A FC-GSEA Approach to Identify Significant Gene-Sets Using Microarray Gene Expression Data - Advances in Computational Science and Engineering - page 126

Table 2. Significant pathways identified by original-GSEA and FC-GSEA

KEGG pathway names Original-GSEA FC-GSEA

Glutathione metabolism O O

Metabolism of xenobiotics by cytochrome P450 X O

MAPK signaling pathway X X

Cell cycle O O

mTOR signaling pathway X X

Apoptosis X O

Jak-STAT signaling pathway X O

Hematopoietic cell lineage O O

T cell receptor signaling pathway X O

B cell receptor signaling pathway X O

hsa04660 and hsa04642 were identified. As a result, this shows that FC-GSEA has its
superiority to original-GSEA in identifying biologically significant pathways.
Table 3 shows our experimental results evaluated with the precision and the recall
[20]. The precision indicates the fraction of the pathways that actually turn out to be
positive out of the pathways that the GSEA has predicted to be significant pathways.
On the other hand, the recall indicates the fraction of actually significant pathways
correctly predicted by the GSEA out of the total pathways. Also, the precision and the
recall can be summarized into another metric known as the F 1 measure. The formulas
to calculate the precision, the recall and the F 1 measure [20] are shown below.

TP

Precision, p =

TP + FP

TP

Recall, r =

(6)

TP + FN

2 rp 2 × TP

F = =

1

rp + 2 × TPFPFN + +

Here TP is the number of true positive pathways, which is the number of the identi-
fied significant pathways by GSEA out of the collected 10 Leukemia-related path-
ways. FN is the number of false negative pathways, which is the number of the col-
lected 10 Leukemia-related pathways not identified by GSEA. Also, FP is the number
of false positive pathways, which is the number of the identified significant pathways
by GSEA excluding the 10 Leukemia-related pathways.
Note that in the precision, the recall, and F1 measure, the larger quantity indicates
the better performance. According to Table 3, it is observed that FC-GSEA is also
superior to original GSEA.

Table 3. Original-GSEA and FC-GSEA result's estimation

Original-GSEA FC-GSEA

Precision 0.3 0.8

Recall 0.075 0.2

F 1 0.12 0.32