: /home/biocbuild/bbs-3.14-bioc/R/lib/libRlapack.so
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_GB              LC_COLLATE=C              
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> attached base packages:
#> [1] stats4    stats     graphics  grDevices utils     datasets  methods  
#> [8] base     
#> 
#> other attached packages:
#>  [1] graph_1.72.0                AnnotationHub_3.2.0        
#>  [3] BiocFileCache_2.2.0         dbplyr_2.1.1               
#>  [5] AnnotationDbi_1.56.1        BioPlex_1.0.1              
#>  [7] SummarizedExperiment_1.24.0 Biobase_2.54.0             
#>  [9] GenomicRanges_1.46.0        GenomeInfoDb_1.30.0        
#> [11] IRanges_2.28.0              S4Vectors_0.32.0           
#> [13] BiocGenerics_0.40.0         MatrixGenerics_1.6.0       
#> [15] matrixStats_0.61.0          BiocStyle_2.22.0           
#> 
#> loaded via a namespace (and not attached):
#>  [1] bitops_1.0-7                  bit64_4.0.5                  
#>  [3] filelock_1.0.2                httr_1.4.2                   
#>  [5] tools_4.1.1                   bslib_0.3.1                  
#>  [7] utf8_1.2.2                    R6_2.5.1                     
#>  [9] DBI_1.1.1                     withr_2.4.2                  
#> [11] tidyselect_1.1.1              bit_4.0.4                    
#> [13] curl_4.3.2                    compiler_4.1.1               
#> [15] xml2_1.3.2                    DelayedArray_0.20.0          
#> [17] bookdown_0.24                 sass_0.4.0                   
#> [19] readr_2.0.2                   rappdirs_0.3.3               
#> [21] stringr_1.4.0                 digest_0.6.28                
#> [23] rmarkdown_2.11                R.utils_2.11.0               
#> [25] GEOquery_2.62.0               XVector_0.34.0               
#> [27] pkgconfig_2.0.3               htmltools_0.5.2              
#> [29] fastmap_1.1.0                 limma_3.50.0                 
#> [31] highr_0.9                     rlang_0.4.12                 
#> [33] RSQLite_2.2.8                 shiny_1.7.1                  
#> [35] jquerylib_0.1.4               generics_0.1.1               
#> [37] jsonlite_1.7.2                dplyr_1.0.7                  
#> [39] R.oo_1.24.0                   RCurl_1.98-1.5               
#> [41] magrittr_2.0.1                GenomeInfoDbData_1.2.7       
#> [43] Matrix_1.3-4                  Rcpp_1.0.7                   
#> [45] fansi_0.5.0                   lifecycle_1.0.1              
#> [47] R.methodsS3_1.8.1             stringi_1.7.5                
#> [49] yaml_2.2.1                    zlibbioc_1.40.0              
#> [51] grid_4.1.1                    blob_1.2.2                   
#> [53] promises_1.2.0.1              ExperimentHub_2.2.0          
#> [55] crayon_1.4.1                  lattice_0.20-45              
#> [57] Biostrings_2.62.0             hms_1.1.1                    
#> [59] KEGGREST_1.34.0               knitr_1.36                   
#> [61] pillar_1.6.4                  glue_1.4.2                   
#> [63] BiocVersion_3.14.0            evaluate_0.14                
#> [65] data.table_1.14.2             BiocManager_1.30.16          
#> [67] png_0.1-7                     vctrs_0.3.8                  
#> [69] tzdb_0.2.0                    httpuv_1.6.3                 
#> [71] purrr_0.3.4                   tidyr_1.1.4                  
#> [73] assertthat_0.2.1              cachem_1.0.6                 
#> [75] xfun_0.27                     mime_0.12                    
#> [77] xtable_1.8-4                  later_1.3.0                  
#> [79] tibble_3.1.5                  memoise_2.0.0                
#> [81] ellipsis_0.3.2                interactiveDisplayBase_1.32.0