9. Explore InterProScan profile

Source: vignettes/09_Explore_InterProScan_profile.Rmd

First, make sure the library is loaded

If you want to follow this example, you can download the files from here file.

Now let’s load the long Interpro profile using the “Pfam” database: 

pfam_profile <-read_interpro(data_interpro = "../inst/extdata/Interpro",
                             database = "Pfam",
                             profile = T, 
                             write = F)
head(pfam_profile)
Table 1. InterproScan Profile Overview ( profile = T )
Pfam domain_name 5mSIPHEX1_0 5mSIPHEX1_1 5mSIPHEX1_10 5mSIPHEX1_11 5mSIPHEX1_13 5mSIPHEX1_15 5mSIPHEX1_18 5mSIPHEX1_19 5mSIPHEX1_2 5mSIPHEX1_25 5mSIPHEX1_26 5mSIPHEX1_32 5mSIPHEX1_33 5mSIPHEX1_37 5mSIPHEX1_8 5mSIPHEX1_9 5mSIPHEX2_10 5mSIPHEX2_14 5mSIPHEX2_16 5mSIPHEX2_18 5mSIPHEX2_25 5mSIPHEX2_3 5mSIPHEX2_5 5mSIPHEX2_7 700mSIPHEX1_0 700mSIPHEX1_1 700mSIPHEX1_12 700mSIPHEX1_15 700mSIPHEX1_17 700mSIPHEX1_18 700mSIPHEX1_2 700mSIPHEX1_20 700mSIPHEX1_3 700mSIPHEX1_8 700mSIPHEX2_13 700mSIPHEX2_14 700mSIPHEX2_16 700mSIPHEX2_21 700mSIPHEX2_22 700mSIPHEX2_23 700mSIPHEX2_24 700mSIPHEX2_9
PF00005 ABC transporter 74 42 76 30 54 21 28 26 27 30 20 28 21 61 100 20 69 78 16 31 91 60 29 54 41 98 36 29 29 36 32 33 76 44 44 29 36 29 33 34 34 83
PF08352 Oligopeptide/dipeptide transporter, C-terminal region 13 4 3 1 7 1 1 0 0 1 0 1 1 6 10 0 12 3 0 1 8 6 0 7 6 11 1 1 1 1 1 1 3 3 3 1 1 1 1 1 2 10
PF06242 Transcriptional cell cycle regulator TrcR 1 1 0 0 1 1 0 0 0 0 0 0 0 1 1 0 1 0 0 0 1 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
PF00586 AIR synthase related protein, N-terminal domain 3 1 2 3 2 4 3 1 3 3 2 4 2 2 2 2 3 2 1 3 2 2 2 2 1 3 3 3 2 3 2 3 2 0 0 2 3 3 2 3 2 3
PF02769 AIR synthase related protein, C-terminal domain 3 1 3 3 2 4 4 1 3 3 2 4 2 2 2 3 3 3 2 3 2 2 2 2 2 3 4 4 3 4 3 3 3 0 0 3 4 4 3 4 3 3
PF02021 Uncharacterised protein family UPF0102 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 2 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
PF01654 Cytochrome bd terminal oxidase subunit I 1 0 1 1 0 0 0 1 0 1 0 1 1 0 0 2 1 1 0 1 0 0 1 0 1 2 0 1 1 2 3 1 1 0 0 1 2 1 3 0 1 2
PF00528 Binding-protein-dependent transport system inner membrane component 54 30 39 10 31 3 7 8 4 10 0 9 2 40 78 2 53 39 0 10 67 36 9 31 31 59 2 6 2 8 6 12 39 29 29 2 8 6 7 2 18 52
PF00920 Dehydratase family 4 2 3 2 2 2 2 2 2 2 0 2 0 2 5 2 4 3 0 3 4 2 1 2 2 3 1 2 1 2 2 2 3 1 1 1 2 2 2 1 2 3
PF01458 SUF system FeS cluster assembly, SufBD 2 2 2 2 2 2 4 0 2 2 2 2 2 0 2 0 2 2 2 2 2 0 2 2 1 2 2 2 2 0 2 2 2 0 0 2 0 2 2 2 0 2

To explore the Interpro profiles we can use the following function:

  • get_subset_pca: which performs a PCA analysis to reduce the dimensions of the contributing families, resulting in a new table with the most represented Pfam families (for this example) of the bins/genome samples.

