diff --git a/NAMESPACE b/NAMESPACE
index 691642f..448ebb2 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -5,6 +5,7 @@ export(getSubnetworkFromIndra)
 export(visualizeNetworks)
 importFrom(RCy3,createNetworkFromDataFrames)
 importFrom(RCy3,createVisualStyle)
+importFrom(RCy3,layoutNetwork)
 importFrom(RCy3,mapVisualProperty)
 importFrom(RCy3,setVisualStyle)
 importFrom(httr,POST)
diff --git a/R/annotateProteinInfoFromIndra.R b/R/annotateProteinInfoFromIndra.R
index a03c204..5d39135 100644
--- a/R/annotateProteinInfoFromIndra.R
+++ b/R/annotateProteinInfoFromIndra.R
@@ -2,7 +2,7 @@
 #'
 #' This function annotates a data frame with protein information from Indra.
 #'
-#' @param input output of \code{\link[MSstats]{groupComparison}} function's 
+#' @param df output of \code{\link[MSstats]{groupComparison}} function's 
 #'      comparisonResult table, which contains a list of proteins and their 
 #'      corresponding p-values, logFCs, along with additional HGNC ID and HGNC 
 #'      name columns
diff --git a/R/getSubnetworkFromIndra.R b/R/getSubnetworkFromIndra.R
index 7c20dda..40b2d33 100644
--- a/R/getSubnetworkFromIndra.R
+++ b/R/getSubnetworkFromIndra.R
@@ -25,6 +25,7 @@
 #'
 getSubnetworkFromIndra <- function(input, pvalueCutoff = NULL) {
     input <- .filterGetSubnetworkFromIndraInput(input, pvalueCutoff)
+    .validateGetSubnetworkFromIndraInput(input)
     res <- .callIndraCogexApi(input$HgncId)
     nodes <- .constructNodesDataFrame(input)
     edges <- .constructEdgesDataFrame(res, input)
diff --git a/R/utils_getSubnetworkFromIndra.R b/R/utils_getSubnetworkFromIndra.R
index 4743734..4e92aaf 100644
--- a/R/utils_getSubnetworkFromIndra.R
+++ b/R/utils_getSubnetworkFromIndra.R
@@ -1,3 +1,13 @@
+#' Validate input for MSstatsBioNet getSubnetworkFromIndra
+#' @param input dataframe from MSstats groupComparison output
+#' @keywords internal
+#' @noRd
+.validateGetSubnetworkFromIndraInput <- function(input) {
+    if (nrow(input) >= 400) {
+        stop("Invalid Input Error: INDRA query must contain less than 400 proteins.  Consider adding a p-value cutoff")
+    }
+}
+
 #' Call INDRA Cogex API and return response
 #' @param hgncIds list of hgnc ids
 #' @return list of INDRA statements
diff --git a/R/visualizeNetworks.R b/R/visualizeNetworks.R
index b146986..a74c76b 100644
--- a/R/visualizeNetworks.R
+++ b/R/visualizeNetworks.R
@@ -14,7 +14,7 @@
 #' @param logfcCutoff log fold change cutoff for coloring significant
 #' proteins. Default is 0.5
 #' @importFrom RCy3 createNetworkFromDataFrames mapVisualProperty
-#' createVisualStyle setVisualStyle
+#' createVisualStyle setVisualStyle layoutNetwork
 #'
 #' @export
 #'
@@ -56,7 +56,7 @@ visualizeNetworks <- function(nodes, edges,
             mapVisualProperty(
                 "Node Fill Color", "logFC_color", "c",
                 c(-logfcCutoff, 0.0, logfcCutoff),
-                c("#5588DD", "#5588DD", "#D3D3D3", "#DD8855", "#DD8855")
+                c("#ADD8E6", "#ADD8E6", "#D3D3D3", "#FFA590", "#FFA590")
             )
         )
         createVisualStyle(
diff --git a/man/annotateProteinInfoFromIndra.Rd b/man/annotateProteinInfoFromIndra.Rd
index 2cb5e64..35d2767 100644
--- a/man/annotateProteinInfoFromIndra.Rd
+++ b/man/annotateProteinInfoFromIndra.Rd
@@ -7,7 +7,10 @@
 annotateProteinInfoFromIndra(df, proteinIdType)
 }
 \arguments{
-\item{df}{A data frame containing protein information.}
+\item{df}{output of \code{\link[MSstats]{groupComparison}} function's 
+comparisonResult table, which contains a list of proteins and their 
+corresponding p-values, logFCs, along with additional HGNC ID and HGNC 
+name columns}
 
 \item{proteinIdType}{A character string specifying the type of protein ID. 
