3. Advanced Analysis and Visualization

Advanced Analysis Workflow

Once you have a ComplexMap object, the package provides several functions for deeper analysis and interpretation of the network structure. This vignette covers:

Optimizing Parameters: Using evaluateComplexes() to tune the refineComplexList step.
Summarizing & Querying Themes: A streamlined workflow using summarizeThemes() and queryMap() to identify and investigate biological clusters.

library(ComplexMap)
library(dplyr)

1. Optimizing Refinement with `evaluateComplexes`

The mergeThreshold in refineComplexList determines how aggressively redundant complexes are merged. The default is a conservative Jaccard similarity of 0.90 to preserve biological variants.

The evaluateComplexes() function can score a refined complex list against a gold standard, helping you tune this parameter.

# Load the package's demo and reference data
data(demoComplexes)
data(referenceComplexes)

# 1. Run Refinement
refinement_output <- refineComplexList(
  demoComplexes,
  mergeThreshold = 0.90,
  similarityMethod = "jaccard",
  verbose = FALSE
)

# 2. Evaluate
# Pass the $refinedComplexes element to the evaluation function
metrics <- evaluateComplexes(
  predictedComplexes = refinement_output$refinedComplexes,
  referenceComplexes = referenceComplexes,
  nCores = 2, # Use multiple cores if available
  verbose = FALSE
)

# Display the resulting metrics
knitr::kable(as.data.frame(metrics))

PPV	Sn	Acc	MMR
0.8005051	0.2510583	0.4483006	0.0940346

For more systematic tuning, see the documentation for benchmarkParameters(), which automates this process over a range of thresholds.

2. A Streamlined Workflow for Theme Analysis

A key goal of ComplexMap is to organize complexes into a functional landscape. summarizeThemes() uses community detection to find densely connected physical neighborhoods (themes) and, by default, adds this information directly to your ComplexMap object. This makes querying by theme simple and intuitive.

First, let’s generate a map object for this example.

gmtPath <- getExampleGmt()
gmt <- getGmtFromFile(gmtPath, verbose = FALSE)

cm_obj_adv <- createComplexMap(
  complexList = demoComplexes,
  gmt = gmt,
  mergeThreshold = 0.85, 
  verbose = FALSE
)

Step 2.1: Summarize Themes and Add to Object

Now, we run summarizeThemes(). The default add_to_object = TRUE returns the modified ComplexMap object, now containing theme information in its node table.

# Ensure reproducibility of community detection
set.seed(123)

# This single command finds themes AND adds them to the object
cm_obj_adv <- summarizeThemes(cm_obj_adv, verbose = FALSE)

# We can inspect the new columns in the node table
getNodeTable(cm_obj_adv) %>%
  select(complexId, primaryFunctionalDomain, themeId, themeLabel) %>%
  head() %>%
  knitr::kable()

complexId	primaryFunctionalDomain	themeId	themeLabel
CpxMap_0414	BIOCARTA_CIRCADIAN_PATHWAY	1	BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY
CpxMap_0401	BIOCARTA_RNA_PATHWAY	1	BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY
CpxMap_0359	BIOCARTA_AGPCR_PATHWAY	2	BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY
CpxMap_0501	BIOCARTA_SUMO_PATHWAY	3	BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY
CpxMap_0508	Unenriched	3	BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY
CpxMap_0090	BIOCARTA_SALMONELLA_PATHWAY	2	BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY

The returned object is now “theme-aware”.

Step 2.2: Querying the Map for Specific Information

The queryMap() function can now be used with type = "theme" to easily retrieve all complexes belonging to a specific biological theme.

Query by Protein

Find all complexes that contain a specific protein.

# Find all complexes containing the protein "UBA1"
queryMap(cm_obj_adv, query = "UBA1", type = "protein") %>%
  select(complexId, primaryFunctionalDomain, proteinCount, themeLabel, proteins) %>%
  knitr::kable()

complexId	primaryFunctionalDomain	proteinCount	themeLabel	proteins
CpxMap_0497	BIOCARTA_PROTEASOME_PATHWAY	18	BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY	UBA1,TRMT1,RARS1,QARS1,NARS1,MARS1,LARS1,KARS1,IARS1,GARS1,EPRS1,DARS1,AARS1,VBP1,EEF1E1,ASNS,AIMP2,AIMP1
CpxMap_0195	BIOCARTA_PROTEASOME_PATHWAY	4	BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY	WDR73,USH1C,UBA1,NMD3

Query by Complex ID

Retrieve the data for a single complex.

