There are times, we come across to

1. Find common genes between two pathways/lists
2. Find genes that are unique to list 1 excluding common genes between two lists
3. Find genes that are unique to list 2, excluding common genes between two lists

Following note is an R code examples to do above tasks. For this you would need to R (grab latest version) and  dplyr package (again, grab latest package).

Before we dive into the code execution, let me briefly explain join function we will be using below. Join function does what it says. It joins.  When we say join, we need to tell program how to join two gene lists (L1 and L2). Both the gene lists (L1 and L2) should have same column names for gene lists and other columns. For eg. If list 1 has gene names under column named "Genes", list2 column with gene names should have title "Genes".

When joining, there can be three types of joining: Genes  common between two lists (called inner_join),Genes unique to list 1 only (exclude common genes and list2 genes) and Genes unique to list 2 only (exclude common genes and list2 genes). Common genes are those genes which are common between list1 and list 2. Now let us get to work:

Let us assume that we have two gene lists: L1 and L2 with following genes and they also have expression trends.

------------------------------------------------------------------------------
L1
------------------------------------------------------------------------------
            gene           Expression

1. RARA            up
2. RNF40          down
3. RUVBL2       down
4. SETD1A       down
5. ACTR8         down

------------------------------------------------------------------------------
L2
------------------------------------------------------------------------------

               gene         Expression

1. ACTL6A         down
2. ACTL6B         up
3. ACTR5           up
4. ACTR8           down

 -------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Common genes between L1 and L2:
------------------------------------------------------------------------------
Let us find out the common genes between L1 and L2:

_____________________________________________

Code
______________________________________________
$ library(dplyr)
$ inner_join(L1,L2)
 
Output:
 Joining, by = c("gene", "Expression")
    gene            Expression
1 ACTR8         down
==================================================

--------------------------------------------------------------------------------
Genes unique to L1 (exclude common genes and genes in L2)
--------------------------------------------------------------------------------
Let us find out the unique genes to L1:
_____________________________________________

Code
______________________________________________
$ library(dplyr)
$ anti_join(L1,L2) #Note L1 is on left side
 
Output:
 Joining, by = c("gene", "Expression")
    gene            Expression
1 SETD1A       down
2 RUVBL2       down
3 RNF40          down
4 RARA           up


==================================================

----------------------------------------------------------------------------------
Genes unique to L2 (exclude common genes and genes in L1)
-----------------------------------------------------------------------------------
Let us find out the unique genes to L2:
_____________________________________________

Code
______________________________________________
$ library(dplyr)
$ anti_join(L2,L1) #Note L1 is on right side
 
Output:
 Joining, by = c("gene", "Expression")
    gene            Expression
1  ACTR5         up
2 ACTL6B        up
3 ACTL6A        down