Integrated analysis for delineation of cooperative effects of signature miRNAs and DNA methylation on gene expression

load miRNA data

load gene expression data

Prepare clinical data

Clinical data

Approach predicted miRNA targets

## [1] TRUE

## 
##  TRUE 
## 23207

## Searching diana_microt ...
## Searching elmmo ...
## Searching microcosm ...
## Searching miranda ...
## Searching mirdb ...
## Searching pictar ...
## Searching pita ...
## Searching targetscan ...
## Searching diana_microt ...
## Searching elmmo ...
## Searching microcosm ...
## Searching miranda ...
## Searching mirdb ...
## Searching pictar ...
## Searching pita ...
## Searching targetscan ...
## Searching diana_microt ...
## Searching elmmo ...
## Searching microcosm ...
## Searching miranda ...
## Searching mirdb ...
## Searching pictar ...
## Searching pita ...
## Searching targetscan ...
## Searching diana_microt ...
## Searching elmmo ...
## Searching microcosm ...
## Searching miranda ...
## Searching mirdb ...
## Searching pictar ...
## Searching pita ...
## Searching targetscan ...

## 
## FALSE  TRUE 
##  2658     9

## 
## FALSE  TRUE 
##  2701    16

## 
## FALSE  TRUE 
##  1607     3

## 
## FALSE  TRUE 
##  2605     8

## [1] AGBL2    C11orf57 C15orf52 EFEMP1   EIF4G2   LNX1     PAX6     PHB2    
## [9] SLC7A8  
## 12792 Levels: A2BP1 A2ML1 A4GALT A4GNT AAAS AACS AADACL2 AADAT AAGAB AAK1 ... ZZZ3

##  [1] CREBZF  DNAH10  ELF5    IFIT5   LIMD2   LYPLA2  MGEA5   MLF2    NFASC  
## [10] ONECUT2 RNF121  RPS6KL1 RRM2    TOMM40  TTC1    ZNF445 
## 12792 Levels: A2BP1 A2ML1 A4GALT A4GNT AAAS AACS AADACL2 AADAT AAGAB AAK1 ... ZZZ3

## [1] KCNQ1 KRT8  PLEK 
## 12792 Levels: A2BP1 A2ML1 A4GALT A4GNT AAAS AACS AADACL2 AADAT AAGAB AAK1 ... ZZZ3

## [1] ADHFE1 BCAN   EIF4G2 PAWR   SF3B1  TCF4   ZNF282 ZNF555
## 12792 Levels: A2BP1 A2ML1 A4GALT A4GNT AAAS AACS AADACL2 AADAT AAGAB AAK1 ... ZZZ3

table output integrated analysis mRNA miRNA DNAmeth predicted miRNA targets

## Finished

## Finished

## Finished

## Finished

Get Pubmedresults for predicted miRNA targets

data table predicted miRNA targets

Approach with cancer gene census genes

## 
## FALSE 
##   546

## 
## FALSE  TRUE 
##   537     9

## 
## FALSE  TRUE 
##   545     1

## 
## FALSE  TRUE 
##   544     2

## factor(0)
## 12792 Levels: A2BP1 A2ML1 A4GALT A4GNT AAAS AACS AADACL2 AADAT AAGAB AAK1 ... ZZZ3

## [1] BRCA1  DNM2   ESR1   LMO2   MDM4   MLLT10 PTEN   SND1   WT1   
## 12792 Levels: A2BP1 A2ML1 A4GALT A4GNT AAAS AACS AADACL2 AADAT AAGAB AAK1 ... ZZZ3

## [1] CSF1R
## 12792 Levels: A2BP1 A2ML1 A4GALT A4GNT AAAS AACS AADACL2 AADAT AAGAB AAK1 ... ZZZ3

## [1] PTEN  SF3B1
## 12792 Levels: A2BP1 A2ML1 A4GALT A4GNT AAAS AACS AADACL2 AADAT AAGAB AAK1 ... ZZZ3

Generate table oputput cancer gene consensus

## Finished

## Finished
## Pass returnall=TRUE to return lists of duplicate or missing query terms.

## Finished

Get Pubmedresults for CGC genes

data table CGC genes