# Get the data for complex "CpxMap_0001"
queryMap(cm_obj_adv, query = "CpxMap_0001", type = "complex") %>%
  # Use glimpse to see all columns, including theme info
  glimpse()
#> Rows: 1
#> Columns: 14
#> $ complexId               <chr> "CpxMap_0001"
#> $ proteinCount            <int> 3
#> $ proteins                <chr> "WDR82,ULK3,UCHL1"
#> $ primaryFunctionalDomain <chr> "Unenriched"
#> $ topEnrichedFunctions    <chr> NA
#> $ colorHex                <chr> "#CCCCCC"
#> $ sizeMapping             <dbl> 1.584963
#> $ x                       <dbl> -10.84864
#> $ y                       <dbl> 12.73338
#> $ betweenness             <dbl> 0
#> $ degree                  <dbl> 0
#> $ themeId                 <int> 36
#> $ themeLabel              <chr> "Unenriched"
#> $ themePurity             <dbl> 0

Query by Theme

Because we added theme labels to the object, we can now query them directly.

# First, let's find a valid theme label to query from our map
node_table <- getNodeTable(cm_obj_adv)
if (nrow(node_table) > 0 && "themeLabel" %in% names(node_table)) {
  target_theme <- na.omit(node_table$themeLabel)

  cat("Querying for all nodes in theme:", target_theme, "\n\n")

  # Query the map using the theme label
  theme_nodes <- queryMap(cm_obj_adv, query = target_theme, type = "theme")
  
  theme_nodes %>%
    select(complexId, primaryFunctionalDomain, themeLabel) %>%
    head() %>%
    knitr::kable()
}
#> Querying for all nodes in theme: BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_SAM68_PATHWAY BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_SM_PATHWAY BIOCARTA_LIS1_PATHWAY / BIOCARTA_EPO_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_SM_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_SM_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_S1P_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_LIS1_PATHWAY / BIOCARTA_EPO_PATHWAY BIOCARTA_MRP_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_MRP_PATHWAY BIOCARTA_SAM68_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY Unenriched BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY Unenriched BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_EDG1_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_LIS1_PATHWAY / BIOCARTA_EPO_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_EDG1_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_RAB_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_LIS1_PATHWAY / BIOCARTA_EPO_PATHWAY BIOCARTA_BIOPEPTIDES_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY Unenriched BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_EDG1_PATHWAY BIOCARTA_S1P_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_SM_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_LIS1_PATHWAY / BIOCARTA_EPO_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_SM_PATHWAY BIOCARTA_S1P_PATHWAY BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_NUCLEARRS_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_SM_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_S1P_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_BTG2_PATHWAY / BIOCARTA_ALK_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_RAB_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_SAM68_PATHWAY BIOCARTA_MRP_PATHWAY BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_EDG1_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY Unenriched BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY Unenriched BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_LIS1_PATHWAY / BIOCARTA_EPO_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_SM_PATHWAY BIOCARTA_S1P_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_MRP_PATHWAY BIOCARTA_BIOPEPTIDES_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_NUCLEARRS_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_LIS1_PATHWAY / BIOCARTA_EPO_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY Unenriched BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY Unenriched BIOCARTA_LIS1_PATHWAY / BIOCARTA_EPO_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_NUCLEARRS_PATHWAY BIOCARTA_RAB_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_EDG1_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_RAB_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_SM_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY Unenriched BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_NUCLEARRS_PATHWAY BIOCARTA_MRP_PATHWAY Unenriched BIOCARTA_EDG1_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_EDG1_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_NUCLEARRS_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_NUCLEARRS_PATHWAY BIOCARTA_SM_PATHWAY Unenriched BIOCARTA_RAB_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_BIOPEPTIDES_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_MRP_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_SM_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_RAB_PATHWAY Unenriched BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_SM_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_BTG2_PATHWAY / BIOCARTA_ALK_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_BTG2_PATHWAY / BIOCARTA_ALK_PATHWAY BIOCARTA_SM_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_BTG2_PATHWAY / BIOCARTA_ALK_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_BTG2_PATHWAY / BIOCARTA_ALK_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_LIS1_PATHWAY / BIOCARTA_EPO_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_BTG2_PATHWAY / BIOCARTA_ALK_PATHWAY BIOCARTA_RAB_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_LIS1_PATHWAY / BIOCARTA_EPO_PATHWAY BIOCARTA_EDG1_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_LIS1_PATHWAY / BIOCARTA_EPO_PATHWAY BIOCARTA_LIS1_PATHWAY / BIOCARTA_EPO_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_SM_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_EEA1_PATHWAY BIOCARTA_SM_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_LIS1_PATHWAY / BIOCARTA_EPO_PATHWAY BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_BTG2_PATHWAY / BIOCARTA_ALK_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_EDG1_PATHWAY BIOCARTA_LIS1_PATHWAY / BIOCARTA_EPO_PATHWAY BIOCARTA_LIS1_PATHWAY / BIOCARTA_EPO_PATHWAY BIOCARTA_EEA1_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_S1P_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_SM_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_S1P_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY Unenriched BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_LIS1_PATHWAY / BIOCARTA_EPO_PATHWAY BIOCARTA_BTG2_PATHWAY / BIOCARTA_ALK_PATHWAY BIOCARTA_SM_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_EDG1_PATHWAY BIOCARTA_BIOPEPTIDES_PATHWAY BIOCARTA_SM_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_RAB_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_BIOPEPTIDES_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_MRP_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY Unenriched BIOCARTA_SM_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_EDG1_PATHWAY BIOCARTA_S1P_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_BTG2_PATHWAY / BIOCARTA_ALK_PATHWAY BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_LIS1_PATHWAY / BIOCARTA_EPO_PATHWAY BIOCARTA_SAM68_PATHWAY BIOCARTA_SM_PATHWAY BIOCARTA_NUCLEARRS_PATHWAY BIOCARTA_BIOPEPTIDES_PATHWAY BIOCARTA_EDG1_PATHWAY BIOCARTA_S1P_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY Unenriched BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_S1P_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_EDG1_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY Unenriched BIOCARTA_EDG1_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY Unenriched BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY Unenriched Unenriched BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_GABA_PATHWAY Unenriched Unenriched BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_RAB_PATHWAY BIOCARTA_RAB_PATHWAY Unenriched BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY Unenriched BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_LDL_PATHWAY Unenriched BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY Unenriched BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY Unenriched Unenriched BIOCARTA_SAM68_PATHWAY BIOCARTA_SM_PATHWAY BIOCARTA_LIS1_PATHWAY / BIOCARTA_EPO_PATHWAY Unenriched BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_EDG1_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_LIS1_PATHWAY / BIOCARTA_EPO_PATHWAY BIOCARTA_TID_PATHWAY / BIOCARTA_CARM_ER_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY BIOCARTA_MTA3_PATHWAY / BIOCARTA_PRC2_PATHWAY BIOCARTA_MRP_PATHWAY BIOCARTA_RAB_PATHWAY BIOCARTA_LDL_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY Unenriched BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY Unenriched BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY Unenriched Unenriched BIOCARTA_SM_PATHWAY BIOCARTA_LIS1_PATHWAY / BIOCARTA_EPO_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_CELL2CELL_PATHWAY / BIOCARTA_TEL_PATHWAY Unenriched BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY Unenriched BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_SM_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY Unenriched BIOCARTA_KREB_PATHWAY / BIOCARTA_ETC_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY BIOCARTA_RANMS_PATHWAY / BIOCARTA_NPC_PATHWAY BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY BIOCARTA_GABA_PATHWAY Unenriched Unenriched BIOCARTA_IRES_PATHWAY / BIOCARTA_MCM_PATHWAY Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched Unenriched BIOCARTA_ARAP_PATHWAY Unenriched Unenriched Unenriched

