Table 2 The downstream effects of the upstream regulators from the comparison of m vs. p.

From: Combating viral contaminants in CHO cells by engineering innate immunity

Virus

Consis-tency score*a

Total nodes (TF, TG, BP)

Transcription factors (TF)*b

Target gene (TG)*c

Biological Process (BP)*d

Relations*e

30 h

5.82

21

(5, 13, 3)

STAT1, IRF3, IRF5, IRF7, NFATC2

CASP1, CXCL10, DDX58, EIF2AK2, IFIH1, IL15, ISG15, Mx1/Mx2, OASL2, PELI1, PML, SOCS1, TNFSF10

Inhibit

Replication of virus.

Activate

Activation of phagocytes; Apoptosis of antigen presenting cells.

6/15 (40%)

54 h

22.47

48

(7.29.12)

STAT1, IRF3, IRF5, IRF7, NFATC2,

TRIM24, NCOA2

BST2, C3, CASP1, CXCL10, DDX58, EGR2, EIF2AK2, GBP2, IFIH1, IFIT1B, IFIT2, IFITM3 (IITMP3), Igtp, IL15, ISG15, Mx1/Mx2, MYC, OASL2, PML, PSMB10, PSMB8, PSME2, PTGS2, SPP1, STAT2, TAP1, TLR3, TNFSF10, TRAFD1

Inhibit

Replication of virus; Infection by RNA virus; Infection of central nervous system.

Activate

Antiviral response; Clearance of virus; Immune response of antigen presenting cells; Immune response of phagocytes; Cytotoxicity of leukocytes; Function of leukocytes; Infiltration by T lymphocytes; Quantity of MHC Class I of cell surface; Cell death of myeloid cells.

21/84 (25%)

78 h

27.80

30

(8, 14, 8)

STAT1, IRF5, NFATC2, NR3C1, PPARD,

ZBTB16, CDKN2A, EBF1

C3, CCL2, CCL7, CD36, CXCL10, CXCL9, DDX58, EIF2AK2, ISG15, MYC, THBS1, TLR3, TNFSF10, VEGFA

Activate

Activation of macrophages;

Apoptosis of myeloid cells; Cell movement of T lymphocytes; Cellular infiltration by leukocytes;

Damage of lung; Recruitment of leukocytes; Response of myeloid cells; Response of phagocytes.

11/64 (17%)

78 h

7.56

12

(2, 7, 3)

CDKN2A, ZBTB16

C3, CCL2, CCL7, CXCL10, CXCL9, MYC, VEGFA

Activate

Cell movement of T lymphocytes; Recruitment of leukocytes; Survival of organism.

1/6 (17%)

  1. *aConsistency score is to measure the consistency of a predicted network by IPA with the literature evidences.
  2. *b,cThe upstream regulators (STAT1 is highlighted in bold face) and the antiviral relating genes.
  3. *dThe biological functions known to associated with the regulatory networks annotated by the IPA.
  4. *eThe number of identified relationships and the total relationships that represent the known regulatory relationships between regulators and functions supported by literatures annotated by the IPA.
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