diff --git a/R/getSubnetworkFromIndra.R b/R/getSubnetworkFromIndra.R
index ab3e232..09f1f30 100644
--- a/R/getSubnetworkFromIndra.R
+++ b/R/getSubnetworkFromIndra.R
@@ -32,7 +32,9 @@
 #' as "namespace:identifier", e.g. "HGNC:1234" or "CHEBI:4911".
 #' @param filter_by_curation logical, whether to filter out statements that
 #' have been curated as incorrect in INDRA.  Default is FALSE.
-#' @param api_key string of INDRA API key for accessing curated statements.
+#' @param filter_by_ptm_site logical, whether to filter edges based on whether the 
+#' site information from INDRA matches with the PTM site in the input.  Default is FALSE.  
+#' Only applicable for differential PTM abundance results.
 #'
 #' @return list of 2 data.frames, nodes and edges
 #'
@@ -57,15 +59,17 @@ getSubnetworkFromIndra <- function(input,
                                    sources_filter = NULL,
                                    logfc_cutoff = NULL,
                                    force_include_other = NULL, 
-                                   filter_by_curation = FALSE, 
-                                   api_key = "") {
+                                   filter_by_curation = FALSE,
+                                   filter_by_ptm_site = FALSE) {
     input <- .filterGetSubnetworkFromIndraInput(input, pvalueCutoff, logfc_cutoff, force_include_other)
     .validateGetSubnetworkFromIndraInput(input, protein_level_data, sources_filter, force_include_other)
     res <- .callIndraCogexApi(input$HgncId, force_include_other)
-    res <- .filterIndraResponse(res, statement_types, evidence_count_cutoff, sources_filter, filter_by_curation, api_key)
+    res <- .filterIndraResponse(res, statement_types, evidence_count_cutoff, sources_filter)
     edges <- .constructEdgesDataFrame(res, input, protein_level_data)
     edges <- .filterEdgesDataFrame(edges, paper_count_cutoff, correlation_cutoff)
     nodes <- .constructNodesDataFrame(input, edges)
+    subnetwork = .filterByPtmSite(nodes, edges, filter_by_ptm_site)
+    subnetwork = .filterByCuration(subnetwork$nodes, subnetwork$edges, evidence_count_cutoff, filter_by_curation)
     warning(
         "NOTICE: This function includes third-party software components
         that are licensed under the BSD 2-Clause License. Please ensure to
@@ -73,5 +77,5 @@ getSubnetworkFromIndra <- function(input,
         package or utilizing the results based on this package.
         See the LICENSE file for more details."
     )
-    return(list(nodes = nodes, edges = edges))
+    return(subnetwork)
 }
diff --git a/R/utils_getSubnetworkFromIndra.R b/R/utils_getSubnetworkFromIndra.R
index 3f3a674..a5a717c 100644
--- a/R/utils_getSubnetworkFromIndra.R
+++ b/R/utils_getSubnetworkFromIndra.R
@@ -68,9 +68,9 @@
 
 #' @importFrom httr GET status_code content
 #' @importFrom jsonlite fromJSON
-.get_incorrect_curation_count <- function(stmt_hash, api_key) {
+.get_incorrect_curation_count <- function(stmt_hash) {
     stmt_hash_char <- as.character(stmt_hash)
-    url <- paste0("https://db.indra.bio/curation/list/", stmt_hash_char, "?api_key=", api_key)
+    url <- paste0("https://db.indra.bio/curation/list/", stmt_hash_char)
 
