eTME_signatures: Empirically-defined Immune Signature Genes in RCC Bulk Tumor

In DisHet: Estimate the Gene Expression Levels and Component Proportions of the Normal, Stroma (Immune) and Tumor Components of Bulk Tumor Samples

Description

Based on DisHet analysis of 35 RCC trio RNA-Seq data, we defined immune-specific genes with empirical evidence, named eTME, for empirically-defined immune signature of tumor. Using eTME, we refined previously published Immunome signatures. We also assigned other eTME genes to specific immune cell types using the BLUEPRINT project data. These two sets of refined gene signatures were consolidated and documented in the DisHet R package as the "eTME" immune cell gene signatures.

Usage

data("eTME_signatures")

Format

A List contains 2 lists of signatures:the 1st list "signatures_gene" contains the signatures on gene level, and the 2nd list "signatures_mRNA" contains the signatures on mRNA level. Both lists contain 25 items/vectors.

'M2 macrophages'

: a vector of genes/mRNA that are abundantly expressed in M2 macrophages

'M1 macrophages'

: a vector of genes/mRNA that are abundantly expressed in M1 macrophages

Macrophages

: a vector of genes/mRNA that are abundantly expressed in Macrophages

Monocytes

: a vector of genes/mRNA that are abundantly expressed in Monocytes

'B cells'

: a vector of genes/mRNA that are abundantly expressed in B cells

'CD8 T cells'

: a vector of genes/mRNA that are abundantly expressed in CD8 T cells

'T cells'

: a vector of genes/mRNA that are abundantly expressed in T cells

'Dendritic cells'

: a vector of genes/mRNA that are abundantly expressed in Dendritic cells

'CD56dim NK cells'

: a vector of genes/mRNA that are abundantly expressed in CD56dim NK cells

'CD56bright NK cells'

: a vector of genes/mRNA that are abundantly expressed in CD56bright NK cells

'NK cells'

: a vector of genes/mRNA that are abundantly expressed in NK cells

'Endothelial cells'

: a vector of genes/mRNA that are abundantly expressed in Endothelial cells

Eosinophils

: a vector of genes/mRNA that are abundantly expressed in Eosinophils

Neutrophils

: a vector of genes/mRNA that are abundantly expressed in Neutrophils

'Treg cells'

: a vector of genes/mRNA that are abundantly expressed in Treg cells

'Th1 cells'

: a vector of genes/mRNA that are abundantly expressed in Th1 cells

'Th2 cells'

: a vector of genes/mRNA that are abundantly expressed in Th2 cells

'Tfh cells'

: a vector of genes/mRNA that are abundantly expressed in Tfh cells

'Th cells'

: a vector of genes/mRNA that are abundantly expressed in Th cells

aDCs

: a vector of genes/mRNA that are abundantly expressed in aDCs

iDCs

: a vector of genes/mRNA that are abundantly expressed in iDCs

pDCs

: a vector of genes/mRNA that are abundantly expressed in pDCs

'Mast cells'

: a vector of genes/mRNA that are abundantly expressed in Mast cells

'Tm cells'

: a vector of genes/mRNA that are abundantly expressed in Tm cells

Pericytes

: a vector of genes/mRNA that are abundantly expressed in Pericytes

Examples

data(eTME_signatures)
eTME_signatures$signatures_gene$Macrophages
eTME_signatures$signatures_mRNA$Macrophages
eTME_signatures$signatures_gene$`T cells`
eTME_signatures$signatures_mRNA$`T cells`