Some considerations:

  • To better visualize the results we recommend the loading of metadata, which essentially could include:

  • The clean names of the bins

  • Type of sampling

  • Environment

  • Hierarchical order

metadata <- read_excel("../inst/extdata/metadata_SIPH.xlsx")
head(metadata)
Table 2. Metadata overview
Clean_name Bin_name Name Depth Short_name Phylum Class Genus Database name
g_Flavobacterium_5m_16 5mSIPHEX2_16 SIP_5_Bin16-g_Flavobacterium Depth_5_meters SIP_5_Bin16 Bacteroidota Flavobacteriia Flavobacterium 5mSIPHEX1_0.faa
g_Flavobacterium_5m_26 5mSIPHEX1_26 SIP_5_Bin26-g_Flavobacterium Depth_5_meters SIP_5_Bin26 Bacteroidota Flavobacteriia Flavobacterium 5mSIPHEX1_1.faa
g_Henriciella_5m_15 5mSIPHEX1_15 SIP_5_Bin15-g_Henriciella Depth_5_meters SIP_5_Bin15 Pseudomonadota Alphaproteobacteria Henriciella 5mSIPHEX1_10.faa
g_Hyphomonas_5m_32 5mSIPHEX1_32 SIP_5_Bin32-g_Hyphomonas Depth_5_meters SIP_5_Bin32 Pseudomonadota Alphaproteobacteria Hyphomonas 5mSIPHEX1_11.faa
g_Hyphomonas_5m_33 5mSIPHEX1_33 SIP_5_Bin33-g_Hyphomonas Depth_5_meters SIP_5_Bin33 Pseudomonadota Alphaproteobacteria Hyphomonas 5mSIPHEX1_13.faa
g_Celeribacter_5m_10 5mSIPHEX2_10 SIP2_5_Bin10-g_Celeribacter Depth_5_meters SIP2_5_Bin10 Pseudomonadota Alphaproteobacteria Celeribacter 5mSIPHEX1_15.faa
g_Celeribacter_5m_0 5mSIPHEX1_0 SIP_5_Bin0-g_Celeribacter Depth_5_meters SIP_5_Bin0 Pseudomonadota Alphaproteobacteria Celeribacter 5mSIPHEX1_18.faa
s_Planktomarina_temperata_5m_1 5mSIPHEX1_1 SIP_5_Bin1-s_Planktomarina temperata Depth_5_meters SIP_5_Bin1 Pseudomonadota Alphaproteobacteria Planktomarina 5mSIPHEX1_19.faa
s_Lentibacter_algarum_5m_13 5mSIPHEX1_13 SIP_5_Bin13-s_Lentibacter algarum Depth_5_meters SIP_5_Bin13 Pseudomonadota Alphaproteobacteria Lentibacter 5mSIPHEX1_2.faa
s_Lentibacter_algarum_5m_7 5mSIPHEX2_7 SIP_5_Bin7-s_Lentibacter algarum Depth_5_meters SIP_5_Bin7 Pseudomonadota Alphaproteobacteria Lentibacter 5mSIPHEX1_25.faa 
#Extra commands to clean the bin names 

lookup <- setNames(metadata$Bin_name, metadata$Clean_name)

pfam_profile_renamed <- pfam_profile %>% 
  rename(!!!lookup) 
important_PFAMs<-get_subset_pca(tibble_rbims=pfam_profile_renamed,
                                cos2_val=0.96,
                                analysis="Pfam")
head(important_PFAMs)

To visualize the InterproScan subset we can use the following functions:

Use plot_heatmap with the argument distance = T to visualize the clustering of the bins/genome samples based on the InterproScan domains.


plot_heatmap(important_PFAMs, 
             y_axis=Pfam, 
             analysis = "INTERPRO", 
             distance = T)
Figure 1. Clustering of InterproScan families across bins.

Figure 1. Clustering of InterproScan families across bins.

Use plot_heatmap with the argument distance = F to visualize the abundance of InterproScan domains across the bins/genome samples.


plot_heatmap(important_PFAMs, 
             y_axis=Pfam, 
             analysis = "INTERPRO", 
             distance = F)
Figure 2. Presence/Absence of InterproScan families across bins.

Figure 2. Presence/Absence of InterproScan families across bins.

