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Table 2 Names of genes and proteins

From: Mining and state-space modeling and verification of sub-networks from large-scale biomolecular networks

1:

G(V, E) is the input graph with vertex set V and edge set E.

2:

s is the seed vertex; f is the affinity threshold; d is the distance threshold.

3:

N ← {Adjacency list of s} {s}

4:

C ← FindCore(N)

5:

C' ← ExpandCore(C, f, d)

6:

return C'

7:

FindCore(N)

8:

   for each v N

9:

      calculate k v i n MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGRbWAdaqhaaWcbaGaemODayhabaGaemyAaKMaemOBa4gaaaaa@326D@ (N)

10:

   end for

11:

   K min ← min { k v i n MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGRbWAdaqhaaWcbaGaemODayhabaGaemyAaKMaemOBa4gaaaaa@326D@ (N), v N}

12:

   K max ← max { k v i n MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGRbWAdaqhaaWcbaGaemODayhabaGaemyAaKMaemOBa4gaaaaa@326D@ (N), v N}

13:

   if K min = K max or ( k i i n ( N ) = k j i n ( N ) , i , j N , i , j s , i j MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGRbWAdaqhaaWcbaGaemyAaKgabaGaemyAaKMaemOBa4gaaOGaeiikaGIaemOta4KaeiykaKIaeyypa0Jaem4AaS2aa0baaSqaaiabdQgaQbqaaiabdMgaPjabd6gaUbaakiabcIcaOiabd6eaojabcMcaPiabcYcaSiabbccaGiabgcGiIiabdMgaPjabcYcaSiabdQgaQjabgIGiolabd6eaojabcYcaSiabdMgaPjabcYcaSiabdQgaQjabgcMi5kabdohaZjabcYcaSiabdMgaPjabgcMi5kabdQgaQbaa@5489@ ) then return N

14:

   else return FindCore(N - {v}, k v i n MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGRbWAdaqhaaWcbaGaemODayhabaGaemyAaKMaemOBa4gaaaaa@326D@ (N) = K min )

15:

ExpandCore(C, f, d)

16:

    D ( v , w ) E , v C , w C { v , w } MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGebarcqGHsgIRdaWfqaqaaiabgQIiidWcbaGaeiikaGIaemODayNaeiilaWIaem4DaCNaeiykaKIaeyicI4SaemyrauKaeiilaWIaemODayNaeyicI4Saem4qamKaeiilaWIaem4DaCNaeyycI8Saem4qameabeaakiabcUha7jabdAha2jabcYcaSiabdEha3jabc2ha9baa@4A42@

17:

   C'C

18:

   for each t D, t C, and distance(t, s) <= d

19:

      calculate k t i n MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGRbWAdaqhaaWcbaGaemiDaqhabaGaemyAaKMaemOBa4gaaaaa@3269@ (D)

20:

      calculate k t o u t MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGRbWAdaqhaaWcbaGaemiDaqhabaGaem4Ba8MaemyDauNaemiDaqhaaaaa@33F4@ (D)

21:

      if k t i n MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGRbWAdaqhaaWcbaGaemiDaqhabaGaemyAaKMaemOBa4gaaaaa@3269@ (D) > k t o u t MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGRbWAdaqhaaWcbaGaemiDaqhabaGaem4Ba8MaemyDauNaemiDaqhaaaaa@33F4@ (D) or k t i n MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGRbWAdaqhaaWcbaGaemiDaqhabaGaemyAaKMaemOBa4gaaaaa@3269@ (D)/|D| > f then C'C' {t}

22:

   end for

23:

   if C' = C then return C

24:

   else return ExpandCore(C', f, d)