Identification of Essential Proteins Based on Improved HITS Algorithm

. 2019 Feb 25;10(2):177. doi: 10.3390/genes10020177

Algorithm 1 HSEP essential proteins identification.

Require: A PPI network

G = (V, E)

, Gene expression data, Subcellular location data Gene Ontology GO.
Ensure: Essential protein set.
Step 1

1:
Convert G to Bidirectional Digraph $G^{'} (V, E^{'})$
2:
for each interacting protein pair $(a, b)$ in PPI do
3:
Calculate $E C C$ /*The closeness of the two nodes*/
4:
Calculate $P C C$ /*the importance of two nodes based on Gene expression */
5:
Calculate $G O_s i m$ /*The functional similarity of the two nodes based on GO annotation*/
6:
Calculate $S L$ /*the reliable of two nodes based on subcellular localization */
7:
end for
8:
for each interacting protein pair (a,b) in $G^{'}$ do
9:
edge $(a, b)$ = $E C C (a, b)$
10:
edge $(b, a)$ = $P C C (b, a)$ + $G O_s i m (b, a)$ + $S L (b, a)$
11:
end for

Step 2
12:
form in $[1, m a x i t e r]$ do
13:
for each node v in V do
14:
$a_{m} (v) = \sum_{(u, v) \in E} h_{m - 1} (u)$
15:
$h_{m} (v) = \sum_{(u, v) \in E} a_{m - 1} (u)$
16:
$a_{m} = \frac{a_{m}}{m a x (a_{m})}$
17:
$a_{m} = \frac{h_{m}}{m a x (h_{m})}$
18:
$m = m + 1$
19:
until $| a_{m} - a_{m - 1} | + | h_{m} - h_{m - 1} | < γ$
20:
return $(a_{m}, h_{m})$
21:
end for
22:
end for
23:
calculate ensemble score $E M$
24:
a essential proteins set= $E M > T$