For plot_bubble, the user has two options for the argument calc:

  • Binary

plot_bubble(important_PFAMs, 
            y_axis=Pfam, 
            x_axis=Bin_name, 
            calc = "Binary",
            analysis = "INTERPRO", 
            data_experiment = metadata_renamed, 
            color_character = Depth,
            order_bins = ordered,
            y_labs = "Most contributing InterproScan families",
            text_y = 10,
            x_labs = "Bins",
            text_x = 9)
#> Scale for size is already present.
#> Adding another scale for size, which will replace the existing scale.
Figure 3. Presence of InterproScan families across bins.

Figure 3. Presence of InterproScan families across bins.

Or

  • Abundance


plot_bubble(important_PFAMs, 
            y_axis=Pfam, 
            x_axis=Bin_name, 
            calc = "Abundance",
            analysis = "INTERPRO", 
            data_experiment = metadata_renamed, 
            color_character = Class,
            y_labs = "Most contributing InterproScan families",
            text_y = 10,
            x_labs = "Bins",
            text_x = 9,
            range_size = c(1,15))
Figure 4. Abundance of InterproScan families across bins.

Figure 4. Abundance of InterproScan families across bins.

Exploring other databases within InterproScan

Because the annotation with InterproScan recovers data from different databases, rbims can also explore not only Pfams, but also TigerFams, Superamilies or InterproScan ID’s. First, we will reload the InterProScan output in a wide format and extract the PFAM abundance information.

Let’s load the long Interpro profile using the “INTERPRO” database: 

interpro_profile <-read_interpro(data_interpro ="../inst/extdata/Interpro",
                                 profile = T, 
                                 database = "INTERPRO",
                                 write = F)
head(interpro_profile)
Table 1. dbCAN Profile Overview ( profile = T )
INTERPRO domain_name 5mSIPHEX1_0 5mSIPHEX1_1 5mSIPHEX1_10 5mSIPHEX1_11 5mSIPHEX1_13 5mSIPHEX1_15 5mSIPHEX1_18 5mSIPHEX1_19 5mSIPHEX1_2 5mSIPHEX1_25 5mSIPHEX1_26 5mSIPHEX1_32 5mSIPHEX1_33 5mSIPHEX1_37 5mSIPHEX1_8 5mSIPHEX1_9 5mSIPHEX2_10 5mSIPHEX2_14 5mSIPHEX2_16 5mSIPHEX2_18 5mSIPHEX2_25 5mSIPHEX2_3 5mSIPHEX2_5 5mSIPHEX2_7 700mSIPHEX1_0 700mSIPHEX1_1 700mSIPHEX1_12 700mSIPHEX1_15 700mSIPHEX1_17 700mSIPHEX1_18 700mSIPHEX1_2 700mSIPHEX1_20 700mSIPHEX1_3 700mSIPHEX1_8 700mSIPHEX2_13 700mSIPHEX2_14 700mSIPHEX2_16 700mSIPHEX2_21 700mSIPHEX2_22 700mSIPHEX2_23 700mSIPHEX2_24 700mSIPHEX2_9
2391 1580 3106 2391 2133 2316 2021 2238 1892 2424 1320 2665 1785 1905 3346 1963 2286 3437 1494 2533 3002 1844 2221 2137 1513 2583 2394 2444 2287 2858 2657 2595 3062 1281 1277 2287 2851 2442 2664 2292 1843 2422
IPR003593 AAA+ ATPase domain 100 64 126 61 84 51 59 62 53 67 29 57 43 79 137 50 95 132 33 67 124 78 65 83 52 129 59 66 54 80 70 72 126 59 58 54 80 66 70 57 71 114
IPR003439 ABC transporter-like, ATP-binding domain 75 43 77 31 55 22 29 27 28 31 20 28 21 64 104 21 70 79 17 32 94 63 30 55 41 98 36 30 31 37 34 34 77 46 46 31 37 30 35 34 35 83
IPR017871 ABC transporter-like, conserved site 63 34 63 24 49 15 20 19 24 24 10 21 15 49 85 18 59 65 10 25 76 50 21 49 34 83 26 22 23 31 30 27 63 35 35 23 31 22 31 25 30 71
IPR027417 P-loop containing nucleoside triphosphate hydrolase 198 132 243 156 166 142 148 171 144 168 99 155 109 167 267 137 181 277 104 185 231 162 163 168 111 228 153 176 149 196 182 171 240 110 110 149 196 176 172 141 151 209
IPR013563 Oligopeptide/dipeptide ABC transporter, C-terminal 13 4 3 1 7 1 1 0 0 1 0 1 1 6 10 0 12 3 0 1 8 6 0 7 6 11 1 1 1 1 1 1 3 3 3 1 1 1 1 1 2 10
IPR010421 Transcriptional cell cycle regulator TrcR 1 1 0 0 1 1 0 0 0 0 0 0 0 1 1 0 1 0 0 0 1 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
IPR016188 PurM-like, N-terminal domain 3 1 2 3 2 4 3 1 3 3 2 4 2 2 2 2 3 2 1 3 2 2 2 2 1 3 3 3 2 3 2 3 2 0 0 2 3 3 2 3 2 3
IPR036921 PurM-like, N-terminal domain superfamily 3 1 3 4 2 4 4 2 4 4 3 4 2 2 2 3 3 3 2 4 2 2 3 2 1 3 4 4 3 4 3 4 3 0 0 3 4 4 3 4 3 3
IPR010918 PurM-like, C-terminal domain 3 1 3 3 2 4 4 1 3 3 2 4 2 2 2 3 3 3 2 3 2 2 2 2 2 3 4 4 3 4 3 3 3 0 0 3 4 4 3 4 3 3

