####################################################################
# Name: John Palomino
# Lab 8: Intro to RNA-Seq and Xena
# Turn in a Notebook that answers the questions below
####################################################################
#loading required packages
library(edgeR)
## Loading required package: limma
library(UCSCXenaTools)
## =========================================================================================
## UCSCXenaTools version 1.4.5
## Project URL: https://github.com/ropensci/UCSCXenaTools
## Usages: https://cran.r-project.org/web/packages/UCSCXenaTools/vignettes/USCSXenaTools.html
##
## If you use it in published research, please cite:
## Wang et al., (2019). The UCSCXenaTools R package: a toolkit for accessing genomics data
## from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq.
## Journal of Open Source Software, 4(40), 1627, https://doi.org/10.21105/joss.01627
## =========================================================================================
## --Enjoy it--
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(ggplot2)
##########################################################################
Question 1 -- [2 / 5 points] ❌The read count is the number of reads (GGG, AAC, etc) that align to each gene. I'll go over this in class.
# 1) Consider a reference genome with genes as follows:
# AGAGAGAG|AACAACAACAAC|GGGAAAGGGAAA
# gene 1 | gene 2 | gene 3
# Suppose that mRNA is extracted from a sample, and during sequencing is
# broken into the following fragments: GGG, AAC, ACA, GAA, and GAG
#
# What are the read counts for each of the 3 genes?
# Gene 1: GGG=0, AAC=0, ACA=0, GAA=0, and GAG=3
# Gene 2: GGG=0, AAC=4, ACA=4, GAA=0, and GAG=0
# Gene 3:GGG=2, AAC=0, ACA, GAA=2, and GAG=0
# Include your answers in the comment above. Note that you should NOT use
# R to answer this question.
##########################################################################
Question 2 -- [10 / 10 points] ✅
# 2) Consider the matrix 'm' below, and complete the following steps so
# that each column has mean 0.
m <- matrix(c(1:10, c(1:3, 10, 4), rep(17,5)), ncol=4)
# (a) Use the 'colMeans' function to create a vector containing the mean of
# each column
c_means=colMeans(m)
c_means
## [1] 3 8 4 17
# (b) Use the 'sweep' function to subtract the mean of each column, and
# store the result.
df_mean=sweep(m, 2, c_means)
df_mean
## [,1] [,2] [,3] [,4]
## [1,] -2 -2 -3 0
## [2,] -1 -1 -2 0
## [3,] 0 0 -1 0
## [4,] 1 1 6 0
## [5,] 2 2 0 0
# (c) Use the 'colMeans' function to verify that the mean of each column is 0
c_means1=colMeans(df_mean)
c_means1
## [1] 0 0 0 0
##########################################################################
Question 3 -- [8 / 15 points] ❌Part (d) is correct, but refer to the notes to correctly calculate rpkm manually.
# 3) Consider the matrix of read counts below, where the relative
# expression between samples 1 and 2 are the same (but the total read
# counts are twice as high for sample 2), and gene 3 has higher
# expression in sample 3 than in sample 1.
read_counts <- data.frame(s1 = c(10, 20, 15)) %>%
mutate(s2 = 2*s1, s3 = s1)
rownames(read_counts) <- paste0("gene", 1:3)
read_counts$s3[3] <- read_counts$s3[3] * 2
read_counts$s3[1:2] <- read_counts$s3[1:2] - 15/2
# (a) Calculate the vector containing total reads per sample, per million mapped reads.
# Note: this is 'N' from the class example.
N=colSums(read_counts)
N
## s1 s2 s3
## 45 90 45
# (b) The length of the three genes are 100, 200, and 100 bases. Create a vector containing
# the gene lengths in kilobases. Note: this is 'L' from the class example.
L <- data.frame(s1 =100) %>%
mutate(s2= 2*s1, s3 = s1)
L
## s1 s2 s3
## 1 100 200 100
# (c) Use the 'sweep' function multiple times to calculate the RPKM values, which gives
# the Reads Per Kilobase of transcript, per Million mapped reads.
# (d) Use the 'rpkm' function from the edgeR package to calculate the RPKM values (these
# results should be the same as your calculation in (c))
rpkmMatrix <- rpkm(read_counts,c(100,200,100))
rpkmMatrix
## s1 s2 s3
## gene1 2222222 2222222 555555.6
## gene2 2222222 2222222 1388888.9
## gene3 3333333 3333333 6666666.7
Question 4 -- [3 / 6 points] ❌For (a), you need to divide each rpkm value by the sum of its column, then multiply by 1 million; part (b) did not answer the question -- are they comparable?
# 4) Consider the rpkm values in the matrix below
rpkm_values <- data.frame(s1 = c(5,10,5), s2 = c(5,10,30))
rownames(rpkm_values) <- paste0('gene', 1:3)
# (a) Calculate the TPM values from the rpkm values matrix
head(rpkm_values)
## s1 s2
## gene1 5 5
## gene2 10 10
## gene3 5 30
r_tpm <- function(dfr,len)
{
dfr1 <- sweep(dfr,MARGIN=1,(len/10^4),`/`)
scf <- colSums(dfr1)/(10^6)
return(sweep(dfr1,2,scf,`/`))
}
r_tpm(rpkm_values,c(100,200,100))
## s1 s2
## gene1 333333.3 125000
## gene2 333333.3 125000
## gene3 333333.3 750000
# (b) The rpkm value of gene1 is 5 in both samples. Does this mean that the
# expression of gene1 is the same across samples? Why or why not? Recall
# the following interpretations
# - an rpkm value 'r': for every 1 million mapped reads, we expect to find 'r'
# reads for every kilobase of the transcript
# - a tpm value of 't': for the given gene, we expect to observe 't' reads for
# every 1 million full length transcripts that are sequenced.
# rpkm value of 5 in both samples means implies that for every 1 million mapped reads, we expect to find 5
# reads for every kilobase of the transcript
Question 5 -- [0 / 4 points] ❌
# 5) Show that the number of cohorts available with read count data from the 'gdcHub'
# is 41. Note that the column 'XenaHostNames' contains the hub information while the
# read count data is labeled as 'HTSeq - Counts' in the 'Label' column.
data(XenaData) # load the XenaData data frame
head(XenaData)
## # A tibble: 6 x 17
## XenaHosts XenaHostNames XenaCohorts XenaDatasets SampleCount DataSubtype Label
## <chr> <chr> <chr> <chr> <int> <chr> <chr>
## 1 https://… publicHub Breast Can… ucsfNeve_pu… 51 gene expre… Neve…
## 2 https://… publicHub Breast Can… ucsfNeve_pu… 57 phenotype Phen…
## 3 https://… publicHub Glioma (Ko… kotliarov20… 194 copy number Kotl…
## 4 https://… publicHub Glioma (Ko… kotliarov20… 194 phenotype Phen…
## 5 https://… publicHub Lung Cance… weir2007_pu… 383 copy number CGH
## 6 https://… publicHub Lung Cance… weir2007_pu… 383 phenotype Phen…
## # … with 10 more variables: Type <chr>, AnatomicalOrigin <chr>,
## # SampleType <chr>, Tags <chr>, ProbeMap <chr>, LongTitle <chr>,
## # Citation <chr>, Version <chr>, Unit <chr>, Platform <chr>
show(XenaData$XenaCohorts)
## [1] "Breast Cancer Cell Lines (Neve 2006)"
## [2] "Breast Cancer Cell Lines (Neve 2006)"
## [3] "Glioma (Kotliarov 2006)"
## [4] "Glioma (Kotliarov 2006)"
## [5] "Lung Cancer CGH (Weir 2007)"
## [6] "Lung Cancer CGH (Weir 2007)"
## [7] "Cancer Cell Line Encyclopedia (Breast)"
## [8] "Cancer Cell Line Encyclopedia (Breast)"
## [9] "Cancer Cell Line Encyclopedia (Breast)"
## [10] "Cancer Cell Line Encyclopedia (Breast)"
## [11] "Breast Cancer (Chin 2006)"
## [12] "Breast Cancer (Chin 2006)"
## [13] "Breast Cancer (Chin 2006)"
## [14] "Melanoma (Lin 2008)"
## [15] "Melanoma (Lin 2008)"
## [16] "Melanoma (Lin 2008)"
## [17] "MET500 (expression centric)"
## [18] "MET500 (expression centric)"
## [19] "MET500 (expression centric)"
## [20] "MET500 (expression centric)"
## [21] "Normal Breast (Benz 2020)"
## [22] "Normal Breast (Benz 2020)"
## [23] "Normal Breast (Benz 2020)"
## [24] "Normal Breast (Benz 2020)"
## [25] "Normal Breast (Benz 2020)"
## [26] "lymph-node-negative breast cancer (Wang 2005)"
## [27] "lymph-node-negative breast cancer (Wang 2005)"
## [28] "Breast Cancer (vantVeer 2002)"
## [29] "Breast Cancer (vantVeer 2002)"
## [30] "Neuroblastoma (Khan)"
## [31] "Neuroblastoma (Khan)"
## [32] "Connectivity Map"
## [33] "Connectivity Map"
## [34] "NCI-60"
## [35] "NCI-60"
## [36] "NCI-60"
## [37] "NCI-60"
## [38] "Lung Cancer (Raponi 2006)"
## [39] "Lung Cancer (Raponi 2006)"
## [40] "Ovarian Cancer (Etemadmoghadam 2009)"
## [41] "Ovarian Cancer (Etemadmoghadam 2009)"
## [42] "Ovarian Cancer (Etemadmoghadam 2009)"
## [43] "Cancer Cell Line Encyclopedia (CCLE)"
## [44] "Cancer Cell Line Encyclopedia (CCLE)"
## [45] "Cancer Cell Line Encyclopedia (CCLE)"
## [46] "Cancer Cell Line Encyclopedia (CCLE)"
## [47] "Cancer Cell Line Encyclopedia (CCLE)"
## [48] "Cancer Cell Line Encyclopedia (CCLE)"
## [49] "Cancer Cell Line Encyclopedia (CCLE)"
## [50] "Cancer Cell Line Encyclopedia (CCLE)"
## [51] "Cancer Cell Line Encyclopedia (CCLE)"
## [52] "Breast Cancer (Hess 2006)"
## [53] "Breast Cancer (Hess 2006)"
## [54] "Pediatric diffuse intrinsic pontine gliomas (Puget 2012)"
## [55] "Pediatric diffuse intrinsic pontine gliomas (Puget 2012)"
## [56] "Pediatric diffuse intrinsic pontine gliomas (Puget 2012)"
## [57] "Breast Cancer (Yau 2010)"
## [58] "Breast Cancer (Yau 2010)"
## [59] "St Jude PCGP pan-cancer"
## [60] "St Jude PCGP pan-cancer"
## [61] "St Jude PCGP pan-cancer"
## [62] "St Jude PCGP pan-cancer"
## [63] "Head and Neck Cancer (Puram 2017)"
## [64] "Head and Neck Cancer (Puram 2017)"
## [65] "Head and Neck Cancer (Puram 2017)"
## [66] "Head and Neck Cancer (Puram 2017)"
## [67] "Head and Neck Cancer (Puram 2017)"
## [68] "Head and Neck Cancer (Puram 2017)"
## [69] "Head and Neck Cancer (Puram 2017)"
## [70] "Head and Neck Cancer (Puram 2017)"
## [71] "Head and Neck Cancer (Puram 2017)"
## [72] "TARGET Acute Lymphoblastic Leukemia"
## [73] "TARGET Acute Lymphoblastic Leukemia"
## [74] "TARGET Acute Lymphoblastic Leukemia"
## [75] "Node-negative breast cancer (Desmedt 2007)"
## [76] "Node-negative breast cancer (Desmedt 2007)"
## [77] "Breast Cancer (Caldas 2007)"
## [78] "Breast Cancer (Caldas 2007)"
## [79] "Breast Cancer (Caldas 2007)"
## [80] "Pediatric tumor (Khan)"
## [81] "Pediatric tumor (Khan)"
## [82] "Breast Cancer (Miller 2005)"
## [83] "Breast Cancer (Miller 2005)"
## [84] "Pancreatic Cancer (Harada 2008)"
## [85] "Pancreatic Cancer (Harada 2008)"
## [86] "GBM (Parsons 2008)"
## [87] "GBM (Parsons 2008)"
## [88] "MAGIC"
## [89] "MAGIC"
## [90] "MAGIC"
## [91] "MAGIC"
## [92] "Breast Cancer (Vijver 2002)"
## [93] "Breast Cancer (Vijver 2002)"
## [94] "Lung