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Update oncoplots (11/11) #116

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Oct 28, 2024
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Update oncoplots (11/11) #116

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36cd348
update oncoplots
komalsrathi Jun 24, 2024
d9d7f10
rerun on docker
komalsrathi Jun 26, 2024
e0c8584
update with sinai data
komalsrathi Sep 9, 2024
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178 changes: 178 additions & 0 deletions analyses/oncoplots/10-figure_1c.R
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# Function: Script to generate Figure 1C
suppressPackageStartupMessages({
library(ComplexHeatmap)
library(tidyverse)
library(circlize)
})

# set directories
root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
analyses_dir <- file.path(root_dir, "analyses", "oncoplots")
input_dir <- file.path(analyses_dir, "results")
output_dir <- file.path(analyses_dir, "results", "cascade_plots_sinai_data")
dir.create(output_dir, recursive = T, showWarnings = F)

# read matrix
dat <- read_tsv(file.path(analyses_dir, "input", "harmonized_mutation_data_090224.txt"))
dat <- dat %>%
column_to_rownames("geneID")
dat[dat == 0] <- ""
dat[dat != ""] <- "Mutation"
keep = apply(
dat,
1,
FUN = function(x)
length(unique(x)) == 2
)
dat = dat[keep, ]

alter_fun = list(
background = function(x, y, w, h) {
grid.rect(x, y, w, h, gp = gpar(fill = "#ffffff", col = "#595959"))
},
Mutation = function(x, y, w, h) {
grid.rect(x,
y,
w - unit(0.3, "mm"),
h - unit(0.3, "mm"),
gp = gpar(fill = "black", col = NA))
}
)
col = c("Mutation" = "black")

# read annotation
annot_info <- read.delim(
file.path(input_dir, "annotation_add_tumor_only.txt"),
header = TRUE,
check.names = TRUE
)
annot_info <- annot_info %>%
filter(Sample %in% colnames(dat), Sequencing_Experiment != "RNA-Seq") %>%
dplyr::select(-c(CNS_region)) %>%
remove_rownames() %>%
column_to_rownames('Sample') %>%
as.data.frame()
samples_to_use <- intersect(rownames(annot_info), colnames(dat))
dat <- dat[, samples_to_use]
annot_info <- annot_info[samples_to_use, ]

# convert to two age groups
annot_info <- annot_info %>%
mutate(Age = as.character(Age)) %>%
mutate(Age = ifelse(Age %in% c("(15,26]", "(26,40]"), "(15,40]", Age))
annot_info$Age <- factor(annot_info$Age, levels = c("[0,15]", "(15,40]"))

# color code for TMB
col_fun_tmb = colorRamp2(c(0, max(annot_info$TMB, na.rm = T)), c("white", "magenta3"))

# remove Molecular_Subtype
annot_info$Molecular_Subtype <- NULL

# replace NA values with "Flag"
annot_info$Cancer_Group[is.na(annot_info$Cancer_Group)] <- "Flag"

# remove underscore from column names
colnames(annot_info) <- gsub("_", " ", colnames(annot_info))

# oncoprint annotation color code
ha = HeatmapAnnotation(
df = annot_info %>% dplyr::select(-c(`Sequencing Experiment`)),
col = list(
TMB = col_fun_tmb,
Diagnosis = c(
"High-grade glioma/astrocytoma (WHO grade III/IV)" = "lightseagreen",
"Diffuse Midline Glioma (WHO grade III/IV)" = "darkgreen",
"Astrocytoma;Oligoastrocytoma (WHO grade III)" = "mediumorchid2",
"Astrocytoma (WHO grade III/IV)" = "#5fff57",
"Glioblastoma (WHO grade IV)" = "#f268d6",
"Pleomorphic xanthoastrocytoma (WHO grade III)" = "#005082"
),
`Molecular Subtype` = c(
"DMG, H3 K28" = "#053061",
"DHG, H3 G35, TP53" = "#A6761D",
"HGG, H3 wildtype" = "#4393c3",
"HGG, H3 wildtype, TP53" = "darkgreen",
"DMG, H3 K28, TP53" = "#BC80BD",
"HGG, IDH, TP53" = "#FFFF99",
"IHG, NTRK-altered, TP53" = "#E7298A",
"IHG, NTRK-altered" = "#f4a582",
"IHG, ROS1-altered" = "#d6604d",
"IHG, ALK-altered" = "#E31A1C",
"PXA" = "#67001f",
"HGG, IDH" = "#B3DE69",
"Flag" = "#f1f1f1"
),
`Diagnosis Type` = c(
"Initial CNS Tumor" = "#cee397",
"Progressive" = "#827397",
"Recurrence" = "#363062",
"Second Malignancy" = "#005082"
),
`Tumor Location` = c(
"Cortical" = "#D4806C",
"Other/Multiple locations/NOS" = "#7C8F97",
"Midline" = "#344C68",
"Cerebellar" = "#94004C"
),
`CNS region` = c(
"Posterior fossa" = "#D4806C",
"Other" = "#7C8F97",
"Midline" = "#344C68",
"Hemispheric" = "#94004C",
"Mixed" = "darkgreen"
),
`Cancer Group` = c(
"(DMG) Diffuse Midline Glioma" = "#053061",
"(DHG) Diffuse Hemispheric Glioma" = "#A6761D",
"(HGG) High Grade Glioma (not otherwise specified)" = "#4393c3",
"(IHG) Infantile Hemispheric Glioma" = "#E7298A",
"(PXA) Pleomorphic Xanthoastrocytoma" = "#67001f",
"Flag" = "#f1f1f1"
),
Sex = c("Male" = "#0707CF", "Female" = "#CC0303"),
Age = c("[0,15]" = "#C7E9C0", "(15,40]" = "#238B45")
),
annotation_name_gp = gpar(fontsize = 10),
gp = gpar(col = "#595959"),
simple_anno_size = unit(4, "mm"),
annotation_name_side = "left"
)