We are going to look for the InterProScan IDs that conform the DNA topoisomerase 1. To do this, we will create a vector of the IDs associated to that enzyme. 

DNA_topoisomerase_1<-c("IPR013497", "IPR023406", "IPR013824")

With the function get_subset_pathway we can create a subset of the INTERPRO table. 

DNA_topo_INTERPRO<-get_subset_pathway(interpro_profile,
                                      type_of_interest_feature=INTERPRO,
                                      interest_feature=DNA_topoisomerase_1)
head(DNA_topo_INTERPRO)
Table 4. InterproScan Profile Overview ( profile = T )
INTERPRO domain_name 5mSIPHEX1_0 5mSIPHEX1_1 5mSIPHEX1_10 5mSIPHEX1_11 5mSIPHEX1_13 5mSIPHEX1_15 5mSIPHEX1_18 5mSIPHEX1_19 5mSIPHEX1_2 5mSIPHEX1_25 5mSIPHEX1_26 5mSIPHEX1_32 5mSIPHEX1_33 5mSIPHEX1_37 5mSIPHEX1_8 5mSIPHEX1_9 5mSIPHEX2_10 5mSIPHEX2_14 5mSIPHEX2_16 5mSIPHEX2_18 5mSIPHEX2_25 5mSIPHEX2_3 5mSIPHEX2_5 5mSIPHEX2_7 700mSIPHEX1_0 700mSIPHEX1_1 700mSIPHEX1_12 700mSIPHEX1_15 700mSIPHEX1_17 700mSIPHEX1_18 700mSIPHEX1_2 700mSIPHEX1_20 700mSIPHEX1_3 700mSIPHEX1_8 700mSIPHEX2_13 700mSIPHEX2_14 700mSIPHEX2_16 700mSIPHEX2_21 700mSIPHEX2_22 700mSIPHEX2_23 700mSIPHEX2_24 700mSIPHEX2_9
IPR023406 DNA topoisomerase, type IA, active site 1 1 2 0 1 1 2 2 2 2 1 1 0 1 1 0 1 3 1 1 1 1 2 1 0 1 1 2 1 1 2 1 2 1 1 1 1 2 2 1 2 1
IPR013497 DNA topoisomerase, type IA, central 1 2 2 0 1 1 2 2 2 2 1 1 0 1 1 0 1 4 1 1 1 1 2 1 0 1 1 2 2 1 2 1 2 1 1 2 1 2 2 1 2 1
IPR013824 DNA topoisomerase, type IA, central region, subdomain 1 1 2 2 0 1 1 2 2 2 2 1 1 0 1 1 0 1 4 1 1 1 1 2 1 0 1 1 2 2 1 2 1 2 1 1 2 1 2 2 1 2 1

To visualize it, we can create a bubble plot to explore the distribution of these enzymes across the bins. 


plot_bubble(DNA_topo_INTERPRO, 
            y_axis=INTERPRO,
            x_axis=Bin_name,
            calc = "Abundance",
            analysis = "INTERPRO", 
            data_experiment = metadata, 
            color_character = Depth)
Figure 5. Abundance of InterproScan families conforming the DNA topoisomerase pathway across bins.

Figure 5. Abundance of InterproScan families conforming the DNA topoisomerase pathway across bins.