Adenocarcinoma (Ding 2008)"
## [95] "Lung Adenocarcinoma (Ding 2008)"
## [96] "Breast Cancer Cell Lines (Heiser 2012)"
## [97] "Breast Cancer Cell Lines (Heiser 2012)"
## [98] "Breast Cancer Cell Lines (Heiser 2012)"
## [99] "Breast Cancer Cell Lines (Heiser 2012)"
## [100] "Breast Cancer (Haverty 2008)"
## [101] "Breast Cancer (Haverty 2008)"
## [102] "Pancreatic Cancer (Jones 2008)"
## [103] "Pancreatic Cancer (Jones 2008)"
## [104] "Acute lymphoblastic leukemia (Mullighan 2008)"
## [105] "Acute lymphoblastic leukemia (Mullighan 2008)"
## [106] "Acute lymphoblastic leukemia (Mullighan 2008)"
## [107] "TARGET neuroblastoma"
## [108] "TARGET neuroblastoma"
## [109] "TARGET neuroblastoma"
## [110] "TARGET neuroblastoma"
## [111] "TARGET neuroblastoma"
## [112] "TARGET neuroblastoma"
## [113] "Pancreatic Cancer (Balagurunathan 2008)"
## [114] "Pancreatic Cancer (Balagurunathan 2008)"
## [115] "TCGA Ovarian Cancer (OV)"
## [116] "TCGA Ovarian Cancer (OV)"
## [117] "TCGA Ovarian Cancer (OV)"
## [118] "TCGA Ovarian Cancer (OV)"
## [119] "TCGA Ovarian Cancer (OV)"
## [120] "TCGA Ovarian Cancer (OV)"
## [121] "TCGA Ovarian Cancer (OV)"
## [122] "TCGA Ovarian Cancer (OV)"
## [123] "TCGA Ovarian Cancer (OV)"
## [124] "TCGA Ovarian Cancer (OV)"
## [125] "TCGA Ovarian Cancer (OV)"
## [126] "TCGA Ovarian Cancer (OV)"
## [127] "TCGA Ovarian Cancer (OV)"
## [128] "TCGA Ovarian Cancer (OV)"
## [129] "TCGA Ovarian Cancer (OV)"
## [130] "TCGA Ovarian Cancer (OV)"
## [131] "TCGA Ovarian Cancer (OV)"
## [132] "TCGA Ovarian Cancer (OV)"
## [133] "TCGA Ovarian Cancer (OV)"
## [134] "TCGA Ovarian Cancer (OV)"
## [135] "TCGA Ovarian Cancer (OV)"
## [136] "TCGA Ovarian Cancer (OV)"
## [137] "TCGA Ovarian Cancer (OV)"
## [138] "TCGA Ovarian Cancer (OV)"
## [139] "TCGA Ovarian Cancer (OV)"
## [140] "TCGA Ovarian Cancer (OV)"
## [141] "TCGA Ovarian Cancer (OV)"
## [142] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [143] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [144] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [145] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [146] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [147] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [148] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [149] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [150] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [151] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [152] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [153] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [154] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [155] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [156] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [157] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [158] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [159] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [160] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [161] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [162] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [163] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [164] "TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [165] "TCGA Lower Grade Glioma (LGG)"
## [166] "TCGA Lower Grade Glioma (LGG)"
## [167] "TCGA Lower Grade Glioma (LGG)"
## [168] "TCGA Lower Grade Glioma (LGG)"
## [169] "TCGA Lower Grade Glioma (LGG)"
## [170] "TCGA Lower Grade Glioma (LGG)"
## [171] "TCGA Lower Grade Glioma (LGG)"
## [172] "TCGA Lower Grade Glioma (LGG)"
## [173] "TCGA Lower Grade Glioma (LGG)"
## [174] "TCGA Lower Grade Glioma (LGG)"
## [175] "TCGA Lower Grade Glioma (LGG)"
## [176] "TCGA Lower Grade Glioma (LGG)"
## [177] "TCGA Lower Grade Glioma (LGG)"
## [178] "TCGA Lower Grade Glioma (LGG)"
## [179] "TCGA Lower Grade Glioma (LGG)"
## [180] "TCGA Lower Grade Glioma (LGG)"
## [181] "TCGA Lower Grade Glioma (LGG)"
## [182] "TCGA Lower Grade Glioma (LGG)"
## [183] "TCGA Lower Grade Glioma (LGG)"
## [184] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [185] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [186] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [187] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [188] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [189] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [190] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [191] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [192] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [193] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [194] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [195] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [196] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [197] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [198] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [199] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [200] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [201] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [202] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [203] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [204] "TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [205] "TCGA Pan-Cancer (PANCAN)"
## [206] "TCGA Pan-Cancer (PANCAN)"
## [207] "TCGA Pan-Cancer (PANCAN)"
## [208] "TCGA Pan-Cancer (PANCAN)"
## [209] "TCGA Pan-Cancer (PANCAN)"
## [210] "TCGA Pan-Cancer (PANCAN)"
## [211] "TCGA Pan-Cancer (PANCAN)"
## [212] "TCGA Pan-Cancer (PANCAN)"
## [213] "TCGA Pan-Cancer (PANCAN)"
## [214] "TCGA Bile Duct Cancer (CHOL)"
## [215] "TCGA Bile Duct Cancer (CHOL)"
## [216] "TCGA Bile Duct Cancer (CHOL)"
## [217] "TCGA Bile Duct Cancer (CHOL)"
## [218] "TCGA Bile Duct Cancer (CHOL)"
## [219] "TCGA Bile Duct Cancer (CHOL)"
## [220] "TCGA Bile Duct Cancer (CHOL)"
## [221] "TCGA Bile Duct Cancer (CHOL)"
## [222] "TCGA Bile Duct Cancer (CHOL)"
## [223] "TCGA Bile Duct Cancer (CHOL)"
## [224] "TCGA Bile Duct Cancer (CHOL)"
## [225] "TCGA Bile Duct Cancer (CHOL)"
## [226] "TCGA Bile Duct Cancer (CHOL)"
## [227] "TCGA Bile Duct Cancer (CHOL)"
## [228] "TCGA Bile Duct Cancer (CHOL)"
## [229] "TCGA Bile Duct Cancer (CHOL)"
## [230] "TCGA Bile Duct Cancer (CHOL)"
## [231] "TCGA Colon and Rectal Cancer (COADREAD)"
## [232] "TCGA Colon and Rectal Cancer (COADREAD)"
## [233] "TCGA Colon and Rectal Cancer (COADREAD)"
## [234] "TCGA Colon and Rectal Cancer (COADREAD)"
## [235] "TCGA Colon and Rectal Cancer (COADREAD)"
## [236] "TCGA Colon and Rectal Cancer (COADREAD)"
## [237] "TCGA Colon and Rectal Cancer (COADREAD)"
## [238] "TCGA Colon and Rectal Cancer (COADREAD)"
## [239] "TCGA Colon and Rectal Cancer (COADREAD)"
## [240] "TCGA Colon and Rectal Cancer (COADREAD)"
## [241] "TCGA Colon and Rectal Cancer (COADREAD)"
## [242] "TCGA Colon and Rectal Cancer (COADREAD)"
## [243] "TCGA Colon and Rectal Cancer (COADREAD)"
## [244] "TCGA Colon and Rectal Cancer (COADREAD)"
## [245] "TCGA Colon and Rectal Cancer (COADREAD)"
## [246] "TCGA Adrenocortical Cancer (ACC)"
## [247] "TCGA Adrenocortical Cancer (ACC)"
## [248] "TCGA Adrenocortical Cancer (ACC)"
## [249] "TCGA Adrenocortical Cancer (ACC)"
## [250] "TCGA Adrenocortical Cancer (ACC)"
## [251] "TCGA Adrenocortical Cancer (ACC)"
## [252] "TCGA Adrenocortical Cancer (ACC)"
## [253] "TCGA Adrenocortical Cancer (ACC)"
## [254] "TCGA Adrenocortical Cancer (ACC)"
## [255] "TCGA Adrenocortical Cancer (ACC)"
## [256] "TCGA Adrenocortical Cancer (ACC)"
## [257] "TCGA Adrenocortical Cancer (ACC)"
## [258] "TCGA Adrenocortical Cancer (ACC)"
## [259] "TCGA Adrenocortical Cancer (ACC)"
## [260] "TCGA Adrenocortical Cancer (ACC)"
## [261] "TCGA Adrenocortical Cancer (ACC)"
## [262] "TCGA Adrenocortical Cancer (ACC)"
## [263] "TCGA Cervical Cancer (CESC)"
## [264] "TCGA Cervical Cancer (CESC)"
## [265] "TCGA Cervical Cancer (CESC)"
## [266] "TCGA Cervical Cancer (CESC)"
## [267] "TCGA Cervical Cancer (CESC)"
## [268] "TCGA Cervical Cancer (CESC)"
## [269] "TCGA Cervical Cancer (CESC)"
## [270] "TCGA Cervical Cancer (CESC)"
## [271] "TCGA Cervical Cancer (CESC)"
## [272] "TCGA Cervical Cancer (CESC)"
## [273] "TCGA Cervical Cancer (CESC)"
## [274] "TCGA Cervical Cancer (CESC)"
## [275] "TCGA Cervical Cancer (CESC)"
## [276] "TCGA Cervical Cancer (CESC)"
## [277] "TCGA Cervical Cancer (CESC)"
## [278] "TCGA Cervical Cancer (CESC)"
## [279] "TCGA Cervical Cancer (CESC)"
## [280] "TCGA Cervical Cancer (CESC)"
## [281] "TCGA Rectal Cancer (READ)"
## [282] "TCGA Rectal Cancer (READ)"
## [283] "TCGA Rectal Cancer (READ)"
## [284] "TCGA Rectal Cancer (READ)"
## [285] "TCGA Rectal Cancer (READ)"
## [286] "TCGA Rectal Cancer (READ)"
## [287] "TCGA Rectal Cancer (READ)"
## [288] "TCGA Rectal Cancer (READ)"
## [289] "TCGA Rectal Cancer (READ)"
## [290] "TCGA Rectal Cancer (READ)"
## [291] "TCGA Rectal Cancer (READ)"
## [292] "TCGA Rectal Cancer (READ)"
## [293] "TCGA Rectal Cancer (READ)"
## [294] "TCGA Rectal Cancer (READ)"
## [295] "TCGA Rectal Cancer (READ)"
## [296] "TCGA Rectal Cancer (READ)"
## [297] "TCGA Rectal Cancer (READ)"
## [298] "TCGA Rectal Cancer (READ)"
## [299] "TCGA Rectal Cancer (READ)"
## [300] "TCGA Rectal Cancer (READ)"
## [301] "TCGA Rectal Cancer (READ)"
## [302] "TCGA Rectal Cancer (READ)"
## [303] "TCGA Rectal Cancer (READ)"
## [304] "TCGA Rectal Cancer (READ)"
## [305] "TCGA Rectal Cancer (READ)"
## [306] "TCGA Sarcoma (SARC)"
## [307] "TCGA Sarcoma (SARC)"
## [308] "TCGA Sarcoma (SARC)"
## [309] "TCGA Sarcoma (SARC)"
## [310] "TCGA Sarcoma (SARC)"
## [311] "TCGA Sarcoma (SARC)"
## [312] "TCGA Sarcoma (SARC)"
## [313] "TCGA Sarcoma (SARC)"
## [314] "TCGA Sarcoma (SARC)"
## [315] "TCGA Sarcoma (SARC)"
## [316] "TCGA Sarcoma (SARC)"
## [317] "TCGA Sarcoma (SARC)"
## [318] "TCGA Sarcoma (SARC)"
## [319] "TCGA Sarcoma (SARC)"
## [320] "TCGA Sarcoma (SARC)"
## [321] "TCGA Sarcoma (SARC)"
## [322] "TCGA Sarcoma (SARC)"
## [323] "TCGA Large B-cell Lymphoma (DLBC)"
## [324] "TCGA Large B-cell Lymphoma (DLBC)"
## [325] "TCGA Large B-cell Lymphoma (DLBC)"
## [326] "TCGA Large B-cell Lymphoma (DLBC)"
## [327] "TCGA Large B-cell Lymphoma (DLBC)"
## [328] "TCGA Large B-cell Lymphoma (DLBC)"
## [329] "TCGA Large B-cell Lymphoma (DLBC)"
## [330] "TCGA Large B-cell Lymphoma (DLBC)"
## [331] "TCGA Large B-cell Lymphoma (DLBC)"