 It can be either "Uniprot" or "Uniprot_Mnemonic".}
diff --git a/man/dot-populateHgncIdsInDataFrame.Rd b/man/dot-populateHgncIdsInDataFrame.Rd
new file mode 100644
index 0000000..886c686
--- /dev/null
+++ b/man/dot-populateHgncIdsInDataFrame.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/annotateProteinInfoFromIndra.R
+\name{.populateHgncIdsInDataFrame}
+\alias{.populateHgncIdsInDataFrame}
+\title{Populate HGNC IDs in Data Frame}
+\usage{
+.populateHgncIdsInDataFrame(df)
+}
+\arguments{
+\item{df}{A data frame containing protein information.}
+}
+\value{
+A data frame with populated HGNC IDs.
+}
+\description{
+This function populates the HGNC IDs in the data frame based on the Uniprot IDs.
+}
diff --git a/man/dot-populateHgncNamesInDataFrame.Rd b/man/dot-populateHgncNamesInDataFrame.Rd
new file mode 100644
index 0000000..23d91d8
--- /dev/null
+++ b/man/dot-populateHgncNamesInDataFrame.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/annotateProteinInfoFromIndra.R
+\name{.populateHgncNamesInDataFrame}
+\alias{.populateHgncNamesInDataFrame}
+\title{Populate HGNC Names in Data Frame}
+\usage{
+.populateHgncNamesInDataFrame(df)
+}
+\arguments{
+\item{df}{A data frame containing protein information.}
+}
+\value{
+A data frame with populated HGNC names.
+}
+\description{
+This function populates the HGNC names in the data frame based on the HGNC IDs.
+}
diff --git a/man/dot-populateKinaseInfoInDataFrame.Rd b/man/dot-populateKinaseInfoInDataFrame.Rd
new file mode 100644
index 0000000..aa8dddd
--- /dev/null
+++ b/man/dot-populateKinaseInfoInDataFrame.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/annotateProteinInfoFromIndra.R
+\name{.populateKinaseInfoInDataFrame}
+\alias{.populateKinaseInfoInDataFrame}
+\title{Populate Kinase Info in Data Frame}
+\usage{
+.populateKinaseInfoInDataFrame(df)
+}
+\arguments{
+\item{df}{A data frame containing protein information.}
+}
+\value{
+A data frame with populated kinase information.
+}
+\description{
+This function populates the kinase information in the data frame based on the HGNC names.
+}
diff --git a/man/dot-populatePhophataseInfoInDataFrame.Rd b/man/dot-populatePhophataseInfoInDataFrame.Rd
new file mode 100644
index 0000000..e0cd5b5
--- /dev/null
+++ b/man/dot-populatePhophataseInfoInDataFrame.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/annotateProteinInfoFromIndra.R
+\name{.populatePhophataseInfoInDataFrame}
+\alias{.populatePhophataseInfoInDataFrame}
+\title{Populate Phosphatase Info in Data Frame}
+\usage{
+.populatePhophataseInfoInDataFrame(df)
+}
+\arguments{
+\item{df}{A data frame containing protein information.}
+}
+\value{
+A data frame with populated phosphatase information.
+}
+\description{
+This function populates the phosphatase information in the data frame based on the HGNC names.
+}
diff --git a/man/dot-populateTranscriptionFactorInfoInDataFrame.Rd b/man/dot-populateTranscriptionFactorInfoInDataFrame.Rd
new file mode 100644
index 0000000..e54c6f3
--- /dev/null
+++ b/man/dot-populateTranscriptionFactorInfoInDataFrame.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/annotateProteinInfoFromIndra.R
+\name{.populateTranscriptionFactorInfoInDataFrame}
+\alias{.populateTranscriptionFactorInfoInDataFrame}
+\title{Populate Transcription Factor Info in Data Frame}
+\usage{
+.populateTranscriptionFactorInfoInDataFrame(df)
+}
+\arguments{
+\item{df}{A data frame containing protein information.}
+}
+\value{
+A data frame with populated transcription factor information.