     tryCatch({
         response <- GET(url)
@@ -96,21 +96,18 @@
 
 #' Call INDRA Cogex API and return response
 #' @param res response from INDRA
-#' @param interaction_types interaction types to filter by
+#' @param statement_types interaction types to filter by
 #' @param evidence_count_cutoff number of evidence to filter on for each paper
 #' @param sources_filter list of sources to filter by. Default is NULL, i.e. no filter
-#' @param filter_by_curation logical, whether to filter out statements that
-#' have been curated as incorrect in INDRA.  Default is FALSE.
-#' @param api_key string of INDRA API key for accessing curated statements.
 #' @return filtered list of INDRA statements
 #' @importFrom jsonlite fromJSON
 #' @keywords internal
 #' @noRd
-.filterIndraResponse <- function(res, interaction_types, evidence_count_cutoff, 
-                                 sources_filter = NULL, filter_by_curation = FALSE, api_key = "") {
-    if (!is.null(interaction_types)) {
+.filterIndraResponse <- function(res, statement_types, evidence_count_cutoff, 
+                                 sources_filter = NULL) {
+    if (!is.null(statement_types)) {
         res = Filter(
-            function(statement) statement$data$stmt_type %in% interaction_types, 
+            function(statement) statement$data$stmt_type %in% statement_types, 
             res)
     }
     if (!is.null(sources_filter)) {
@@ -123,16 +120,6 @@
             res
         )
     }
-    if (filter_by_curation) {
-        for (i in seq_along(res)) {
-            stmt_json <- fromJSON(res[[i]]$data$stmt_json)
-            stmt_hash <- stmt_json$matches_hash
-            incorrect_count <- .get_incorrect_curation_count(stmt_hash, api_key)
-            res[[i]]$data$evidence_count <- res[[i]]$data$evidence_count - incorrect_count
-            # Todo: Also subtract source_counts accordingly if requested
-            Sys.sleep(0.1)
-        }
-    }
     res = Filter(
         function(statement) statement$data$evidence_count >= evidence_count_cutoff, 
         res
@@ -373,6 +360,31 @@
     return(edges)
 }
 
+.filterByCuration = function(nodes, edges, evidence_count_cutoff, filter_by_curation) {
+    if (filter_by_curation) {
+        incorrect_counts <- numeric(nrow(edges))
+        for (i in seq_len(nrow(edges))) {
+            incorrect_counts[i] <- .get_incorrect_curation_count(edges$stmt_hash[i])
+            Sys.sleep(0.1)
+        }
+        edges$evidenceCount <- edges$evidenceCount - incorrect_counts
+        edges <- edges[edges$evidenceCount >= evidence_count_cutoff, ]
+        nodes <- nodes[nodes$id %in% c(edges$source, edges$target), ]
+    }
+    return(list(nodes = nodes, edges = edges))
+}
+
+.filterByPtmSite = function(nodes, edges, filter_by_ptm_site) {
+    if (filter_by_ptm_site && nrow(nodes[!is.na(nodes$Site), ]) > 0) {
+        ptm_overlap <- .calculatePTMOverlapAggregated(edges, nodes)
+        keep <- ptm_overlap[paste(edges$source, edges$target, edges$interaction, sep = "-")]
+        edges <- edges[!is.na(keep) & keep != "", ]
+        edges <- edges[!is.na(edges$site),]
+        nodes <- nodes[nodes$id %in% c(edges$source, edges$target), ]
+    }
+    return(list(nodes = nodes, edges = edges))
+}
+
 #' Construct correlation matrix from MSstats
 #' @param protein_level_data output of dataProcess
 #' @importFrom tidyr pivot_wider
diff --git a/R/visualizeNetworksWithHTML.R b/R/visualizeNetworksWithHTML.R
index 1c13cfa..db8b64c 100644
--- a/R/visualizeNetworksWithHTML.R
+++ b/R/visualizeNetworksWithHTML.R
@@ -78,8 +78,9 @@ getRelationshipProperties <- function() {
 #' @param edges Data frame with edge information including 'target' and 'site' columns
 #' @param nodes Data frame with node information including 'id' and 'Site' columns
 #' @return Vector of overlap descriptions for each unique edge (after consolidation)
+#' @keywords internal
 #' @noRd
-calculatePTMOverlapAggregated <- function(edges, nodes) {
+.calculatePTMOverlapAggregated <- function(edges, nodes) {
     if (nrow(edges) == 0) return(character(0))
     
     # Group edges by source-target-interaction to match consolidation logic
@@ -153,7 +154,7 @@ consolidateEdges <- function(edges, nodes = NULL) {
     