complexId	primaryFunctionalDomain	themeLabel
CpxMap_0414	BIOCARTA_CIRCADIAN_PATHWAY	BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY
CpxMap_0401	BIOCARTA_RNA_PATHWAY	BIOCARTA_CPSF_PATHWAY / BIOCARTA_G2_PATHWAY
CpxMap_0359	BIOCARTA_AGPCR_PATHWAY	BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY
CpxMap_0501	BIOCARTA_SUMO_PATHWAY	BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY
CpxMap_0508	Unenriched	BIOCARTA_PROTEASOME_PATHWAY / BIOCARTA_ERAD_PATHWAY
CpxMap_0090	BIOCARTA_SALMONELLA_PATHWAY	BIOCARTA_SALMONELLA_PATHWAY / BIOCARTA_PGC1A_PATHWAY

This streamlined workflow makes exploring the thematic structure of the complex map efficient and powerful.

Qingzhou Zhang

2025-12-03

Advanced Analysis Workflow

1. Optimizing Refinement with `evaluateComplexes`

2. A Streamlined Workflow for Theme Analysis

Step 2.1: Summarize Themes and Add to Object

Step 2.2: Querying the Map for Specific Information

3. Advanced Analysis and Visualization

Qingzhou Zhang

2025-12-03

Advanced Analysis Workflow

1. Optimizing Refinement with evaluateComplexes

2. A Streamlined Workflow for Theme Analysis

Step 2.1: Summarize Themes and Add to Object

Step 2.2: Querying the Map for Specific Information

1. Optimizing Refinement with `evaluateComplexes`