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Table 6 The top-AID/APOBEC signature-linked Functional Annotations identified by systems biology approach (algorithm II; overlap with 4 individual target genes)

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

Functional Annotations-top-output_mixed_and_4_individual

Pos.

Functional Annotations

Mixed

APOBEC3G

ESR1

ID2

ID3

PTPRC (CD45)

P-value

Molecules

Molecules

Molecules

Molecules

Molecules

Molecules

1

arthritis

1.53E-17

AIF1, ALOX5, AR, BGN, C3AR1, CASP1, CCL5, CCR5, CD86, CDH11, CDKN1A, CIITA, COL6A1, CSF2RB, CTSS, FAS, 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, TNFSF13B, ZFP36

ALOX5, CASP1, CCL5, CIITA, CTSS, GBP2, HLA-DOA, HLA-DPA1, HLA-DPB1, IL15, IRF1, ITGAM, MS4A6A, PSMB9, SAMD9L, TAGAP, TLR3, TNFSF13B

 

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

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

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

2

cell death of immune cells

8.52E-15

CASP1, CCL5, CCR5, CD2, CD47, CD86, CDKN1A, CIITA, COL1A1, CSF2RB, CYBB, EGFR, ESR1, EYA2, FAS, FCER1G, FN1, GIMAP4, GZMA, HCK, ID2, ID3, IFIH1, IL15, IRF1, ITGAM, ITPR1, LAIR1, LRIG1, MEIS1, PTPRC, SNAI2, TIMP1, TLR3, TNFSF13B

CASP1, CCL5, CIITA, IFIH1, IL15, IRF1, ITGAM, TLR3, TNFSF13B

CD47, ESR1, EYA2, LRIG1, MEIS1

CDKN1A, COL1A1, EGFR, FAS, ID2, ID3, SNAI2

 

CCL5, CCR5, CD2, CD86, CSF2RB, CYBB, FCER1G, GIMAP4, GZMA, LAIR1, PTPRC

3

rheumatoid arthritis

2.2E-13

AIF1, ALOX5, BGN, C3AR1, CCL5, CCR5, CD86, CDH11, CIITA, CSF2RB, FCGRT, GBP2, GZMA, HCK, HLA-DOA, HLA-DPA1, HLA-DPB1, IGFBP4, IGFBP7, IL10RA, ITPR1, JAM3, LST1, MS4A6A, PSMB9, PTPRC, SAMD9L, SDC2, SNAI2, SPOCK1, TAGAP, TIMP1, TLR3, TNFSF13B, ZFP36

ALOX5, CCL5, CIITA, GBP2, HLA-DOA, HLA-DPA1, HLA-DPB1, MS4A6A, PSMB9, SAMD9L, TAGAP, TLR3, TNFSF13B

 

CDH11, FCGRT, IGFBP4, IGFBP7, SDC2, SNAI2, TIMP1, ZFP36

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

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

4

apoptosis

2.9E-12

AIF1, ALOX5, ANTXR2, APOL6, AR, ARMC10, BGN, CASP1, CCL5, CCR5, CD2, CD47, CD48, CD53, CDH11, CDKN1A, CIITA, COL1A1, CSF2RB, CTGF, CTSS, CYBB, DKK3, DLC1, 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, LRIG1, MNDA, MUC16, PMEPA1, PMP22, PTPRC, RHOB, SDC2, SGPP1, SNAI2, SOX17, SPOCK1, SULF2, TIMP1, TLR3, TNFRSF14, TNFSF13B, VCAN, XAF1, ZFP36

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

 

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

BGN, DKK3, DLC1, FBN1, FN1, FSTL1, ID1, ID2, ID3, IGFBP4, ITPR1, PMEPA1, PMP22, RHOB, SDC2, SNAI2, SPOCK1, SULF2

CCL5, CCR5, CD2, CD48, CD53, CSF2RB, CYBB, FCER1G, GZMA, HCK, LAIR1, MNDA, PTPRC

5

necrosis

1.36E-11

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

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

 

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

BGN, DKK3, FN1, FSTL1, ID1, ID2, ID3, IGFBP4, ITPR1, PMEPA1, PMP22, RHOB, SDC2, SNAI2, SPOCK1, SULF2

CCL5, CCR5, CD2, CD48, CD86, CSF2RB, CYBB, FCER1G, GIMAP4, GZMA, HCK, LAIR1, PTPRC

  1. IPA nomenclature was used for Functional Annotations. Since analysis for the 10-top-output_mixed_and_5 individual revealed only one functional annotation, the results of the top-output_mixed_and_4 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