gene-gene correlation from two different Tissues
You can use mapply(). ta and tb being transposed data frames of your A and B data frames respectively:
&gt; mapply(cor, ta, tb)[mapply(cor, ta, tb) &gt; 0.5]

      G_3       G_5       G_9      G_10      G_11      G_15      G_20      G_23      G_25      G_26      G_33      G_40      G_43      G_48      G_57      G_60 
0.5346591 0.8066507 0.8379777 0.6752681 0.7221359 0.5285787 0.7333045 0.5627962 0.6533379 0.7256878 0.5996492 0.6486557 0.5108215 0.7386332 0.6596823 0.6919915 
     G_63      G_72      G_76      G_80      G_81      G_90      G_97      G_98      G_99 
0.5589583 0.8391917 0.7608801 0.8003665 0.6364557 0.5030968 0.7298439 0.5693024 0.5709411