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Table 7 The 10-top-AID/APOBEC signature-linked Functional Annotations identified by systems biology approach (algorithm II; overlap with 3 individual target genes)

From: AID/APOBEC-network reconstruction identifies pathways associated with survival in ovarian cancer

Functional Annotations-10-top-output_mixed_and_3_individual

Pos.

Functional Annotations

Mixed

APOBEC3G

ESR1

ID2

ID3

PTPRC (CD45)

P-value

Molecules

Molecules

Molecules

Molecules

Molecules

Molecules

1

Rheumatic Disease

1.66E-18

ACTA2, AIF1, ALOX5, AR, BGN, C3AR1, CASP1, CCL5, CCR5, CD86, CDH11, CDKN1A, CIITA, COL1A1, COL6A1, CSF2RB, CTSS, FAS, FBN1, FCER1G, FCGRT, FN1, FSTL1, GBP2, GZMA, HCK, HLA-DOA, HLA-DPA1, HLA-DPB1, IGFBP4, IGFBP7, IL10RA, IL15, IRF1, ITGAM, ITPR1, JAM3, LST1, MS4A6A, PSMB9, PTPRC, SAMD9L, SDC2, SNAI2, SPOCK1, TAGAP, TIMP1, TLR3, TLR8, TNFSF13B, ZFP36

  

ACTA2, CDH11, CDKN1A, COL1A1, COL6A1, FAS, FCGRT, IGFBP4, IGFBP7, SDC2, SNAI2, TIMP1, ZFP36

BGN, CDH11, FBN1, FN1, IGFBP4, ITPR1, JAM3, SDC2, SNAI2, SPOCK1

AIF1, C3AR1, CCL5, CCR5, CD86, CSF2RB, FCER1G, GZMA, HCK, IL10RA, LST1, MS4A6A, PTPRC, TLR8

2

cell movement of leukocytes

8.68E-17

AIF1, ALOX5, AR, BGN, C3AR1, CASP1, CCL5, CCR5, CD2, CD47, CD48, CD86, CDKN1A, CIITA, COL1A1, CTGF, CTSS, CYBB, DOCK2, EGFR, ENG, EPS8, ESR1, FAS, FCER1G, FN1, FYB, HCK, IL10RA, IL15, ITGAM, JAM3, LCP2, PTPRC, RHOB, ROCK2, TIMP1, TLR3, TNFRSF14, TNFSF13B

ALOX5, CASP1, CCL5, CIITA, CTSS, IL15, ITGAM, TLR3, TNFSF13B

 

CDKN1A, COL1A1, EGFR, ENG, EPS8, FAS, RHOB, ROCK2, TIMP1

 

AIF1, C3AR1, CCL5, CCR5, CD2, CD48, CD86, CYBB, DOCK2, FCER1G, FYB, HCK, IL10RA, LCP2

3

quantity of leukocytes

1.51E-16

ALOX5, C3AR1, CCL5, CCR5, CD47, CD48, CD84, CD86, CDKN1A, CIITA, CLEC7A, CSF2RB, CTSS, CYBB, DKK3, DOCK2, ESR1, FAS, FCER1G, FOXP1, FYB, HCK, HEXB, ID1, ID2, IL10RA, IL15, IRF1, ITGAM, JAM3, LAIR1, LCP2, MEIS1, PSMB10, PSMB9, PTPRC, SAMSN1, SASH3, SLA, SNAI2, TIMP1, TLR3, TNFSF13B, ZFP36

ALOX5, CCL5, CIITA, CLEC7A, CTSS, IL15, IRF1, ITGAM, PSMB10, PSMB9, TLR3, TNFSF13B

 

CDKN1A, FAS, FOXP1, HEXB, ID1, ID2, SNAI2, TIMP1, ZFP36

 

C3AR1, CCL5, CCR5, CD48, CD84, CD86, CSF2RB, CYBB, DOCK2, FCER1G, FYB, HCK, IL10RA, LAIR1, LCP2, PTPRC, SAMSN1, SASH3, SLA

4

cell movement of myeloid cells

4.14E-13

AIF1, ALOX5, AR, C3AR1, CASP1, CCL5, CCR5, CD2, CD47, CD48, CDKN1A, COL1A1, CTGF, CTSS, CYBB, DOCK2, EGFR, ENG, FAS, FCER1G, FN1, HCK, IL15, ITGAM, JAM3, PTPRC, RHOB, ROCK2, TLR3

ALOX5, CASP1, CCL5, CTSS, IL15, ITGAM, TLR3

 

CDKN1A, COL1A1, EGFR, ENG, FAS, RHOB, ROCK2

 

AIF1, C3AR1, CCL5, CCR5, CD2, CD48, CYBB, DOCK2, FCER1G, HCK

5

cell movement of phagocytes

9.33E-13

AIF1, ALOX5, AR, C3AR1, CASP1, CCL5, CCR5, CD47, CD86, CDKN1A, COL1A1, CTGF, CTSS, CYBB, DOCK2, EGFR, ENG, EPS8, FAS, FCER1G, FN1, HCK, IL10RA, IL15, ITGAM, JAM3, RHOB, TIMP1, TLR3