## [332] "TCGA Large B-cell Lymphoma (DLBC)"
## [333] "TCGA Large B-cell Lymphoma (DLBC)"
## [334] "TCGA Large B-cell Lymphoma (DLBC)"
## [335] "TCGA Large B-cell Lymphoma (DLBC)"
## [336] "TCGA Large B-cell Lymphoma (DLBC)"
## [337] "TCGA Large B-cell Lymphoma (DLBC)"
## [338] "TCGA Large B-cell Lymphoma (DLBC)"
## [339] "TCGA Large B-cell Lymphoma (DLBC)"
## [340] "TCGA Prostate Cancer (PRAD)"
## [341] "TCGA Prostate Cancer (PRAD)"
## [342] "TCGA Prostate Cancer (PRAD)"
## [343] "TCGA Prostate Cancer (PRAD)"
## [344] "TCGA Prostate Cancer (PRAD)"
## [345] "TCGA Prostate Cancer (PRAD)"
## [346] "TCGA Prostate Cancer (PRAD)"
## [347] "TCGA Prostate Cancer (PRAD)"
## [348] "TCGA Prostate Cancer (PRAD)"
## [349] "TCGA Prostate Cancer (PRAD)"
## [350] "TCGA Prostate Cancer (PRAD)"
## [351] "TCGA Prostate Cancer (PRAD)"
## [352] "TCGA Prostate Cancer (PRAD)"
## [353] "TCGA Prostate Cancer (PRAD)"
## [354] "TCGA Prostate Cancer (PRAD)"
## [355] "TCGA Prostate Cancer (PRAD)"
## [356] "TCGA Prostate Cancer (PRAD)"
## [357] "TCGA Prostate Cancer (PRAD)"
## [358] "TCGA Lung Cancer (LUNG)"
## [359] "TCGA Lung Cancer (LUNG)"
## [360] "TCGA Lung Cancer (LUNG)"
## [361] "TCGA Lung Cancer (LUNG)"
## [362] "TCGA Lung Cancer (LUNG)"
## [363] "TCGA Lung Cancer (LUNG)"
## [364] "TCGA Lung Cancer (LUNG)"
## [365] "TCGA Lung Cancer (LUNG)"
## [366] "TCGA Lung Cancer (LUNG)"
## [367] "TCGA Lung Cancer (LUNG)"
## [368] "TCGA Lung Cancer (LUNG)"
## [369] "TCGA Lung Cancer (LUNG)"
## [370] "TCGA Lung Cancer (LUNG)"
## [371] "TCGA Lung Cancer (LUNG)"
## [372] "TCGA Lung Cancer (LUNG)"
## [373] "TCGA Liver Cancer (LIHC)"
## [374] "TCGA Liver Cancer (LIHC)"
## [375] "TCGA Liver Cancer (LIHC)"
## [376] "TCGA Liver Cancer (LIHC)"
## [377] "TCGA Liver Cancer (LIHC)"
## [378] "TCGA Liver Cancer (LIHC)"
## [379] "TCGA Liver Cancer (LIHC)"
## [380] "TCGA Liver Cancer (LIHC)"
## [381] "TCGA Liver Cancer (LIHC)"
## [382] "TCGA Liver Cancer (LIHC)"
## [383] "TCGA Liver Cancer (LIHC)"
## [384] "TCGA Liver Cancer (LIHC)"
## [385] "TCGA Liver Cancer (LIHC)"
## [386] "TCGA Liver Cancer (LIHC)"
## [387] "TCGA Liver Cancer (LIHC)"
## [388] "TCGA Liver Cancer (LIHC)"
## [389] "TCGA Liver Cancer (LIHC)"
## [390] "TCGA Liver Cancer (LIHC)"
## [391] "TCGA Liver Cancer (LIHC)"
## [392] "TCGA Kidney Chromophobe (KICH)"
## [393] "TCGA Kidney Chromophobe (KICH)"
## [394] "TCGA Kidney Chromophobe (KICH)"
## [395] "TCGA Kidney Chromophobe (KICH)"
## [396] "TCGA Kidney Chromophobe (KICH)"
## [397] "TCGA Kidney Chromophobe (KICH)"
## [398] "TCGA Kidney Chromophobe (KICH)"
## [399] "TCGA Kidney Chromophobe (KICH)"
## [400] "TCGA Kidney Chromophobe (KICH)"
## [401] "TCGA Kidney Chromophobe (KICH)"
## [402] "TCGA Kidney Chromophobe (KICH)"
## [403] "TCGA Kidney Chromophobe (KICH)"
## [404] "TCGA Kidney Chromophobe (KICH)"
## [405] "TCGA Kidney Chromophobe (KICH)"
## [406] "TCGA Kidney Chromophobe (KICH)"
## [407] "TCGA Kidney Chromophobe (KICH)"
## [408] "TCGA Kidney Chromophobe (KICH)"
## [409] "TCGA Kidney Chromophobe (KICH)"
## [410] "TCGA Head and Neck Cancer (HNSC)"
## [411] "TCGA Head and Neck Cancer (HNSC)"
## [412] "TCGA Head and Neck Cancer (HNSC)"
## [413] "TCGA Head and Neck Cancer (HNSC)"
## [414] "TCGA Head and Neck Cancer (HNSC)"
## [415] "TCGA Head and Neck Cancer (HNSC)"
## [416] "TCGA Head and Neck Cancer (HNSC)"
## [417] "TCGA Head and Neck Cancer (HNSC)"
## [418] "TCGA Head and Neck Cancer (HNSC)"
## [419] "TCGA Head and Neck Cancer (HNSC)"
## [420] "TCGA Head and Neck Cancer (HNSC)"
## [421] "TCGA Head and Neck Cancer (HNSC)"
## [422] "TCGA Head and Neck Cancer (HNSC)"
## [423] "TCGA Head and Neck Cancer (HNSC)"
## [424] "TCGA Head and Neck Cancer (HNSC)"
## [425] "TCGA Head and Neck Cancer (HNSC)"
## [426] "TCGA Head and Neck Cancer (HNSC)"
## [427] "TCGA Head and Neck Cancer (HNSC)"
## [428] "TCGA Head and Neck Cancer (HNSC)"
## [429] "TCGA Head and Neck Cancer (HNSC)"
## [430] "TCGA Head and Neck Cancer (HNSC)"
## [431] "TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [432] "TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [433] "TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [434] "TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [435] "TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [436] "TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [437] "TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [438] "TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [439] "TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [440] "TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [441] "TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [442] "TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [443] "TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [444] "TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [445] "TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [446] "TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [447] "TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [448] "TCGA Esophageal Cancer (ESCA)"
## [449] "TCGA Esophageal Cancer (ESCA)"
## [450] "TCGA Esophageal Cancer (ESCA)"
## [451] "TCGA Esophageal Cancer (ESCA)"
## [452] "TCGA Esophageal Cancer (ESCA)"
## [453] "TCGA Esophageal Cancer (ESCA)"
## [454] "TCGA Esophageal Cancer (ESCA)"
## [455] "TCGA Esophageal Cancer (ESCA)"
## [456] "TCGA Esophageal Cancer (ESCA)"
## [457] "TCGA Esophageal Cancer (ESCA)"
## [458] "TCGA Esophageal Cancer (ESCA)"
## [459] "TCGA Esophageal Cancer (ESCA)"
## [460] "TCGA Esophageal Cancer (ESCA)"
## [461] "TCGA Esophageal Cancer (ESCA)"
## [462] "TCGA Esophageal Cancer (ESCA)"
## [463] "TCGA Esophageal Cancer (ESCA)"
## [464] "TCGA Esophageal Cancer (ESCA)"
## [465] "TCGA Esophageal Cancer (ESCA)"
## [466] "TCGA Esophageal Cancer (ESCA)"
## [467] "TCGA Thyroid Cancer (THCA)"
## [468] "TCGA Thyroid Cancer (THCA)"
## [469] "TCGA Thyroid Cancer (THCA)"
## [470] "TCGA Thyroid Cancer (THCA)"
## [471] "TCGA Thyroid Cancer (THCA)"
## [472] "TCGA Thyroid Cancer (THCA)"
## [473] "TCGA Thyroid Cancer (THCA)"
## [474] "TCGA Thyroid Cancer (THCA)"
## [475] "TCGA Thyroid Cancer (THCA)"
## [476] "TCGA Thyroid Cancer (THCA)"
## [477] "TCGA Thyroid Cancer (THCA)"
## [478] "TCGA Thyroid Cancer (THCA)"
## [479] "TCGA Thyroid Cancer (THCA)"
## [480] "TCGA Thyroid Cancer (THCA)"
## [481] "TCGA Thyroid Cancer (THCA)"
## [482] "TCGA Thyroid Cancer (THCA)"
## [483] "TCGA Thyroid Cancer (THCA)"
## [484] "TCGA Thyroid Cancer (THCA)"
## [485] "TCGA Thyroid Cancer (THCA)"
## [486] "TCGA Lung Adenocarcinoma (LUAD)"
## [487] "TCGA Lung Adenocarcinoma (LUAD)"
## [488] "TCGA Lung Adenocarcinoma (LUAD)"
## [489] "TCGA Lung Adenocarcinoma (LUAD)"
## [490] "TCGA Lung Adenocarcinoma (LUAD)"
## [491] "TCGA Lung Adenocarcinoma (LUAD)"
## [492] "TCGA Lung Adenocarcinoma (LUAD)"
## [493] "TCGA Lung Adenocarcinoma (LUAD)"
## [494] "TCGA Lung Adenocarcinoma (LUAD)"
## [495] "TCGA Lung Adenocarcinoma (LUAD)"
## [496] "TCGA Lung Adenocarcinoma (LUAD)"
## [497] "TCGA Lung Adenocarcinoma (LUAD)"
## [498] "TCGA Lung Adenocarcinoma (LUAD)"
## [499] "TCGA Lung Adenocarcinoma (LUAD)"
## [500] "TCGA Lung Adenocarcinoma (LUAD)"
## [501] "TCGA Lung Adenocarcinoma (LUAD)"
## [502] "TCGA Lung Adenocarcinoma (LUAD)"
## [503] "TCGA Lung Adenocarcinoma (LUAD)"
## [504] "TCGA Lung Adenocarcinoma (LUAD)"
## [505] "TCGA Lung Adenocarcinoma (LUAD)"
## [506] "TCGA Lung Adenocarcinoma (LUAD)"
## [507] "TCGA Lung Adenocarcinoma (LUAD)"
## [508] "TCGA Lung Adenocarcinoma (LUAD)"
## [509] "TCGA Acute Myeloid Leukemia (LAML)"
## [510] "TCGA Acute Myeloid Leukemia (LAML)"
## [511] "TCGA Acute Myeloid Leukemia (LAML)"
## [512] "TCGA Acute Myeloid Leukemia (LAML)"
## [513] "TCGA Acute Myeloid Leukemia (LAML)"
## [514] "TCGA Acute Myeloid Leukemia (LAML)"
## [515] "TCGA Acute Myeloid Leukemia (LAML)"
## [516] "TCGA Acute Myeloid Leukemia (LAML)"
## [517] "TCGA Acute Myeloid Leukemia (LAML)"
## [518] "TCGA Acute Myeloid Leukemia (LAML)"
## [519] "TCGA Acute Myeloid Leukemia (LAML)"
## [520] "TCGA Acute Myeloid Leukemia (LAML)"
## [521] "TCGA Acute Myeloid Leukemia (LAML)"
## [522] "TCGA Acute Myeloid Leukemia (LAML)"
## [523] "TCGA Acute Myeloid Leukemia (LAML)"
## [524] "TCGA Acute Myeloid Leukemia (LAML)"
## [525] "TCGA Acute Myeloid Leukemia (LAML)"
## [526] "TCGA Acute Myeloid Leukemia (LAML)"
## [527] "TCGA Acute Myeloid Leukemia (LAML)"
## [528] "TCGA Bladder Cancer (BLCA)"
## [529] "TCGA Bladder Cancer (BLCA)"
## [530] "TCGA Bladder Cancer (BLCA)"
## [531] "TCGA Bladder Cancer (BLCA)"
## [532] "TCGA Bladder Cancer (BLCA)"
## [533] "TCGA Bladder Cancer (BLCA)"
## [534] "TCGA Bladder Cancer (BLCA)"
## [535] "TCGA Bladder Cancer (BLCA)"
## [536] "TCGA Bladder Cancer (BLCA)"
## [537] "TCGA Bladder Cancer (BLCA)"
## [538] "TCGA Bladder Cancer (BLCA)"
## [539] "TCGA Bladder Cancer (BLCA)"
## [540] "TCGA Bladder Cancer (BLCA)"
## [541] "TCGA Bladder Cancer (BLCA)"
## [542] "TCGA Bladder Cancer (BLCA)"
## [543] "TCGA Bladder Cancer (BLCA)"
## [544] "TCGA Bladder Cancer (BLCA)"
## [545] "TCGA Bladder Cancer (BLCA)"
## [546] "TCGA Bladder Cancer (BLCA)"
## [547] "TCGA Bladder Cancer (BLCA)"
## [548] "TCGA Bladder Cancer (BLCA)"
## [549] "TCGA Melanoma (SKCM)"
## [550] "TCGA Melanoma (SKCM)"
## [551] "TCGA Melanoma (SKCM)"
## [552] "TCGA Melanoma (SKCM)"
## [553] "TCGA Melanoma (SKCM)"
## [554] "TCGA Melanoma (SKCM)"
## [555] "TCGA Melanoma (SKCM)"
## [556] "TCGA Melanoma (SKCM)"
## [557] "TCGA Melanoma (SKCM)"
## [558] "TCGA Melanoma (SKCM)"
## [559] "TCGA Melanoma (SKCM)"
## [560] "TCGA Melanoma (SKCM)"
## [561] "TCGA Melanoma (SKCM)"
## [562] "TCGA Melanoma (SKCM)"
## [563] "TCGA Melanoma (SKCM)"
## [564] "TCGA Melanoma (SKCM)"
## [565] "TCGA Melanoma (SKCM)"