# order by Age
ht = oncoPrint(
dat,
get_type = function(x)
strsplit(x, ";")[[1]],
alter_fun = alter_fun,
column_split = annot_info$Age,
col = col,
show_column_names = TRUE,
column_names_gp = gpar(fontsize = 10),
row_names_gp = gpar(fontsize = 10),
column_names_side = "top",
top_annotation = ha,
right_annotation = NULL,
row_names_side = "left",
pct_side = "right",
remove_empty_rows = TRUE,
heatmap_legend_param = list(
title = "Alteration",
nrow = 9,
title_position = "topleft",
direction = "horizontal",
at = c("Mutation"),
labels = c("SNV")
)
)
pdf(
file = file.path(output_dir, "figure_1c.pdf"),
width = 16,
height = 8
)
draw(
ht,
merge_legend = TRUE,
heatmap_legend_side = "right",
annotation_legend_side = "right"
)
dev.off()
32 changes: 32 additions & 0 deletions analyses/oncoplots/input/harmonized_mutation_data_090224.txt
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geneID 7316-895 7316-4466 7316-1106 7316-4432 7316-4552 7316-3771 7316UP-1962 7316-1099 7316-2069 7316UP-2035 7316UP-2333 7316-3521 7316-3075 7316-3765 7316-114 7316-4337 7316-913 7316-1774 7316-3058 7316-5928 7316-161 7316-204 7316-1956 7316-1763 7316-2274 7316-6310 7316UP-1104 7316-870 7316UP-2403 7316-195 7316-2140 7316-5087 7316-4917 7316-37 7316-4516 7316-466 7316-1746 7316-409 7316-371 7316-2092 7316-3636 7316-1946 7316-2660 7316-1769 7316-4293 7316-3000 7316-2152 7316-89 7316-194 7316-4723 7316-445 7316-3303 7316-2737 7316-2176 7316-3769 7316-2810 7316-4844 7316-4993 7316-2146 7316-2857 7316UP-2058 7316-4842 7316-3935 7316-85 7316-5267 7316-4215 7316UP-759 7316-2594 7316UP-310 7316-2151 7316-388 7316-4942 7316-1844 7316-1889 7316-2536 7316-622 7316-2777 7316-231 7316-287 7316-1052 7316-2241 7316-1455 7316-255 7316-1723 7316-288 7316-619 7316-620 7316-624 7316-2599 C3L-00104 C3L-00365 C3L-00674 C3L-00677 C3L-01040 C3L-01043 C3L-01045 C3L-01046 C3L-01048 C3L-01049 C3L-01061 C3L-01142 C3L-01146 C3L-01149 C3L-01154 C3L-01155 C3L-01156 C3L-01157 C3L-01327 C3L-01834 C3L-01887 C3L-02041 C3L-02465 C3L-02504 C3L-02542 C3L-02642 C3L-02704 C3L-02705 C3L-02707 C3L-02708 C3L-02900 C3L-02955 C3L-02970 C3L-02984 C3L-03260 C3L-03266 C3L-03387 C3L-03390 C3L-03392 C3L-03400 C3L-03405 C3L-03407 C3L-03681 C3L-03727 C3L-03728 C3L-03744 C3L-03748 C3L-03968 C3L-04084 C3N-00661 C3N-00662 C3N-00663 C3N-00665 C3N-01192 C3N-01196 C3N-01334 C3N-01364 C3N-01366 C3N-01367 C3N-01368 C3N-01369 C3N-01505 C3N-01515 C3N-01517 C3N-01518 C3N-01798 C3N-01814 C3N-01815 C3N-01816 C3N-01818 C3N-01851 C3N-01852 C3N-01856 C3N-01857 C3N-02181 C3N-02183 C3N-02185 C3N-02186 C3N-02188 C3N-02190 C3N-02255 C3N-02256 C3N-02769 C3N-02770 C3N-02782 C3N-02783 C3N-02784 C3N-02785 C3N-02786 C3N-02788 C3N-03070 C3N-03088 C3N-03180 C3N-03182 C3N-03183 C3N-03184 C3N-03186 C3N-03188 C3N-03473
BRAF 0 1 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
MT-ND5 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
PIK3CA 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
AHNAK2 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
H3-3A 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 0 1 1 0 0 1 1 0 0 1 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 1 0 0 1 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1 0 1 0 0 1 0 0 1 0 1 1 1 0 0 1 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
PIK3R1 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
DNAH5 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
TSC2 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
TP53 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 1 1 1 1 0 0 1 0 0 1 0 1 1 1 0 1 0 1 0 1 1 1 1 1 1 0 0 1 0 1 0 0 1 0 1 0 0 0 1 0 1 0 0 0 0 1 0 1 1 0 0 0 0 1 1 1 0 1 1 0 0 1 1 0 1 0 0 0 0 0 0 0 1 1 0 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1 0 0 0 1 1 0 1 1 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 1 1 0 1 0 1 1 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 0 1 1 1 0 0 1 0 0 0 0 1
RAMP2 0 0 0 0 0 0 0 1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
MYO16 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NF1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 1 1 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 1 0 0 0 0 1 0 0 1 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1
TTN 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 1 1 1 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 0 0 1 1 0 0 0 0 0 1 0 0 1 0 1 0 0 0 0 1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0
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SP8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
MUC17 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
ATM 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
MACF1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
PDGFRA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
SLC12A9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
MSH6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
MUC16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
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