Example output

Loading required package: gtools
Loading required package: matrixStats
 [1] "COL8A2"    "CTSK"      "CD84"      "CHI3L1"    "CHIT1"     "MARCO"    
 [7] "JAKMIP2"   "GPNMB"     "CLEC5A"    "MSR1"      "MS4A4A"    "LINC00900"
[13] "KCNJ5"     "CD163"     "EMP1"      "BCAT1"     "RGCC"      "COLEC12"  
[19] "APOE"      "CECR1"     "CYBB"     
  [1] "NM_005202"    "AK074129"     "NM_001294347" "BC096296"     "NM_000396"   
  [6] "CU677571"     "NM_001184882" "NM_003874"    "AK296290"     "NM_001184879"
 [11] "Y12632"       "NM_001184881" "U96627"       "AF054818"     "AK095458"    
 [16] "NM_001276"    "BC038354"     "BX648308"     "E01500"       "AK131093"    
 [21] "NM_003465"    "U62662"       "NM_001256125" "AK309341"     "KJ896600"    
 [26] "NM_001243266" "NM_148975"    "AK075081"     "CU676600"     "AB013102"    
 [31] "AK090602"     "AK309234"     "AK307308"     "NM_000890"    "BC069571"    
 [36] "L47208"       "NM_004244"    "Z22970"       "BC051281"     "Z22968"      
 [41] "Z22971"       "NM_203416"    "DQ058615"     "NM_001423"    "AK310798"    
 [46] "Y07909"       "AK308505"     "AK299388"     "BC047300"     "U43916"      
 [51] "NM_005504"    "NM_001178094" "NM_001178092" "NM_001178093" "AK294879"    
 [56] "NM_001178091" "BC033864"     "KJ901300"     "AK056255"     "NM_014059"   
 [61] "AK095079"     "NM_130386"    "AB052103"     "NM_001302691" "AK314898"    
 [66] "AK308546"     "NM_001302688" "NM_006770"    "AK301407"     "AF035819"    
 [71] "NM_001282226" "NM_001282229" "NM_001282228" "BC051755"     "NM_177405"   
 [76] "AF190746"     "AB462971"     "AK292689"     "AK314321"     "NM_001270941"
 [81] "NM_001270934" "NM_014790"    "NM_001282282" "KJ892861"     "BC003189"    
 [86] "CU689536"     "CU679974"     "NM_002510"    "NM_001005340" "AJ505015"    
 [91] "AK297051"     "AK312279"     "AK297055"     "AK303071"     "NM_013252"   
 [96] "AK307095"     "NM_001301167" "AK292766"     "AK313703"     "KJ893413"    
[101] "NM_138716"    "NM_138715"    "AK293217"     "AF037351"     "AK293409"    
[106] "NM_002445"    "E03268"       "NM_000397"    "AK301476"    
 [1] "LCK"    "CD2"    "CD28"   "TRAT1"  "CD96"   "TRBC1"  "GIMAP5" "CD6"   
 [9] "CD3E"   "CD3D"   "CD3G"   "TRAC"   "BCL11B" "ITM2A"  "SH2D1A"
 [1] "U23852"       "NM_005356"    "AJ865079"     "X05027"       "NM_001042771"
 [6] "AK303073"     "BC013200"     "AF228313"     "NM_001767"    "AK313614"    
[11] "NM_006725"    "AK312749"     "BC078669"     "DQ786330"     "U66145"      
[16] "NM_001254750" "NM_001254751" "U66146"       "AK126159"     "NM_000733"   
[21] "AK301255"     "AK311641"     "BC033578"     "X03884"       "NM_000732"   
[26] "BC070321"     "NM_001040651" "AK299997"     "AK313966"     "AK310622"    
[31] "NM_000073"    "AK310578"     "BC063385"     "BC020840"     "NM_138576"   
[36] "NM_022898"    "AB057670"     "NM_001243078" "AJ517504"     "NM_006139"   
[41] "NM_016388"    "AK291991"     "AJ240085"     "NM_005816"    "NM_198196"   
[46] "BC020749"     "AK290719"     "KJ902078"     "X63456"       "BC073797"    
[51] "AK002158"     "NM_018384"    "BC033688"     "BC011732"     "DQ341455"    
[56] "NM_004867"    "NM_001171581" "AY359051"     "AK303238"     "CU691874"    
[61] "AL023657"     "NM_002351"    "NM_001114937" "AF100542"     "AF100540"    
[66] "AF100543"    

DisHet documentation built on May 2, 2019, 2:42 a.m.