## [566] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [567] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [568] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [569] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [570] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [571] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [572] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [573] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [574] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [575] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [576] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [577] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [578] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [579] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [580] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [581] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [582] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [583] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [584] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [585] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [586] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [587] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [588] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [589] "TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [590] "TCGA Testicular Cancer (TGCT)"
## [591] "TCGA Testicular Cancer (TGCT)"
## [592] "TCGA Testicular Cancer (TGCT)"
## [593] "TCGA Testicular Cancer (TGCT)"
## [594] "TCGA Testicular Cancer (TGCT)"
## [595] "TCGA Testicular Cancer (TGCT)"
## [596] "TCGA Testicular Cancer (TGCT)"
## [597] "TCGA Testicular Cancer (TGCT)"
## [598] "TCGA Testicular Cancer (TGCT)"
## [599] "TCGA Testicular Cancer (TGCT)"
## [600] "TCGA Testicular Cancer (TGCT)"
## [601] "TCGA Testicular Cancer (TGCT)"
## [602] "TCGA Testicular Cancer (TGCT)"
## [603] "TCGA Testicular Cancer (TGCT)"
## [604] "TCGA Testicular Cancer (TGCT)"
## [605] "TCGA Testicular Cancer (TGCT)"
## [606] "TCGA Testicular Cancer (TGCT)"
## [607] "TCGA Pancreatic Cancer (PAAD)"
## [608] "TCGA Pancreatic Cancer (PAAD)"
## [609] "TCGA Pancreatic Cancer (PAAD)"
## [610] "TCGA Pancreatic Cancer (PAAD)"
## [611] "TCGA Pancreatic Cancer (PAAD)"
## [612] "TCGA Pancreatic Cancer (PAAD)"
## [613] "TCGA Pancreatic Cancer (PAAD)"
## [614] "TCGA Pancreatic Cancer (PAAD)"
## [615] "TCGA Pancreatic Cancer (PAAD)"
## [616] "TCGA Pancreatic Cancer (PAAD)"
## [617] "TCGA Pancreatic Cancer (PAAD)"
## [618] "TCGA Pancreatic Cancer (PAAD)"
## [619] "TCGA Pancreatic Cancer (PAAD)"
## [620] "TCGA Pancreatic Cancer (PAAD)"
## [621] "TCGA Pancreatic Cancer (PAAD)"
## [622] "TCGA Pancreatic Cancer (PAAD)"
## [623] "TCGA Pancreatic Cancer (PAAD)"
## [624] "TCGA Glioblastoma (GBM)"
## [625] "TCGA Glioblastoma (GBM)"
## [626] "TCGA Glioblastoma (GBM)"
## [627] "TCGA Glioblastoma (GBM)"
## [628] "TCGA Glioblastoma (GBM)"
## [629] "TCGA Glioblastoma (GBM)"
## [630] "TCGA Glioblastoma (GBM)"
## [631] "TCGA Glioblastoma (GBM)"
## [632] "TCGA Glioblastoma (GBM)"
## [633] "TCGA Glioblastoma (GBM)"
## [634] "TCGA Glioblastoma (GBM)"
## [635] "TCGA Glioblastoma (GBM)"
## [636] "TCGA Glioblastoma (GBM)"
## [637] "TCGA Glioblastoma (GBM)"
## [638] "TCGA Glioblastoma (GBM)"
## [639] "TCGA Glioblastoma (GBM)"
## [640] "TCGA Glioblastoma (GBM)"
## [641] "TCGA Glioblastoma (GBM)"
## [642] "TCGA Glioblastoma (GBM)"
## [643] "TCGA Glioblastoma (GBM)"
## [644] "TCGA Glioblastoma (GBM)"
## [645] "TCGA Glioblastoma (GBM)"
## [646] "TCGA Glioblastoma (GBM)"
## [647] "TCGA Glioblastoma (GBM)"
## [648] "TCGA Glioblastoma (GBM)"
## [649] "TCGA Stomach Cancer (STAD)"
## [650] "TCGA Stomach Cancer (STAD)"
## [651] "TCGA Stomach Cancer (STAD)"
## [652] "TCGA Stomach Cancer (STAD)"
## [653] "TCGA Stomach Cancer (STAD)"
## [654] "TCGA Stomach Cancer (STAD)"
## [655] "TCGA Stomach Cancer (STAD)"
## [656] "TCGA Stomach Cancer (STAD)"
## [657] "TCGA Stomach Cancer (STAD)"
## [658] "TCGA Stomach Cancer (STAD)"
## [659] "TCGA Stomach Cancer (STAD)"
## [660] "TCGA Stomach Cancer (STAD)"
## [661] "TCGA Stomach Cancer (STAD)"
## [662] "TCGA Stomach Cancer (STAD)"
## [663] "TCGA Stomach Cancer (STAD)"
## [664] "TCGA Stomach Cancer (STAD)"
## [665] "TCGA Stomach Cancer (STAD)"
## [666] "TCGA Stomach Cancer (STAD)"
## [667] "TCGA Stomach Cancer (STAD)"
## [668] "TCGA Stomach Cancer (STAD)"
## [669] "TCGA Stomach Cancer (STAD)"
## [670] "TCGA Stomach Cancer (STAD)"
## [671] "TCGA Stomach Cancer (STAD)"
## [672] "TCGA Stomach Cancer (STAD)"
## [673] "TCGA Mesothelioma (MESO)"
## [674] "TCGA Mesothelioma (MESO)"
## [675] "TCGA Mesothelioma (MESO)"
## [676] "TCGA Mesothelioma (MESO)"
## [677] "TCGA Mesothelioma (MESO)"
## [678] "TCGA Mesothelioma (MESO)"
## [679] "TCGA Mesothelioma (MESO)"
## [680] "TCGA Mesothelioma (MESO)"
## [681] "TCGA Mesothelioma (MESO)"
## [682] "TCGA Mesothelioma (MESO)"
## [683] "TCGA Mesothelioma (MESO)"
## [684] "TCGA Mesothelioma (MESO)"
## [685] "TCGA Mesothelioma (MESO)"
## [686] "TCGA Mesothelioma (MESO)"
## [687] "TCGA Mesothelioma (MESO)"
## [688] "TCGA Mesothelioma (MESO)"
## [689] "TCGA Mesothelioma (MESO)"
## [690] "TCGA Ocular melanomas (UVM)"
## [691] "TCGA Ocular melanomas (UVM)"
## [692] "TCGA Ocular melanomas (UVM)"
## [693] "TCGA Ocular melanomas (UVM)"
## [694] "TCGA Ocular melanomas (UVM)"
## [695] "TCGA Ocular melanomas (UVM)"
## [696] "TCGA Ocular melanomas (UVM)"
## [697] "TCGA Ocular melanomas (UVM)"
## [698] "TCGA Ocular melanomas (UVM)"
## [699] "TCGA Ocular melanomas (UVM)"
## [700] "TCGA Ocular melanomas (UVM)"
## [701] "TCGA Ocular melanomas (UVM)"
## [702] "TCGA Ocular melanomas (UVM)"
## [703] "TCGA Ocular melanomas (UVM)"
## [704] "TCGA Ocular melanomas (UVM)"
## [705] "TCGA Ocular melanomas (UVM)"
## [706] "TCGA Ocular melanomas (UVM)"
## [707] "TCGA lower grade glioma and glioblastoma (GBMLGG)"
## [708] "TCGA lower grade glioma and glioblastoma (GBMLGG)"
## [709] "TCGA lower grade glioma and glioblastoma (GBMLGG)"
## [710] "TCGA lower grade glioma and glioblastoma (GBMLGG)"
## [711] "TCGA lower grade glioma and glioblastoma (GBMLGG)"
## [712] "TCGA lower grade glioma and glioblastoma (GBMLGG)"
## [713] "TCGA lower grade glioma and glioblastoma (GBMLGG)"
## [714] "TCGA lower grade glioma and glioblastoma (GBMLGG)"
## [715] "TCGA lower grade glioma and glioblastoma (GBMLGG)"
## [716] "TCGA lower grade glioma and glioblastoma (GBMLGG)"
## [717] "TCGA lower grade glioma and glioblastoma (GBMLGG)"
## [718] "TCGA lower grade glioma and glioblastoma (GBMLGG)"
## [719] "TCGA Thymoma (THYM)"
## [720] "TCGA Thymoma (THYM)"
## [721] "TCGA Thymoma (THYM)"
## [722] "TCGA Thymoma (THYM)"
## [723] "TCGA Thymoma (THYM)"
## [724] "TCGA Thymoma (THYM)"
## [725] "TCGA Thymoma (THYM)"
## [726] "TCGA Thymoma (THYM)"
## [727] "TCGA Thymoma (THYM)"
## [728] "TCGA Thymoma (THYM)"
## [729] "TCGA Thymoma (THYM)"
## [730] "TCGA Thymoma (THYM)"
## [731] "TCGA Thymoma (THYM)"
## [732] "TCGA Thymoma (THYM)"
## [733] "TCGA Thymoma (THYM)"
## [734] "TCGA Thymoma (THYM)"
## [735] "TCGA Thymoma (THYM)"
## [736] "TCGA Endometrioid Cancer (UCEC)"
## [737] "TCGA Endometrioid Cancer (UCEC)"
## [738] "TCGA Endometrioid Cancer (UCEC)"
## [739] "TCGA Endometrioid Cancer (UCEC)"
## [740] "TCGA Endometrioid Cancer (UCEC)"
## [741] "TCGA Endometrioid Cancer (UCEC)"
## [742] "TCGA Endometrioid Cancer (UCEC)"
## [743] "TCGA Endometrioid Cancer (UCEC)"
## [744] "TCGA Endometrioid Cancer (UCEC)"
## [745] "TCGA Endometrioid Cancer (UCEC)"
## [746] "TCGA Endometrioid Cancer (UCEC)"
## [747] "TCGA Endometrioid Cancer (UCEC)"
## [748] "TCGA Endometrioid Cancer (UCEC)"
## [749] "TCGA Endometrioid Cancer (UCEC)"
## [750] "TCGA Endometrioid Cancer (UCEC)"
## [751] "TCGA Endometrioid Cancer (UCEC)"
## [752] "TCGA Endometrioid Cancer (UCEC)"
## [753] "TCGA Endometrioid Cancer (UCEC)"
## [754] "TCGA Endometrioid Cancer (UCEC)"
## [755] "TCGA Endometrioid Cancer (UCEC)"
## [756] "TCGA Endometrioid Cancer (UCEC)"
## [757] "TCGA Endometrioid Cancer (UCEC)"
## [758] "TCGA Endometrioid Cancer (UCEC)"
## [759] "TCGA Endometrioid Cancer (UCEC)"
## [760] "TCGA Endometrioid Cancer (UCEC)"
## [761] "TCGA Endometrioid Cancer (UCEC)"
## [762] "TCGA Breast Cancer (BRCA)"
## [763] "TCGA Breast Cancer (BRCA)"
## [764] "TCGA Breast Cancer (BRCA)"
## [765] "TCGA Breast Cancer (BRCA)"
## [766] "TCGA Breast Cancer (BRCA)"
## [767] "TCGA Breast Cancer (BRCA)"
## [768] "TCGA Breast Cancer (BRCA)"
## [769] "TCGA Breast Cancer (BRCA)"
## [770] "TCGA Breast Cancer (BRCA)"
## [771] "TCGA Breast Cancer (BRCA)"
## [772] "TCGA Breast Cancer (BRCA)"
## [773] "TCGA Breast Cancer (BRCA)"
## [774] "TCGA Breast Cancer (BRCA)"
## [775] "TCGA Breast Cancer (BRCA)"
## [776] "TCGA Breast Cancer (BRCA)"
## [777] "TCGA Breast Cancer (BRCA)"
## [778] "TCGA Breast Cancer (BRCA)"
## [779] "TCGA Breast Cancer (BRCA)"
## [780] "TCGA Breast Cancer (BRCA)"
## [781] "TCGA Breast Cancer (BRCA)"
## [782] "TCGA Breast Cancer (BRCA)"
## [783] "TCGA Breast Cancer (BRCA)"
## [784] "TCGA Breast Cancer (BRCA)"
## [785] "TCGA Breast Cancer (BRCA)"
## [786] "TCGA Uterine Carcinosarcoma (UCS)"
## [787] "TCGA Uterine Carcinosarcoma (UCS)"
## [788] "TCGA Uterine Carcinosarcoma (UCS)"
## [789] "TCGA Uterine Carcinosarcoma (UCS)"
## [790] "TCGA Uterine Carcinosarcoma (UCS)"
## [791] "TCGA Uterine Carcinosarcoma (UCS)"
## [792] "TCGA Uterine Carcinosarcoma (UCS)"
## [793] "TCGA Uterine Carcinosarcoma (UCS)"
## [794] "TCGA Uterine Carcinosarcoma (UCS)"
## [795] "TCGA Uterine Carcinosarcoma (UCS)"
## [796] "TCGA Uterine Carcinosarcoma (UCS)"
## [797] "TCGA Uterine Carcinosarcoma (UCS)"
## [798] "TCGA Uterine Carcinosarcoma (UCS)"
## [799] "TCGA Uterine Carcinosarcoma (UCS)"
## [800] "TCGA Uterine Carcinosarcoma (UCS)"
## [801] "TCGA Uterine Carcinosarcoma (UCS)"
## [802] "TCGA Uterine Carcinosarcoma (UCS)"
## [803] "TCGA Colon Cancer (COAD)"
## [804] "TCGA Colon Cancer (COAD)"
## [805] "TCGA Colon Cancer (COAD)"
## [806] "TCGA Colon Cancer (COAD)"
## [807] "TCGA Colon Cancer (COAD)"
## [808] "TCGA Colon Cancer (COAD)"
## [809] "TCGA Colon Cancer (COAD)"
## [810] "TCGA Colon Cancer (COAD)"
## [811] "TCGA Colon Cancer (COAD)"
## [812] "TCGA Colon Cancer (COAD)"
## [813] "TCGA Colon Cancer (COAD)"
## [814] "TCGA Colon Cancer (COAD)"
## [815] "TCGA Colon Cancer (COAD)"
## [816] "TCGA Colon Cancer (COAD)"
## [817] "TCGA Colon Cancer (COAD)"
## [818] "TCGA Colon Cancer (COAD)"
## [819] "TCGA Colon Cancer (COAD)"
## [820] "TCGA Colon Cancer (COAD)"
## [821] "TCGA Colon Cancer (COAD)"
## [822] "TCGA Colon Cancer (COAD)"
## [823] "TCGA Colon Cancer (COAD)"
## [824] "TCGA Colon Cancer (COAD)"
## [825] "TCGA Colon Cancer (COAD)"
## [826] "TCGA Colon Cancer (COAD)"
## [827] "TCGA Colon Cancer (COAD)"
## [828] "TCGA Formalin Fixed Paraffin-Embedded Pilot Phase II (FPPP)"