+}
+\description{
+This function populates the transcription factor information in the data frame based on the HGNC names.
+}
diff --git a/man/dot-populateUniprotIdsInDataFrame.Rd b/man/dot-populateUniprotIdsInDataFrame.Rd
new file mode 100644
index 0000000..43bee6e
--- /dev/null
+++ b/man/dot-populateUniprotIdsInDataFrame.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/annotateProteinInfoFromIndra.R
+\name{.populateUniprotIdsInDataFrame}
+\alias{.populateUniprotIdsInDataFrame}
+\title{Populate Uniprot IDs in Data Frame}
+\usage{
+.populateUniprotIdsInDataFrame(df, proteinIdType)
+}
+\arguments{
+\item{df}{A data frame containing protein information.}
+
+\item{proteinIdType}{A character string specifying the type of protein ID. 
+It can be either "Uniprot" or "Uniprot_Mnemonic".}
+}
+\value{
+A data frame with populated Uniprot IDs.
+}
+\description{
+This function populates the Uniprot IDs in the data frame based on the protein ID type.
+}
diff --git a/man/dot-validateAnnotateProteinInfoFromIndraInput.Rd b/man/dot-validateAnnotateProteinInfoFromIndraInput.Rd
new file mode 100644
index 0000000..e9f9e2a
--- /dev/null
+++ b/man/dot-validateAnnotateProteinInfoFromIndraInput.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/annotateProteinInfoFromIndra.R
+\name{.validateAnnotateProteinInfoFromIndraInput}
+\alias{.validateAnnotateProteinInfoFromIndraInput}
+\title{Validate Annotate Protein Info Input}
+\usage{
+.validateAnnotateProteinInfoFromIndraInput(df)
+}
+\arguments{
+\item{df}{A data frame containing protein information.}
+}
+\value{
+None. Throws an error if validation fails.
+}
+\description{
+This function validates the input data frame for the annotateProteinInfoFromIndra function.
+}
diff --git a/man/getSubnetworkFromIndra.Rd b/man/getSubnetworkFromIndra.Rd
index d65ffcb..2f5ed5b 100644
--- a/man/getSubnetworkFromIndra.Rd
+++ b/man/getSubnetworkFromIndra.Rd
@@ -7,9 +7,10 @@
 getSubnetworkFromIndra(input, pvalueCutoff = NULL)
 }
 \arguments{
-\item{input}{output of groupComparison function's comparisionResult table,
-which contains a list of proteins and their corresponding p-values, logFCs,
-along with additional HGNC ID and HGNC name columns}
+\item{input}{output of \code{\link[MSstats]{groupComparison}} function's 
+comparisionResult table, which contains a list of proteins and their 
+corresponding p-values, logFCs, along with additional HGNC ID and HGNC 
+name columns}
 
 \item{pvalueCutoff}{p-value cutoff for filtering. Default is NULL, i.e. no
 filtering}
diff --git a/tests/testthat/test-getSubnetworkFromIndra.R b/tests/testthat/test-getSubnetworkFromIndra.R
index b41f297..0c75979 100644
--- a/tests/testthat/test-getSubnetworkFromIndra.R
+++ b/tests/testthat/test-getSubnetworkFromIndra.R
@@ -23,3 +23,15 @@ test_that("getSubnetworkFromIndra with pvalue filter works correctly", {
     expect_equal(nrow(subnetwork$nodes), 6)
     expect_equal(nrow(subnetwork$edges), 1)
 })
+
+test_that("Exception is thrown for 400+ proteins in dataframe", {
+    input_400 <- data.frame(
+        Protein = paste0("Protein", 1:400),
+        issue = NA,
+        adj.pvalue = 0.05
+    )
+    expect_error(
+        getSubnetworkFromIndra(input_400),
+        "Invalid Input Error: INDRA query must contain less than 400 proteins.  Consider adding a p-value cutoff"
+    )
+})