ALOX5, CASP1, CCL5, CTSS, ITGAM, TLR3

 

CDKN1A, COL1A1, EGFR, ENG, EPS8, FAS, RHOB, TIMP1

 

AIF1, C3AR1, CCL5, CCR5, CD86, CYBB, DOCK2, FCER1G, HCK, IL10RA

6

cell death

7.48E-11

AIF1, ALOX5, ANTXR2, APOL6, AR, ARMC10, BGN, CASP1, CCL5, CCR5, CD2, CD47, CD48, CD53, CD86, CDH11, CDKN1A, CIITA, COL1A1, COL6A1, CSF2RB, CTGF, CTSS, CYBB, DKK3, DLC1, DPYD, EGFR, ENG, ESR1, EVA1C, EYA2, FAS, FBN1, FCER1G, FN1, FOXP1, FSTL1, GIMAP4, GZMA, HCK, HEXB, ID1, ID2, ID3, IFIH1, IGFBP4, IGFBP7, IL15, IRF1, ITGAM, ITPR1, LAIR1, LCP2, LRIG1, MEIS1, MNDA, MUC16, PMEPA1, PMP22, PTPRC, RHOB, ROCK2, SDC2, SGPP1, SNAI2, SOX17, SPOCK1, SULF2, TFEC, TIMP1, TLR3, TNFRSF14, TNFSF13B, VCAN, XAF1, ZFP36

ALOX5, APOL6, CASP1, CCL5, CIITA, CTSS, DPYD, EVA1C, IFIH1, IL15, IRF1, ITGAM, TLR3, TNFRSF14, TNFSF13B, XAF1

 

ANTXR2, CDKN1A, COL1A1, COL6A1, CTGF, DLC1, EGFR, ENG, FAS, FOXP1, HEXB, ID1, ID2, ID3, IGFBP4, IGFBP7, RHOB, ROCK2, SDC2, SGPP1, SNAI2, SULF2, TIMP1, ZFP36

 

AIF1, CCL5, CCR5, CD2, CD48, CD53, CD86, CSF2RB, CYBB, FCER1G, GIMAP4, GZMA, HCK, LAIR1, LCP2, MNDA, PTPRC

7

metastasis

1.05E-10

ACTA2, AR, CASP1, CD47, CD86, CDKN1A, CTGF, CYBB, EGFR, ESR1, FN1, FOXP1, ID1, ID2, ID3, IGFBP7, IL15, IRF1, JAM3, MEIS1, NID2, PAPSS2, PRRX1, RAB31, RHOB, TIMP1, TLR8, VCAN

 

AR, CD47, ESR1, MEIS1

ACTA2, CDKN1A, CTGF, EGFR, FOXP1, ID1, ID2, ID3, IGFBP7, PAPSS2, RAB31, TIMP1

FN1, ID1, ID2, ID3, JAM3, PRRX1

 

8

triple-negative breast cancer

1.15E-10

AR, CDH11, CDKN1A, CTGF, DLC1, EGFR, EPS8, ESR1, FAS, HCK, IRF1, LAMB1, TIMP1, WFDC2

 

AR, ESR1, WFDC2

CDH11, CDKN1A, CTGF, DLC1, EGFR, EPS8, FAS, TIMP1

CDH11, DLC1, LAMB1

 

9

binding of cells

1.52E-10

AR, BGN, CCL5, CCR5, CD2, CD47, CD48, CD84, CD86, CLEC7A, CSF2RB, ENG, FAS, FN1, FYB, HCK, HS3ST1, ITGAM, JAM3, LCP2, MUC16, PTPRC, RHOB, SDC2, SNX9

  

ENG, FAS, HS3ST1, RHOB, SDC2, SNX9

BGN, FN1, JAM3, RHOB, SDC2

CCL5, CCR5, CD2, CD48, CD86, CSF2RB, FYB, HCK, LCP2, PTPRC

10

Lymphocyte migration

2.14E-10

ALOX5, CCL5, CCR5, CD2, CD47, CD48, CD86, COL1A1, CTSS, DOCK2, EGFR, ENG, FAS, FN1, FYB, IL15, JAM3, TIMP1, TNFRSF14, TNFSF13B

ALOX5, CCL5, IL15, TNFSF13B

 

COL1A1, EGFR, ENG, FAS, TIMP1

 

CCL5, CCR5, CD2, CD48, CD86, DOCK2, FYB

  1. IPA nomenclature was used for Functional Annotations. Since analysis for the 10-top-output_mixed_and_4 individual revealed only 5 functional annotations, the results of the 10-top-output_mixed_and_3 individual are additionally shown. The ranking is based on the corresponding IPA-based p-value of the output_mixed; the molecules mapped to the Functional Annotation are listed