## [829] "TCGA Formalin Fixed Paraffin-Embedded Pilot Phase II (FPPP)"
## [830] "GDC TCGA Bladder Cancer (BLCA)"
## [831] "GDC TCGA Bladder Cancer (BLCA)"
## [832] "GDC TCGA Bladder Cancer (BLCA)"
## [833] "GDC TCGA Bladder Cancer (BLCA)"
## [834] "GDC TCGA Bladder Cancer (BLCA)"
## [835] "GDC TCGA Bladder Cancer (BLCA)"
## [836] "GDC TCGA Bladder Cancer (BLCA)"
## [837] "GDC TCGA Bladder Cancer (BLCA)"
## [838] "GDC TCGA Bladder Cancer (BLCA)"
## [839] "GDC TCGA Bladder Cancer (BLCA)"
## [840] "GDC TCGA Bladder Cancer (BLCA)"
## [841] "GDC TCGA Bladder Cancer (BLCA)"
## [842] "GDC TCGA Bladder Cancer (BLCA)"
## [843] "GDC TCGA Bladder Cancer (BLCA)"
## [844] "GDC TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [845] "GDC TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [846] "GDC TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [847] "GDC TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [848] "GDC TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [849] "GDC TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [850] "GDC TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [851] "GDC TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [852] "GDC TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [853] "GDC TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [854] "GDC TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [855] "GDC TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [856] "GDC TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [857] "GDC TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [858] "GDC TCGA Lung Squamous Cell Carcinoma (LUSC)"
## [859] "GDC TCGA Esophageal Cancer (ESCA)"
## [860] "GDC TCGA Esophageal Cancer (ESCA)"
## [861] "GDC TCGA Esophageal Cancer (ESCA)"
## [862] "GDC TCGA Esophageal Cancer (ESCA)"
## [863] "GDC TCGA Esophageal Cancer (ESCA)"
## [864] "GDC TCGA Esophageal Cancer (ESCA)"
## [865] "GDC TCGA Esophageal Cancer (ESCA)"
## [866] "GDC TCGA Esophageal Cancer (ESCA)"
## [867] "GDC TCGA Esophageal Cancer (ESCA)"
## [868] "GDC TCGA Esophageal Cancer (ESCA)"
## [869] "GDC TCGA Esophageal Cancer (ESCA)"
## [870] "GDC TCGA Esophageal Cancer (ESCA)"
## [871] "GDC TCGA Esophageal Cancer (ESCA)"
## [872] "GDC TCGA Esophageal Cancer (ESCA)"
## [873] "GDC Pan-Cancer (PANCAN)"
## [874] "GDC Pan-Cancer (PANCAN)"
## [875] "GDC Pan-Cancer (PANCAN)"
## [876] "GDC Pan-Cancer (PANCAN)"
## [877] "GDC Pan-Cancer (PANCAN)"
## [878] "GDC Pan-Cancer (PANCAN)"
## [879] "GDC Pan-Cancer (PANCAN)"
## [880] "GDC Pan-Cancer (PANCAN)"
## [881] "GDC Pan-Cancer (PANCAN)"
## [882] "GDC Pan-Cancer (PANCAN)"
## [883] "GDC Pan-Cancer (PANCAN)"
## [884] "GDC Pan-Cancer (PANCAN)"
## [885] "GDC Pan-Cancer (PANCAN)"
## [886] "GDC TARGET-RT"
## [887] "GDC TARGET-RT"
## [888] "GDC TARGET-RT"
## [889] "GDC TARGET-RT"
## [890] "GDC TARGET-RT"
## [891] "GDC TARGET-RT"
## [892] "GDC MMRF-COMMPASS"
## [893] "GDC MMRF-COMMPASS"
## [894] "GDC MMRF-COMMPASS"
## [895] "GDC MMRF-COMMPASS"
## [896] "GDC MMRF-COMMPASS"
## [897] "GDC MMRF-COMMPASS"
## [898] "GDC TCGA Mesothelioma (MESO)"
## [899] "GDC TCGA Mesothelioma (MESO)"
## [900] "GDC TCGA Mesothelioma (MESO)"
## [901] "GDC TCGA Mesothelioma (MESO)"
## [902] "GDC TCGA Mesothelioma (MESO)"
## [903] "GDC TCGA Mesothelioma (MESO)"
## [904] "GDC TCGA Mesothelioma (MESO)"
## [905] "GDC TCGA Mesothelioma (MESO)"
## [906] "GDC TCGA Mesothelioma (MESO)"
## [907] "GDC TCGA Mesothelioma (MESO)"
## [908] "GDC TCGA Mesothelioma (MESO)"
## [909] "GDC TCGA Mesothelioma (MESO)"
## [910] "GDC TCGA Mesothelioma (MESO)"
## [911] "GDC TCGA Mesothelioma (MESO)"
## [912] "GDC TCGA Lung Adenocarcinoma (LUAD)"
## [913] "GDC TCGA Lung Adenocarcinoma (LUAD)"
## [914] "GDC TCGA Lung Adenocarcinoma (LUAD)"
## [915] "GDC TCGA Lung Adenocarcinoma (LUAD)"
## [916] "GDC TCGA Lung Adenocarcinoma (LUAD)"
## [917] "GDC TCGA Lung Adenocarcinoma (LUAD)"
## [918] "GDC TCGA Lung Adenocarcinoma (LUAD)"
## [919] "GDC TCGA Lung Adenocarcinoma (LUAD)"
## [920] "GDC TCGA Lung Adenocarcinoma (LUAD)"
## [921] "GDC TCGA Lung Adenocarcinoma (LUAD)"
## [922] "GDC TCGA Lung Adenocarcinoma (LUAD)"
## [923] "GDC TCGA Lung Adenocarcinoma (LUAD)"
## [924] "GDC TCGA Lung Adenocarcinoma (LUAD)"
## [925] "GDC TCGA Lung Adenocarcinoma (LUAD)"
## [926] "GDC TCGA Lung Adenocarcinoma (LUAD)"
## [927] "GDC TCGA Stomach Cancer (STAD)"
## [928] "GDC TCGA Stomach Cancer (STAD)"
## [929] "GDC TCGA Stomach Cancer (STAD)"
## [930] "GDC TCGA Stomach Cancer (STAD)"
## [931] "GDC TCGA Stomach Cancer (STAD)"
## [932] "GDC TCGA Stomach Cancer (STAD)"
## [933] "GDC TCGA Stomach Cancer (STAD)"
## [934] "GDC TCGA Stomach Cancer (STAD)"
## [935] "GDC TCGA Stomach Cancer (STAD)"
## [936] "GDC TCGA Stomach Cancer (STAD)"
## [937] "GDC TCGA Stomach Cancer (STAD)"
## [938] "GDC TCGA Stomach Cancer (STAD)"
## [939] "GDC TCGA Stomach Cancer (STAD)"
## [940] "GDC TCGA Stomach Cancer (STAD)"
## [941] "GDC TCGA Stomach Cancer (STAD)"
## [942] "GDC TCGA Testicular Cancer (TGCT)"
## [943] "GDC TCGA Testicular Cancer (TGCT)"
## [944] "GDC TCGA Testicular Cancer (TGCT)"
## [945] "GDC TCGA Testicular Cancer (TGCT)"
## [946] "GDC TCGA Testicular Cancer (TGCT)"
## [947] "GDC TCGA Testicular Cancer (TGCT)"
## [948] "GDC TCGA Testicular Cancer (TGCT)"
## [949] "GDC TCGA Testicular Cancer (TGCT)"
## [950] "GDC TCGA Testicular Cancer (TGCT)"
## [951] "GDC TCGA Testicular Cancer (TGCT)"
## [952] "GDC TCGA Testicular Cancer (TGCT)"
## [953] "GDC TCGA Testicular Cancer (TGCT)"
## [954] "GDC TCGA Testicular Cancer (TGCT)"
## [955] "GDC TCGA Testicular Cancer (TGCT)"
## [956] "GDC TCGA Ocular melanomas (UVM)"
## [957] "GDC TCGA Ocular melanomas (UVM)"
## [958] "GDC TCGA Ocular melanomas (UVM)"
## [959] "GDC TCGA Ocular melanomas (UVM)"
## [960] "GDC TCGA Ocular melanomas (UVM)"
## [961] "GDC TCGA Ocular melanomas (UVM)"
## [962] "GDC TCGA Ocular melanomas (UVM)"
## [963] "GDC TCGA Ocular melanomas (UVM)"
## [964] "GDC TCGA Ocular melanomas (UVM)"
## [965] "GDC TCGA Ocular melanomas (UVM)"
## [966] "GDC TCGA Ocular melanomas (UVM)"
## [967] "GDC TCGA Ocular melanomas (UVM)"
## [968] "GDC TCGA Ocular melanomas (UVM)"
## [969] "GDC TCGA Ocular melanomas (UVM)"
## [970] "GDC TCGA Pancreatic Cancer (PAAD)"
## [971] "GDC TCGA Pancreatic Cancer (PAAD)"
## [972] "GDC TCGA Pancreatic Cancer (PAAD)"
## [973] "GDC TCGA Pancreatic Cancer (PAAD)"
## [974] "GDC TCGA Pancreatic Cancer (PAAD)"
## [975] "GDC TCGA Pancreatic Cancer (PAAD)"
## [976] "GDC TCGA Pancreatic Cancer (PAAD)"
## [977] "GDC TCGA Pancreatic Cancer (PAAD)"
## [978] "GDC TCGA Pancreatic Cancer (PAAD)"
## [979] "GDC TCGA Pancreatic Cancer (PAAD)"
## [980] "GDC TCGA Pancreatic Cancer (PAAD)"
## [981] "GDC TCGA Pancreatic Cancer (PAAD)"
## [982] "GDC TCGA Pancreatic Cancer (PAAD)"
## [983] "GDC TCGA Pancreatic Cancer (PAAD)"
## [984] "GDC TCGA Glioblastoma (GBM)"
## [985] "GDC TCGA Glioblastoma (GBM)"
## [986] "GDC TCGA Glioblastoma (GBM)"
## [987] "GDC TCGA Glioblastoma (GBM)"
## [988] "GDC TCGA Glioblastoma (GBM)"
## [989] "GDC TCGA Glioblastoma (GBM)"
## [990] "GDC TCGA Glioblastoma (GBM)"
## [991] "GDC TCGA Glioblastoma (GBM)"
## [992] "GDC TCGA Glioblastoma (GBM)"
## [993] "GDC TCGA Glioblastoma (GBM)"
## [994] "GDC TCGA Glioblastoma (GBM)"
## [995] "GDC TCGA Glioblastoma (GBM)"
## [996] "GDC TCGA Glioblastoma (GBM)"
## [997] "GDC TCGA Glioblastoma (GBM)"
## [998] "GDC TCGA Glioblastoma (GBM)"
## [999] "GDC TCGA Colon Cancer (COAD)"
## [1000] "GDC TCGA Colon Cancer (COAD)"
## [1001] "GDC TCGA Colon Cancer (COAD)"
## [1002] "GDC TCGA Colon Cancer (COAD)"
## [1003] "GDC TCGA Colon Cancer (COAD)"
## [1004] "GDC TCGA Colon Cancer (COAD)"
## [1005] "GDC TCGA Colon Cancer (COAD)"
## [1006] "GDC TCGA Colon Cancer (COAD)"
## [1007] "GDC TCGA Colon Cancer (COAD)"
## [1008] "GDC TCGA Colon Cancer (COAD)"
## [1009] "GDC TCGA Colon Cancer (COAD)"
## [1010] "GDC TCGA Colon Cancer (COAD)"
## [1011] "GDC TCGA Colon Cancer (COAD)"
## [1012] "GDC TCGA Colon Cancer (COAD)"
## [1013] "GDC TCGA Colon Cancer (COAD)"
## [1014] "GDC TARGET-NBL"
## [1015] "GDC TARGET-NBL"
## [1016] "GDC TARGET-NBL"
## [1017] "GDC TARGET-NBL"
## [1018] "GDC TARGET-NBL"
## [1019] "GDC TCGA Ovarian Cancer (OV)"
## [1020] "GDC TCGA Ovarian Cancer (OV)"
## [1021] "GDC TCGA Ovarian Cancer (OV)"
## [1022] "GDC TCGA Ovarian Cancer (OV)"
## [1023] "GDC TCGA Ovarian Cancer (OV)"
## [1024] "GDC TCGA Ovarian Cancer (OV)"
## [1025] "GDC TCGA Ovarian Cancer (OV)"
## [1026] "GDC TCGA Ovarian Cancer (OV)"
## [1027] "GDC TCGA Ovarian Cancer (OV)"
## [1028] "GDC TCGA Ovarian Cancer (OV)"
## [1029] "GDC TCGA Ovarian Cancer (OV)"
## [1030] "GDC TCGA Ovarian Cancer (OV)"
## [1031] "GDC TCGA Ovarian Cancer (OV)"
## [1032] "GDC TCGA Ovarian Cancer (OV)"
## [1033] "GDC TCGA Ovarian Cancer (OV)"
## [1034] "GDC TCGA Thymoma (THYM)"
## [1035] "GDC TCGA Thymoma (THYM)"
## [1036] "GDC TCGA Thymoma (THYM)"
## [1037] "GDC TCGA Thymoma (THYM)"
## [1038] "GDC TCGA Thymoma (THYM)"
## [1039] "GDC TCGA Thymoma (THYM)"
## [1040] "GDC TCGA Thymoma (THYM)"
## [1041] "GDC TCGA Thymoma (THYM)"
## [1042] "GDC TCGA Thymoma (THYM)"
## [1043] "GDC TCGA Thymoma (THYM)"
## [1044] "GDC TCGA Thymoma (THYM)"
## [1045] "GDC TCGA Thymoma (THYM)"
## [1046] "GDC TCGA Thymoma (THYM)"
## [1047] "GDC TCGA Thymoma (THYM)"
## [1048] "GDC TCGA Breast Cancer (BRCA)"
## [1049] "GDC TCGA Breast Cancer (BRCA)"
## [1050] "GDC TCGA Breast Cancer (BRCA)"
## [1051] "GDC TCGA Breast Cancer (BRCA)"
## [1052] "GDC TCGA Breast Cancer (BRCA)"
## [1053] "GDC TCGA Breast Cancer (BRCA)"
## [1054] "GDC TCGA Breast Cancer (BRCA)"
## [1055] "GDC TCGA Breast Cancer (BRCA)"
## [1056] "GDC TCGA Breast Cancer (BRCA)"
## [1057] "GDC TCGA Breast Cancer (BRCA)"
## [1058] "GDC TCGA Breast Cancer (BRCA)"
## [1059] "GDC TCGA Breast Cancer (BRCA)"
## [1060] "GDC TCGA Breast Cancer (BRCA)"
## [1061] "GDC TCGA Breast Cancer (BRCA)"
## [1062] "GDC TCGA Breast Cancer (BRCA)"
## [1063] "GDC TCGA Endometrioid Cancer (UCEC)"
## [1064] "GDC TCGA Endometrioid Cancer (UCEC)"
## [1065] "GDC TCGA Endometrioid Cancer (UCEC)"
## [1066] "GDC TCGA Endometrioid Cancer (UCEC)"
## [1067] "GDC TCGA Endometrioid Cancer (UCEC)"
## [1068] "GDC TCGA Endometrioid Cancer (UCEC)"
## [1069] "GDC TCGA Endometrioid Cancer (UCEC)"
## [1070] "GDC TCGA Endometrioid Cancer (UCEC)"
## [1071] "GDC TCGA