     # Calculate aggregated PTM overlap information if nodes are provided
     ptm_overlap_map <- if (!is.null(nodes)) {
-        calculatePTMOverlapAggregated(edges, nodes)
+        .calculatePTMOverlapAggregated(edges, nodes)
     } else {
         NULL
     }
@@ -1141,6 +1142,7 @@ createEdgeClickHandler <- function() {
 #' @param edges Data frame with edge information  
 #' @param filename Output HTML filename
 #' @param displayLabelType Type of label to display ("id" or "hgncName")
+#' @param nodeFontSize Font size for node labels (default: 12)
 #' @param ... Additional arguments passed to exportCytoscapeToHTML()
 #' @export
 #' @return Invisibly returns the file path of the created HTML file
diff --git a/man/exportNetworkToHTML.Rd b/man/exportNetworkToHTML.Rd
index 2e9910a..ca8f679 100644
--- a/man/exportNetworkToHTML.Rd
+++ b/man/exportNetworkToHTML.Rd
@@ -9,6 +9,7 @@ exportNetworkToHTML(
   edges,
   filename = "network_visualization.html",
   displayLabelType = "id",
+  nodeFontSize = 12,
   ...
 )
 }
@@ -21,6 +22,8 @@ exportNetworkToHTML(
 
 \item{displayLabelType}{Type of label to display ("id" or "hgncName")}
 
+\item{nodeFontSize}{Font size for node labels (default: 12)}
+
 \item{...}{Additional arguments passed to exportCytoscapeToHTML()}
 }
 \value{
diff --git a/man/generateCytoscapeConfig.Rd b/man/generateCytoscapeConfig.Rd
index 07c70b8..fc6c562 100644
--- a/man/generateCytoscapeConfig.Rd
+++ b/man/generateCytoscapeConfig.Rd
@@ -10,7 +10,8 @@ generateCytoscapeConfig(
   display_label_type = "id",
   container_id = "network-cy",
   event_handlers = NULL,
-  layout_options = NULL
+  layout_options = NULL,
+  node_font_size = 12
 )
 }
 \arguments{
diff --git a/man/getSubnetworkFromIndra.Rd b/man/getSubnetworkFromIndra.Rd
index 94d27f9..a670d6e 100644
--- a/man/getSubnetworkFromIndra.Rd
+++ b/man/getSubnetworkFromIndra.Rd
@@ -16,7 +16,7 @@ getSubnetworkFromIndra(
   logfc_cutoff = NULL,
   force_include_other = NULL,
   filter_by_curation = FALSE,
-  api_key = ""
+  filter_by_ptm_site = FALSE
 )
 }
 \arguments{
@@ -60,7 +60,9 @@ as "namespace:identifier", e.g. "HGNC:1234" or "CHEBI:4911".}
 \item{filter_by_curation}{logical, whether to filter out statements that
 have been curated as incorrect in INDRA.  Default is FALSE.}
 
-\item{api_key}{string of INDRA API key for accessing curated statements.}
+\item{filter_by_ptm_site}{logical, whether to filter edges based on whether the 
+site information from INDRA matches with the PTM site in the input.  Default is FALSE.  
+Only applicable for differential PTM abundance results.}
 }
 \value{
 list of 2 data.frames, nodes and edges
diff --git a/man/previewNetworkInBrowser.Rd b/man/previewNetworkInBrowser.Rd
index 6dde024..d0ac40e 100644
--- a/man/previewNetworkInBrowser.Rd
+++ b/man/previewNetworkInBrowser.Rd
@@ -4,7 +4,13 @@
 \alias{previewNetworkInBrowser}
 \title{Preview network in browser}
 \usage{
-previewNetworkInBrowser(nodes, edges, displayLabelType = "id", ...)
+previewNetworkInBrowser(
+  nodes,
+  edges,
+  displayLabelType = "id",
+  nodeFontSize = 12,
+  ...
+)
 }
 \arguments{
 \item{nodes}{Data frame with node information}