Endometrioid Cancer (UCEC)"
## [1072] "GDC TCGA Endometrioid Cancer (UCEC)"
## [1073] "GDC TCGA Endometrioid Cancer (UCEC)"
## [1074] "GDC TCGA Endometrioid Cancer (UCEC)"
## [1075] "GDC TCGA Endometrioid Cancer (UCEC)"
## [1076] "GDC TCGA Endometrioid Cancer (UCEC)"
## [1077] "GDC TCGA Endometrioid Cancer (UCEC)"
## [1078] "GDC TCGA Uterine Carcinosarcoma (UCS)"
## [1079] "GDC TCGA Uterine Carcinosarcoma (UCS)"
## [1080] "GDC TCGA Uterine Carcinosarcoma (UCS)"
## [1081] "GDC TCGA Uterine Carcinosarcoma (UCS)"
## [1082] "GDC TCGA Uterine Carcinosarcoma (UCS)"
## [1083] "GDC TCGA Uterine Carcinosarcoma (UCS)"
## [1084] "GDC TCGA Uterine Carcinosarcoma (UCS)"
## [1085] "GDC TCGA Uterine Carcinosarcoma (UCS)"
## [1086] "GDC TCGA Uterine Carcinosarcoma (UCS)"
## [1087] "GDC TCGA Uterine Carcinosarcoma (UCS)"
## [1088] "GDC TCGA Uterine Carcinosarcoma (UCS)"
## [1089] "GDC TCGA Uterine Carcinosarcoma (UCS)"
## [1090] "GDC TCGA Uterine Carcinosarcoma (UCS)"
## [1091] "GDC TCGA Uterine Carcinosarcoma (UCS)"
## [1092] "GDC TARGET-WT"
## [1093] "GDC TARGET-WT"
## [1094] "GDC TARGET-WT"
## [1095] "GDC TARGET-WT"
## [1096] "GDC TARGET-WT"
## [1097] "GDC TARGET-WT"
## [1098] "GDC TARGET-AML"
## [1099] "GDC TARGET-AML"
## [1100] "GDC TARGET-AML"
## [1101] "GDC TARGET-AML"
## [1102] "GDC TARGET-AML"
## [1103] "GDC TARGET-AML"
## [1104] "GDC TCGA Bile Duct Cancer (CHOL)"
## [1105] "GDC TCGA Bile Duct Cancer (CHOL)"
## [1106] "GDC TCGA Bile Duct Cancer (CHOL)"
## [1107] "GDC TCGA Bile Duct Cancer (CHOL)"
## [1108] "GDC TCGA Bile Duct Cancer (CHOL)"
## [1109] "GDC TCGA Bile Duct Cancer (CHOL)"
## [1110] "GDC TCGA Bile Duct Cancer (CHOL)"
## [1111] "GDC TCGA Bile Duct Cancer (CHOL)"
## [1112] "GDC TCGA Bile Duct Cancer (CHOL)"
## [1113] "GDC TCGA Bile Duct Cancer (CHOL)"
## [1114] "GDC TCGA Bile Duct Cancer (CHOL)"
## [1115] "GDC TCGA Bile Duct Cancer (CHOL)"
## [1116] "GDC TCGA Bile Duct Cancer (CHOL)"
## [1117] "GDC TCGA Bile Duct Cancer (CHOL)"
## [1118] "GDC TARGET-OS"
## [1119] "GDC TARGET-OS"
## [1120] "GDC TARGET-OS"
## [1121] "GDC TARGET-OS"
## [1122] "GDC TARGET-OS"
## [1123] "GDC TARGET-OS"
## [1124] "GDC TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [1125] "GDC TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [1126] "GDC TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [1127] "GDC TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [1128] "GDC TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [1129] "GDC TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [1130] "GDC TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [1131] "GDC TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [1132] "GDC TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [1133] "GDC TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [1134] "GDC TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [1135] "GDC TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [1136] "GDC TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [1137] "GDC TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [1138] "GDC TCGA Kidney Clear Cell Carcinoma (KIRC)"
## [1139] "GDC TCGA Adrenocortical Cancer (ACC)"
## [1140] "GDC TCGA Adrenocortical Cancer (ACC)"
## [1141] "GDC TCGA Adrenocortical Cancer (ACC)"
## [1142] "GDC TCGA Adrenocortical Cancer (ACC)"
## [1143] "GDC TCGA Adrenocortical Cancer (ACC)"
## [1144] "GDC TCGA Adrenocortical Cancer (ACC)"
## [1145] "GDC TCGA Adrenocortical Cancer (ACC)"
## [1146] "GDC TCGA Adrenocortical Cancer (ACC)"
## [1147] "GDC TCGA Adrenocortical Cancer (ACC)"
## [1148] "GDC TCGA Adrenocortical Cancer (ACC)"
## [1149] "GDC TCGA Adrenocortical Cancer (ACC)"
## [1150] "GDC TCGA Adrenocortical Cancer (ACC)"
## [1151] "GDC TCGA Adrenocortical Cancer (ACC)"
## [1152] "GDC TCGA Adrenocortical Cancer (ACC)"
## [1153] "GDC TCGA Lower Grade Glioma (LGG)"
## [1154] "GDC TCGA Lower Grade Glioma (LGG)"
## [1155] "GDC TCGA Lower Grade Glioma (LGG)"
## [1156] "GDC TCGA Lower Grade Glioma (LGG)"
## [1157] "GDC TCGA Lower Grade Glioma (LGG)"
## [1158] "GDC TCGA Lower Grade Glioma (LGG)"
## [1159] "GDC TCGA Lower Grade Glioma (LGG)"
## [1160] "GDC TCGA Lower Grade Glioma (LGG)"
## [1161] "GDC TCGA Lower Grade Glioma (LGG)"
## [1162] "GDC TCGA Lower Grade Glioma (LGG)"
## [1163] "GDC TCGA Lower Grade Glioma (LGG)"
## [1164] "GDC TCGA Lower Grade Glioma (LGG)"
## [1165] "GDC TCGA Lower Grade Glioma (LGG)"
## [1166] "GDC TCGA Lower Grade Glioma (LGG)"
## [1167] "GDC TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [1168] "GDC TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [1169] "GDC TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [1170] "GDC TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [1171] "GDC TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [1172] "GDC TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [1173] "GDC TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [1174] "GDC TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [1175] "GDC TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [1176] "GDC TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [1177] "GDC TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [1178] "GDC TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [1179] "GDC TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [1180] "GDC TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [1181] "GDC TCGA Kidney Papillary Cell Carcinoma (KIRP)"
## [1182] "GDC TCGA Kidney Chromophobe (KICH)"
## [1183] "GDC TCGA Kidney Chromophobe (KICH)"
## [1184] "GDC TCGA Kidney Chromophobe (KICH)"
## [1185] "GDC TCGA Kidney Chromophobe (KICH)"
## [1186] "GDC TCGA Kidney Chromophobe (KICH)"
## [1187] "GDC TCGA Kidney Chromophobe (KICH)"
## [1188] "GDC TCGA Kidney Chromophobe (KICH)"
## [1189] "GDC TCGA Kidney Chromophobe (KICH)"
## [1190] "GDC TCGA Kidney Chromophobe (KICH)"
## [1191] "GDC TCGA Kidney Chromophobe (KICH)"
## [1192] "GDC TCGA Kidney Chromophobe (KICH)"
## [1193] "GDC TCGA Kidney Chromophobe (KICH)"
## [1194] "GDC TCGA Kidney Chromophobe (KICH)"
## [1195] "GDC TCGA Kidney Chromophobe (KICH)"
## [1196] "GDC TCGA Thyroid Cancer (THCA)"
## [1197] "GDC TCGA Thyroid Cancer (THCA)"
## [1198] "GDC TCGA Thyroid Cancer (THCA)"
## [1199] "GDC TCGA Thyroid Cancer (THCA)"
## [1200] "GDC TCGA Thyroid Cancer (THCA)"
## [1201] "GDC TCGA Thyroid Cancer (THCA)"
## [1202] "GDC TCGA Thyroid Cancer (THCA)"
## [1203] "GDC TCGA Thyroid Cancer (THCA)"
## [1204] "GDC TCGA Thyroid Cancer (THCA)"
## [1205] "GDC TCGA Thyroid Cancer (THCA)"
## [1206] "GDC TCGA Thyroid Cancer (THCA)"
## [1207] "GDC TCGA Thyroid Cancer (THCA)"
## [1208] "GDC TCGA Thyroid Cancer (THCA)"
## [1209] "GDC TCGA Thyroid Cancer (THCA)"
## [1210] "GDC TARGET-ALL-P3"
## [1211] "GDC TARGET-ALL-P3"
## [1212] "GDC TARGET-ALL-P3"
## [1213] "GDC TARGET-ALL-P3"
## [1214] "GDC TARGET-ALL-P3"
## [1215] "GDC TARGET-ALL-P3"
## [1216] "GDC TCGA Liver Cancer (LIHC)"
## [1217] "GDC TCGA Liver Cancer (LIHC)"
## [1218] "GDC TCGA Liver Cancer (LIHC)"
## [1219] "GDC TCGA Liver Cancer (LIHC)"
## [1220] "GDC TCGA Liver Cancer (LIHC)"
## [1221] "GDC TCGA Liver Cancer (LIHC)"
## [1222] "GDC TCGA Liver Cancer (LIHC)"
## [1223] "GDC TCGA Liver Cancer (LIHC)"
## [1224] "GDC TCGA Liver Cancer (LIHC)"
## [1225] "GDC TCGA Liver Cancer (LIHC)"
## [1226] "GDC TCGA Liver Cancer (LIHC)"
## [1227] "GDC TCGA Liver Cancer (LIHC)"
## [1228] "GDC TCGA Liver Cancer (LIHC)"
## [1229] "GDC TCGA Liver Cancer (LIHC)"
## [1230] "GDC TCGA Head and Neck Cancer (HNSC)"
## [1231] "GDC TCGA Head and Neck Cancer (HNSC)"
## [1232] "GDC TCGA Head and Neck Cancer (HNSC)"
## [1233] "GDC TCGA Head and Neck Cancer (HNSC)"
## [1234] "GDC TCGA Head and Neck Cancer (HNSC)"
## [1235] "GDC TCGA Head and Neck Cancer (HNSC)"
## [1236] "GDC TCGA Head and Neck Cancer (HNSC)"
## [1237] "GDC TCGA Head and Neck Cancer (HNSC)"
## [1238] "GDC TCGA Head and Neck Cancer (HNSC)"
## [1239] "GDC TCGA Head and Neck Cancer (HNSC)"
## [1240] "GDC TCGA Head and Neck Cancer (HNSC)"
## [1241] "GDC TCGA Head and Neck Cancer (HNSC)"
## [1242] "GDC TCGA Head and Neck Cancer (HNSC)"
## [1243] "GDC TCGA Head and Neck Cancer (HNSC)"
## [1244] "GDC TCGA Cervical Cancer (CESC)"
## [1245] "GDC TCGA Cervical Cancer (CESC)"
## [1246] "GDC TCGA Cervical Cancer (CESC)"
## [1247] "GDC TCGA Cervical Cancer (CESC)"
## [1248] "GDC TCGA Cervical Cancer (CESC)"
## [1249] "GDC TCGA Cervical Cancer (CESC)"
## [1250] "GDC TCGA Cervical Cancer (CESC)"
## [1251] "GDC TCGA Cervical Cancer (CESC)"
## [1252] "GDC TCGA Cervical Cancer (CESC)"
## [1253] "GDC TCGA Cervical Cancer (CESC)"
## [1254] "GDC TCGA Cervical Cancer (CESC)"
## [1255] "GDC TCGA Cervical Cancer (CESC)"
## [1256] "GDC TCGA Cervical Cancer (CESC)"
## [1257] "GDC TCGA Cervical Cancer (CESC)"
## [1258] "GDC TCGA Rectal Cancer (READ)"
## [1259] "GDC TCGA Rectal Cancer (READ)"
## [1260] "GDC TCGA Rectal Cancer (READ)"
## [1261] "GDC TCGA Rectal Cancer (READ)"
## [1262] "GDC TCGA Rectal Cancer (READ)"
## [1263] "GDC TCGA Rectal Cancer (READ)"
## [1264] "GDC TCGA Rectal Cancer (READ)"
## [1265] "GDC TCGA Rectal Cancer (READ)"
## [1266] "GDC TCGA Rectal Cancer (READ)"
## [1267] "GDC TCGA Rectal Cancer (READ)"
## [1268] "GDC TCGA Rectal Cancer (READ)"
## [1269] "GDC TCGA Rectal Cancer (READ)"
## [1270] "GDC TCGA Rectal Cancer (READ)"
## [1271] "GDC TCGA Rectal Cancer (READ)"
## [1272] "GDC TCGA Rectal Cancer (READ)"
## [1273] "GDC TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [1274] "GDC TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [1275] "GDC TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [1276] "GDC TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [1277] "GDC TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [1278] "GDC TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [1279] "GDC TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [1280] "GDC TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [1281] "GDC TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [1282] "GDC TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [1283] "GDC TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [1284] "GDC TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [1285] "GDC TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [1286] "GDC TCGA Pheochromocytoma & Paraganglioma (PCPG)"
## [1287] "GDC TARGET-CCSK"
## [1288] "GDC TARGET-CCSK"
## [1289] "GDC TARGET-CCSK"
## [1290] "GDC TARGET-CCSK"
## [1291] "GDC TARGET-CCSK"
## [1292] "GDC TARGET-CCSK"
## [1293] "GDC TCGA Sarcoma (SARC)"
## [1294] "GDC TCGA Sarcoma (SARC)"
## [1295] "GDC TCGA Sarcoma (SARC)"
## [1296] "GDC TCGA Sarcoma (SARC)"
## [1297] "GDC TCGA Sarcoma (SARC)"
## [1298] "GDC TCGA Sarcoma (SARC)"
## [1299] "GDC TCGA Sarcoma (SARC)"
## [1300] "GDC TCGA Sarcoma (SARC)"
## [1301] "GDC TCGA Sarcoma (SARC)"
## [1302] "GDC TCGA Sarcoma (SARC)"
## [1303] "GDC TCGA Sarcoma (SARC)"
## [1304] "GDC TCGA Sarcoma (SARC)"
## [1305] "GDC TCGA Sarcoma (SARC)"
## [1306] "GDC TCGA Sarcoma (SARC)"
## [1307] "GDC TCGA Large B-cell Lymphoma (DLBC)"
## [1308] "GDC TCGA Large B-cell Lymphoma (DLBC)"
## [1309] "GDC TCGA Large B-cell Lymphoma (DLBC)"
## [1310] "GDC TCGA Large B-cell Lymphoma (DLBC)"
## [1311] "GDC TCGA Large B-cell Lymphoma (DLBC)"
## [1312] "GDC TCGA Large B-cell Lymphoma (DLBC)"
## [1313] "GDC TCGA Large B-cell Lymphoma (DLBC)"
## [1314] "GDC TCGA Large B-cell Lymphoma (DLBC)"
## [1315] "GDC TCGA Large B-cell Lymphoma (DLBC)"
## [1316] "GDC TCGA Large B-cell Lymphoma (DLBC)"
## [1317] "GDC TCGA Large B-cell Lymphoma (DLBC)"
## [1318] "GDC TCGA Large B-cell Lymphoma (DLBC)"
## [1319] "GDC TCGA Large B-cell Lymphoma (DLBC)"
## [1320] "GDC TCGA Large B-cell Lymphoma (DLBC)"
## [1321] "GDC TCGA Prostate Cancer (PRAD)"
## [1322] "GDC TCGA Prostate Cancer (PRAD)"
## [1323] "GDC TCGA Prostate Cancer (PRAD)"
## [1324] "GDC TCGA Prostate Cancer (PRAD)"
## [1325] "GDC TCGA Prostate Cancer (PRAD)"
## [1326] "GDC TCGA Prostate Cancer (PRAD)"
## [1327] "GDC TCGA Prostate Cancer (PRAD)"
## [1328] "GDC TCGA Prostate Cancer (PRAD)"
## [1329] "GDC TCGA Prostate Cancer (PRAD)"
## [1330] "GDC TCGA Prostate Cancer (PRAD)"
## [1331] "GDC TCGA Prostate Cancer (PRAD)"
## [1332] "GDC TCGA Prostate Cancer (PRAD)"
## [1333] "GDC TCGA Prostate Cancer (PRAD)"
## [1334] "GDC TCGA Prostate Cancer (PRAD)"
## [1335] "GDC TCGA Acute Myeloid Leukemia (LAML)"
## [1336] "GDC TCGA Acute Myeloid Leukemia (LAML)"
## [1337] "GDC TCGA Acute Myeloid Leukemia (LAML)"
## [1338] "GDC TCGA Acute Myeloid Leukemia (LAML)"
## [1339] "GDC TCGA Acute Myeloid Leukemia (LAML)"
## [1340] "GDC TCGA Acute Myeloid Leukemia (LAML)"
## [1341] "GDC TCGA Acute Myeloid Leukemia (LAML)"
## [1342] "GDC TCGA Acute Myeloid Leukemia (LAML)"
## [1343] "GDC TCGA Acute Myeloid Leukemia (LAML)"
## [1344] "GDC TCGA Acute Myeloid Leukemia (LAML)"
## [1345] "GDC TCGA Acute Myeloid Leukemia (LAML)"
## [1346] "GDC TCGA Acute Myeloid Leukemia (LAML)"
## [1347] "GDC TCGA Acute Myeloid Leukemia (LAML)"
## [1348] "GDC TCGA Acute Myeloid Leukemia (LAML)"
## [1349] "GDC TCGA Acute Myeloid Leukemia (LAML)"
## [1350] "GDC TCGA Melanoma (SKCM)"
## [1351] "GDC TCGA Melanoma (SKCM)"
## [1352] "GDC TCGA Melanoma (SKCM)"
## [1353] "GDC TCGA Melanoma (SKCM)"
## [1354] "GDC TCGA Melanoma (SKCM)"
## [1355] "GDC TCGA Melanoma (SKCM)"
## [1356] "GDC TCGA Melanoma (SKCM)"
## [1357] "GDC TCGA Melanoma (SKCM)"
## [1358] "GDC TCGA Melanoma (SKCM)"
## [1359] "GDC TCGA Melanoma (SKCM)"
## [1360] "GDC TCGA Melanoma (SKCM)"
## [1361] "GDC TCGA Melanoma (SKCM)"
## [1362] "GDC TCGA Melanoma (SKCM)"
## [1363] "GDC TCGA Melanoma (SKCM)"
## [1364] "PACA-AU"
## [1365] "PACA-AU"
## [1366] "ICGC (donor centric)"
## [1367] "ICGC (donor centric)"
## [1368] "ICGC (donor centric)"
## [1369] "ICGC (donor centric)"
## [1370] "ICGC (donor centric)"
## [1371] "ICGC (donor centric)"
## [1372] "ICGC (donor centric)"
## [1373] "ICGC (donor centric)"
## [1374] "ICGC (donor centric)"
## [1375] "ICGC (donor centric)"
## [1376] "ICGC (specimen centric)"
## [1377] "ICGC (specimen centric)"
## [1378] "ICGC (specimen centric)"
## [1379] "ICGC (specimen centric)"
## [1380] "ICGC (specimen centric)"
## [1381] "ICGC (specimen centric)"
## [1382] "ICGC (specimen centric)"
## [1383] "ICGC (specimen centric)"
## [1384] "ICGC (specimen centric)"
## [1385] "ICGC (specimen centric)"
## [1386] "ICGC (specimen centric)"
## [1387] "TCGA TARGET GTEx"
## [1388] "TCGA TARGET GTEx"
## [1389] "TCGA TARGET GTEx"
## [1390] "TCGA TARGET GTEx"
## [1391] "TCGA TARGET GTEx"
## [1392] "TCGA TARGET GTEx"
## [1393] "TCGA TARGET GTEx"
## [1394] "TCGA TARGET GTEx"
## [1395] "TCGA TARGET GTEx"
## [1396] "TCGA TARGET GTEx"
## [1397] "TCGA TARGET GTEx"
## [1398] "TCGA TARGET GTEx"
## [1399] "TCGA TARGET GTEx"
## [1400] "TCGA Pan-Cancer (PANCAN)"
## [1401] "TCGA Pan-Cancer (PANCAN)"
## [1402] "TCGA Pan-Cancer (PANCAN)"
## [1403] "TCGA Pan-Cancer (PANCAN)"
## [1404] "TCGA Pan-Cancer (PANCAN)"
## [1405] "TCGA Pan-Cancer (PANCAN)"
## [1406] "TCGA Pan-Cancer (PANCAN)"
## [1407] "TCGA Pan-Cancer (PANCAN)"
## [1408] "TCGA Pan-Cancer (PANCAN)"
## [1409] "TCGA Pan-Cancer (PANCAN)"
## [1410] "TCGA and TARGET Pan-Cancer (PANCAN)"
## [1411] "TCGA and TARGET Pan-Cancer (PANCAN)"
## [1412] "TCGA and TARGET Pan-Cancer (PANCAN)"
## [1413] "TCGA and TARGET Pan-Cancer (PANCAN)"
## [1414] "TARGET Pan-Cancer (PANCAN)"
## [1415] "TARGET Pan-Cancer (PANCAN)"
## [1416] "TARGET Pan-Cancer (PANCAN)"
## [1417] "TARGET Pan-Cancer (PANCAN)"
## [1418] "TARGET Pan-Cancer (PANCAN)"
## [1419] "TARGET Pan-Cancer (PANCAN)"
## [1420] "TARGET Pan-Cancer (PANCAN)"
## [1421] "TARGET Pan-Cancer (PANCAN)"
## [1422] "TARGET Pan-Cancer (PANCAN)"
## [1423] "TARGET Pan-Cancer (PANCAN)"
## [1424] "TARGET Pan-Cancer (PANCAN)"
## [1425] "TARGET Pan-Cancer (PANCAN)"
## [1426] "GTEX"
## [1427] "GTEX"
## [1428] "GTEX"
## [1429] "GTEX"
## [1430] "GTEX"
## [1431] "GTEX"
## [1432] "GTEX"
## [1433] "GTEX"
## [1434] "GTEX"
## [1435] "GTEX"
## [1436] "GTEX"
## [1437] "TCGA Pan-Cancer (PANCAN)"
## [1438] "TCGA Pan-Cancer (PANCAN)"
## [1439] "TCGA Pan-Cancer (PANCAN)"
## [1440] "TCGA Pan-Cancer (PANCAN)"
## [1441] "TCGA Pan-Cancer (PANCAN)"
## [1442] "TCGA Pan-Cancer (PANCAN)"
## [1443] "TCGA Pan-Cancer (PANCAN)"
## [1444] "TCGA Pan-Cancer (PANCAN)"
## [1445] "TCGA Pan-Cancer (PANCAN)"
## [1446] "TCGA Pan-Cancer (PANCAN)"
## [1447] "TCGA Pan-Cancer (PANCAN)"
## [1448] "TCGA Pan-Cancer (PANCAN)"
## [1449] "TCGA Pan-Cancer (PANCAN)"
## [1450] "TCGA Pan-Cancer (PANCAN)"
## [1451] "TCGA Pan-Cancer (PANCAN)"
## [1452] "TCGA Pan-Cancer (PANCAN)"
## [1453] "TCGA Pan-Cancer (PANCAN)"
## [1454] "TCGA Pan-Cancer (PANCAN)"
## [1455] "TCGA Pan-Cancer (PANCAN)"
## [1456] "TCGA Pan-Cancer (PANCAN)"
## [1457] "TCGA Pan-Cancer (PANCAN)"
## [1458] "TCGA Pan-Cancer (PANCAN)"
## [1459] "Treehouse PED v5 April 2018"
## [1460] "Treehouse PED v5 April 2018"
## [1461] "Treehouse PED v5 April 2018"
## [1462] "Treehouse PED v8"
## [1463] "Treehouse PED v8"
## [1464] "Treehouse PED v8"
## [1465] "Vaske 2019 comparative tumor RNA Participants"
## [1466] "Vaske 2019 comparative tumor RNA Participants"
## [1467] "Treehouse Tumor Compendium v11 Public PolyA"
## [1468] "Treehouse Tumor Compendium v11 Public PolyA"
## [1469] "Treehouse Tumor Compendium v11 Public PolyA"
## [1470] "Treehouse Tumor Compendium v10 Public PolyA"
## [1471] "Treehouse Tumor Compendium v10 Public PolyA"
## [1472] "Treehouse Tumor Compendium v10 Public PolyA"
## [1473] "Treehouse PED v9 polyA"
## [1474] "Treehouse PED v9 polyA"
## [1475] "Treehouse PED v9 polyA"
## [1476] "Treehouse PED v9 Ribodeplete"
## [1477] "Treehouse PED v9 Ribodeplete"
## [1478] "Treehouse PED v9 Ribodeplete"
## [1479] "Treehouse Cell Line Compendium v1"
## [1480] "Treehouse Cell Line Compendium v1"
## [1481] "Treehouse Cell Line Compendium v2"
## [1482] "Treehouse Cell Line Compendium v2"
## [1483] "Vaske 2019 comparative tumor RNA Reference Compendium"
## [1484] "Vaske 2019 comparative tumor RNA Reference Compendium"
## [1485] "Treehouse public expression dataset (July 2017)"
## [1486] "Treehouse public expression dataset (July 2017)"
## [1487] "Treehouse public expression dataset (July 2017)"
## [1488] "Treehouse Tumor Compendium 21.02 Public Hybrid Capture"
## [1489] "Treehouse Tumor Compendium 21.02 Public Hybrid Capture"
## [1490] "PCAWG (donor centric)"
## [1491] "PCAWG (donor centric)"
## [1492] "PCAWG (donor centric)"
## [1493] "PCAWG (donor centric)"
## [1494] "PCAWG (donor centric)"
## [1495] "PCAWG (donor centric)"
## [1496] "PCAWG (donor centric)"
## [1497] "PCAWG (donor centric)"
## [1498] "PCAWG (donor centric)"
## [1499] "PCAWG (donor centric)"
## [1500] "PCAWG (donor centric)"
## [1501] "PCAWG (donor centric)"
## [1502] "PCAWG (donor centric)"
## [1503] "PCAWG (donor centric)"
## [1504] "PCAWG (donor centric)"
## [1505] "PCAWG (donor centric)"
## [1506] "PCAWG (donor centric)"
## [1507] "PCAWG (donor centric)"
## [1508] "PCAWG (donor centric)"
## [1509] "PCAWG (donor centric)"
## [1510] "PCAWG (donor centric)"
## [1511] "PCAWG (donor centric)"
## [1512] "PCAWG (donor centric)"
## [1513] "PCAWG (donor centric)"
## [1514] "PCAWG (donor centric)"
## [1515] "PCAWG (donor centric)"
## [1516] "PCAWG (specimen centric)"
## [1517] "PCAWG (specimen centric)"
## [1518] "PCAWG (specimen centric)"
## [1519] "PCAWG (specimen centric)"
## [1520] "PCAWG (specimen centric)"
## [1521] "PCAWG (specimen centric)"
## [1522] "PCAWG (specimen centric)"
## [1523] "PCAWG (specimen centric)"
## [1524] "PCAWG (specimen centric)"
## [1525] "PCAWG (specimen centric)"
## [1526] "PCAWG (specimen centric)"
## [1527] "PCAWG (specimen centric)"
## [1528] "PCAWG (specimen centric)"
## [1529] "PCAWG (specimen centric)"
## [1530] "PCAWG (specimen centric)"
## [1531] "PCAWG (specimen centric)"
## [1532] "PCAWG (specimen centric)"
## [1533] "PCAWG (specimen centric)"
## [1534] "PCAWG (specimen centric)"
## [1535] "PCAWG (specimen centric)"
## [1536] "PCAWG (specimen centric)"
## [1537] "PCAWG (specimen centric)"
## [1538] "PCAWG (specimen centric)"
## [1539] "PCAWG (specimen centric)"
## [1540] "PCAWG (specimen centric)"
## [1541] "PCAWG (specimen centric)"
## [1542] "PCAWG (specimen centric)"
## [1543] "GDC Pan-Cancer (PANCAN)"
## [1544] "GDC Pan-Cancer (PANCAN)"
## [1545] "GDC Pan-Cancer (PANCAN)"
## [1546] "GDC Pan-Cancer (PANCAN)"
## [1547] "GDC TCGA Breast Cancer (BRCA)"
## [1548] "GDC TCGA Breast Cancer (BRCA)"
## [1549] "GDC TCGA Breast Cancer (BRCA)"
## [1550] "GDC TCGA Breast Cancer (BRCA)"
## [1551] "GDC TCGA Breast Cancer (BRCA)"
## [1552] "Human brain (Darmanis 2015)"
## [1553] "Human brain (Darmanis 2015)"
## [1554] "Human brain (Darmanis 2015)"
## [1555] "Longitudinal Lung Cancer scRNA (Bivona 2020)"
## [1556] "Longitudinal Lung Cancer scRNA (Bivona 2020)"
## [1557] "Longitudinal Lung Cancer scRNA (Bivona 2020)"
## [1558] "Longitudinal Lung Cancer scRNA (Bivona 2020)"
## [1559] "Longitudinal Lung Cancer scRNA (Bivona 2020)"
## [1560] "Longitudinal Lung Cancer scRNA (Bivona 2020)"
## [1561] "Longitudinal Lung Cancer scRNA (Bivona 2020)"
## [1562] "Longitudinal Lung Cancer scRNA (Bivona 2020)"
## [1563] "Longitudinal Lung Cancer scRNA (Bivona 2020)"
## [1564] "Longitudinal Lung Cancer scRNA (Bivona 2020)"
## [1565] "Longitudinal Lung Cancer scRNA (Bivona 2020)"
## [1566] "Longitudinal Lung Cancer scRNA (Bivona 2020)"
## [1567] "Longitudinal Lung Cancer scRNA (Bivona 2020)"
## [1568] "Longitudinal Lung Cancer scRNA (Bivona 2020)"
## [1569] "NucSeq from human control eyes (scRNASeq)"
## [1570] "NucSeq from human control eyes (scRNASeq)"
## [1571] "Mouse cortex and hippocampus (Zeisel 2015)"
## [1572] "Mouse cortex and hippocampus (Zeisel 2015)"
## [1573] "Mouse cortex and hippocampus (Zeisel 2015)"
## [1574] "Mouse cortex and hippocampus (Zeisel 2015)"
## [1575] "t-CyCIF RCC (Sorger 2018)"
## [1576] "t-CyCIF RCC (Sorger 2018)"
## [1577] "t-CyCIF RCC (Sorger 2018)"
## [1578] "t-CyCIF RCC (Sorger 2018)"
## [1579] "t-CyCIF RCC (Sorger 2018)"
## [1580] "t-CyCIF RCC (Sorger 2018)"
## [1581] "t-CyCIF PDAC (Sorger 2018)"
## [1582] "t-CyCIF PDAC (Sorger 2018)"
## [1583] "t-CyCIF PDAC (Sorger 2018)"
## [1584] "t-CyCIF PDAC (Sorger 2018)"
## [1585] "t-CyCIF PDAC (Sorger 2018)"
## [1586] "t-CyCIF PDAC (Sorger 2018)"
## [1587] "UCSC Cell Browser Cortex Development"
## [1588] "UCSC Cell Browser Cortex Development"
## [1589] "Visium V1_Adult_Mouse_Brain"
## [1590] "Visium V1_Adult_Mouse_Brain"
## [1591] "Visium V1_Adult_Mouse_Brain"
## [1592] "Visium V1_Adult_Mouse_Brain"
## [1593] "Visium V1_Adult_Mouse_Brain"
## [1594] "Visium V1_Adult_Mouse_Brain"
## [1595] "HCA Adult Retina (Wong)"
## [1596] "HCA Adult Retina (Wong)"
## [1597] "visium V1_Breast_Cancer_Block_A_Section_1"
## [1598] "visium V1_Breast_Cancer_Block_A_Section_1"
## [1599] "visium V1_Breast_Cancer_Block_A_Section_1"
## [1600] "UCSC Cell Browser Autism"
## [1601] "UCSC Cell Browser Autism"
## [1602] "HCA Human Pancreas"
## [1603] "HCA Human Pancreas"
## [1604] "HCA Human Pancreas"
## [1605] "HCA Human Pancreas"
## [1606] "HCA Human Pancreas"
## [1607] "UCSC Cell Browser Multiple Sclerosis"
## [1608] "UCSC Cell Browser Multiple Sclerosis"
## [1609] "HCA Census of Immune Cells"
## [1610] "HCA Census of Immune Cells"
## [1611] "HCA Census of Immune Cells"
## [1612] "Head and Neck Cancer (Puram 2017)"
## [1613] "Head and Neck Cancer (Puram 2017)"
## [1614] "Head and Neck Cancer (Puram 2017)"
## [1615] "Head and Neck Cancer (Puram 2017)"
## [1616] "Head and Neck Cancer (Puram 2017)"
## [1617] "Head and Neck Cancer (Puram 2017)"
## [1618] "Head and Neck Cancer (Puram 2017)"
## [1619] "Head and Neck Cancer (Puram 2017)"
## [1620] "Head and Neck Cancer (Puram 2017)"
## [1621] "osmFish mouse somatosensory cortex (Linnarsson Lab)"
## [1622] "osmFish mouse somatosensory cortex (Linnarsson Lab)"
## [1623] "TCGA TARGET GTEx KidsFirst"
## [1624] "TCGA TARGET GTEx KidsFirst"
## [1625] "TCGA TARGET GTEx KidsFirst"
## [1626] "TCGA TARGET GTEx KidsFirst"
## [1627] "TCGA TARGET GTEx KidsFirst"
## [1628] "TCGA TARGET GTEx KidsFirst"
## [1629] "TCGA TARGET GTEx KidsFirst"
## [1630] "Pediatric Brain Tumor Atlas: PNOC"
## [1631] "Pediatric Brain Tumor Atlas: PNOC"
## [1632] "Pediatric Brain Tumor Atlas: PNOC"
## [1633] "Pediatric Brain Tumor Atlas: PNOC"
## [1634] "Pediatric Brain Tumor Atlas: PNOC"
## [1635] "Pediatric Brain Tumor Atlas: PNOC"
## [1636] "Pediatric Brain Tumor Atlas: PNOC"
## [1637] "Pediatric Brain Tumor Atlas: PNOC"
## [1638] "Pediatric Brain Tumor Atlas: PNOC"
## [1639] "Pediatric Brain Tumor Atlas: PNOC"
## [1640] "Pediatric Brain Tumor Atlas: PNOC"
## [1641] "Pediatric Brain Tumor Atlas: PNOC"
## [1642] "Pediatric Brain Tumor Atlas: PNOC"
## [1643] "Pediatric Brain Tumor Atlas: PNOC"
## [1644] "Pediatric Brain Tumor Atlas: PNOC"
## [1645] "Pediatric Brain Tumor Atlas: PNOC"
## [1646] "Pediatric Brain Tumor Atlas: PNOC"
## [1647] "Pediatric Brain Tumor Atlas: PNOC"
## [1648] "Pediatric Brain Tumor Atlas: PNOC"
## [1649] "Pediatric Brain Tumor Atlas: PNOC"
## [1650] "Pediatric Brain Tumor Atlas: PNOC"
## [1651] "Pediatric Brain Tumor Atlas: PNOC"
## [1652] "Pediatric Brain Tumor Atlas: CBTTC"
## [1653] "Pediatric Brain Tumor Atlas: CBTTC"
## [1654] "Pediatric Brain Tumor Atlas: CBTTC"
## [1655] "Pediatric Brain Tumor Atlas: CBTTC"
## [1656] "Pediatric Brain Tumor Atlas: CBTTC"
## [1657] "Pediatric Brain Tumor Atlas: CBTTC"
## [1658] "Pediatric Brain Tumor Atlas: CBTTC"
## [1659] "Pediatric Brain Tumor Atlas: CBTTC"
## [1660] "Pediatric Brain Tumor Atlas: CBTTC"
## [1661] "Pediatric Brain Tumor Atlas: CBTTC"
## [1662] "Pediatric Brain Tumor Atlas: CBTTC"
## [1663] "Pediatric Brain Tumor Atlas: CBTTC"
## [1664] "Pediatric Brain Tumor Atlas: CBTTC"
## [1665] "Pediatric Brain Tumor Atlas: CBTTC"
## [1666] "Pediatric Brain Tumor Atlas: CBTTC"
## [1667] "Pediatric Brain Tumor Atlas: CBTTC"
## [1668] "Pediatric Brain Tumor Atlas: CBTTC"
## [1669] "Pediatric Brain Tumor Atlas: CBTTC"
## [1670] "Pediatric Brain Tumor Atlas: CBTTC"
## [1671] "Pediatric Brain Tumor Atlas: CBTTC"
## [1672] "Pediatric Brain Tumor Atlas: CBTTC"
# The code below loads the phenotype (clinical) data from the GDC / Bladder Cancer
# patient cohort, which is stored in 'blca_pheno'
blca <- XenaData %>% filter(XenaCohorts == 'GDC TCGA Bladder Cancer (BLCA)')
cli_query = blca %>%
filter(Label == "Phenotype") %>% # select clinical dataset
XenaGenerate() %>% # generate a XenaHub object
XenaQuery() %>% # generate the query
XenaDownload() # download the data
## This will check url status, please be patient.
## All downloaded files will under directory /var/folders/09/wnhgpdlj4nq0h2yqc5hv88rh17kp1y/T//Rtmp4B7M3Y.
## The 'trans_slash' option is FALSE, keep same directory structure as Xena.
## Creating directories for datasets...
## Downloading TCGA-BLCA.GDC_phenotype.tsv.gz
# This prepares (loads) the dataset into R
blca_pheno <- XenaPrepare(cli_query)
head(blca_pheno)
## # A tibble: 6 x 134
## submitter_id.samples additional_pharmac… additional_radia… additional_surgery…
## <chr> <chr> <chr> <chr>
## 1 TCGA-DK-A2I6-01A <NA> <NA> <NA>
## 2 TCGA-FD-A43X-01A <NA> <NA> <NA>
## 3 TCGA-GC-A4ZW-01A <NA> <NA> <NA>
## 4 TCGA-FD-A5C0-01A <NA> <NA> <NA>
## 5 TCGA-GU-AATO-01A <NA> <NA> <NA>
## 6 TCGA-H4-A2HQ-01A <NA> <NA> <NA>
## # … with 130 more variables:
## # additional_treatment_completion_success_outcome <chr>,
## # age_at_initial_pathologic_diagnosis <dbl>,
## # age_began_smoking_in_years <dbl>, batch_number <chr>, bcr <chr>,
## # bcr_followup_barcode <chr>, bcr_followup_uuid <chr>, submitter_id <chr>,
## # bladder_carcinoma_extracapsular_extension_status <chr>,
## # chemical_exposure_text <chr>, clinical_T <chr>, …
Question 6 -- [5 / 5 points] ✅
# 6) Find the mean and median age of a patient from this cohort. The age information
# can be found in the 'age_at_index.demographic' column.
mean_b=mean(blca_pheno$age_at_index.demographic)
mean_b
## [1] 68.15198
median_b=median(blca_pheno$age_at_index.demographic)
median_b
## [1] 69
Question 7 -- [4 / 5 points] ❌You should use ggplot for this. Your graph also needs a title.
# 7) Construct a frequency bar graph showing the race of each patient.
# Race information is contained in the 'race.demographic' column.
table_race=table(blca_pheno$race.demographic)
barplot(table_race,col="sky blue")

Question 8 -- [10 / 10 points] ✅
# 8) (a) Load the phenotype data for the cohort: 'GDC TCGA Thyroid Cancer (THCA)'
# The code below loads the phenotype (clinical) data from the GDC / Bladder Cancer
# patient cohort, which is stored in 'blca_pheno'
thca <- XenaData %>% filter(XenaCohorts == 'GDC TCGA Thyroid Cancer (THCA)')
cli_query = thca %>%
filter(Label == "Phenotype") %>% # select clinical dataset
XenaGenerate() %>% # generate a XenaHub object
XenaQuery() %>% # generate the query
XenaDownload() # download the data
## This will check url status, please be patient.
## All downloaded files will under directory /var/folders/09/wnhgpdlj4nq0h2yqc5hv88rh17kp1y/T//Rtmp4B7M3Y.
## The 'trans_slash' option is FALSE, keep same directory structure as Xena.
## Creating directories for datasets...
## Downloading TCGA-THCA.GDC_phenotype.tsv.gz
# This prepares (loads) the dataset into R
thca_pheno <- XenaPrepare(cli_query)
head(thca_pheno)
## # A tibble: 6 x 114
## submitter_id.samples age_at_initial_pa… batch_number bcr bcr_followup_ba…
## <chr> <dbl> <chr> <chr> <chr>
## 1 TCGA-BJ-A28W-01A 32 149.85.0 Nationw… TCGA-BJ-A28W-F4…
## 2 TCGA-BJ-A28W-11A 32 149.85.0 Nationw… TCGA-BJ-A28W-F4…
## 3 TCGA-EM-A1CT-01A 76 115.87.0 Nationw… TCGA-EM-A1CT-F3…
## 4 TCGA-EM-A1CT-11A 76 115.87.0 Nationw… TCGA-EM-A1CT-F3…
## 5 TCGA-EL-A4JZ-01A 55 270.67.0 Nationw… TCGA-EL-A4JZ-F5…
## 6 TCGA-EL-A4JZ-11A 55 270.67.0 Nationw… TCGA-EL-A4JZ-F5…
## # … with 109 more variables: bcr_followup_uuid <chr>, submitter_id <chr>,
## # braf_gene_genotyping_outcome_lab_results_text <chr>,
## # day_of_dcc_upload <dbl>, day_of_form_completion <dbl>,
## # days_to_initial_pathologic_diagnosis <dbl>,
## # extrathyroid_carcinoma_present_extension_status <chr>, file_uuid <chr>,
## # followup_case_report_form_submission_reason <chr>,
## # genotype_analysis_performed_indicator <chr>, …
# (b) How many patients (rows) are in this cohort?
nrow(thca_pheno)
## [1] 615
# (c) Construct a relative frequency table showing for the anatomical
# site of the thyroid tumor. Note: this information is in the
# column: 'primary_thyroid_gland_neoplasm_location_anatomic_site'
# Note: the thyroid gland is responsible for producing hormones that
# regulate body temperature and heart rate, among others.
# An diagram of the thyroid gland can be seen here:
# https://generalsurgery.ucsf.edu/conditions--procedures/thyroid-cancer.aspx
table_ana=table(thca_pheno$primary_thyroid_gland_neoplasm_location_anatomic_site)
rel_tab=table_ana/615
rel_tab
##
## Bilateral Isthmus Left lobe Right lobe
## 0.15284553 0.04390244 0.35772358 0.43414634