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

Svoboda, Martin; Meshcheryakova, Anastasia; Heinze, Georg; Jaritz, Markus; Pils, Dietmar; Castillo-Tong, Dan Cacsire; Hager, Gudrun; Thalhammer, Theresia; Jensen-Jarolim, Erika; Birner, Peter; Braicu, Ioana; Sehouli, Jalid; Lambrechts, Sandrina; Vergote, Ignace; Mahner, Sven; Zimmermann, Philip; Zeillinger, Robert; Mechtcheriakova, Diana

doi:10.1186/s12864-016-3001-y

BMC Genomics

Table 8 The 10-top-AID/APOBEC signature-linked Upstream Regulators identified by systems biology approach (algorithm I)

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

Upstream Regulators-10-top-output_mixed^a				Upstream Regulators output_individual^b
Upstream Regulators-10-top-output_mixed^a				APOBEC3G		ESR1		ID2		ID3		PTPRC (CD45)
Pos.	Upstream Regulator	P-value	Molecules	Pos.	Molecules	Pos.	Molecules	Pos.	Molecules	Pos.	Molecules	Pos.	Molecules
1	lipopolysaccharide	2.52E-27	ACTA2, ALOX5, APOBEC3F, APOBEC3G, APOL6, AR, BGN, C3AR1, CARD6, CASP1, CCL5, CCR5, CD48, CD53, CD86, CDH11, CDKN1A, CIITA, CLEC7A, COL1A1, COL5A1, COL6A1, CSF2RB, CTGF, CYBB, DKK3, FAS, FBN1, FCER1G, FCGRT, FN1, FYB, GBP2, GZMA, HCK, ID2, IFIH1, IGFBP4, IL10RA, IL15, IRF1, ITGAM, KIAA1551, LAMB1, LCP2, LST1, NID1, NID2, PAPSS2, PLEK, PSMB10, PSMB9, RARRES3, RHOB, SAMSN1, TFEC, TIMP1, TLR3, TLR8, TNFSF13B, TRIM22, VCAN, XAF1, ZFP36
2	Interferon alpha	3.48E-19	APOBEC3F, APOBEC3G, APOL3/APOL4, C3AR1, CASP1, CCL5, CCR5, CD86, CDKN1A, CIITA, CSF2RB, EGFR, FAS, GBP2, IFIH1, IGFBP4, IL10RA, IL15, IRF1, ITGAM, MNDA, PSMB9, RARRES3, TLR3, TLR8, TNFSF13B, TRIM22	4	APOBEC3F, APOBEC3G, APOL3/APOL4, CASP1, CIITA, IL15, IRF1, TLR3, TNFSF13B			591	CDKN1A, IGFBP4			146	CSF2RB, TLR8
3	IFNG	7.59E-18	AIF1, APOBEC3G, APOL6, CARD6, CASP1, CCL5, CCR5, CD2, CD86, CDKN1A, CIITA, COL1A1, CSF2RB, CTGF, CTSS, CYBB, FAS, FCER1G, FN1, GBP2, GMPR, HLA-DOA, ID1, IFIH1, IGFBP4, IL10RA, IL15, IRF1, ITGAM, LCP2, LST1, MNDA, PLEK, PSMB10, PSMB9, RARRES3, RHOB, SNAI2, TIMP1, TLR3, TLR8, TNFRSF14, TNFSF13B, TRIM22, ZFP36	1	APOL6, CARD6, CASP1, CCL5, CIITA, CTSS, GBP2, IFIH1, IL15, IRF1, ITGAM, PSMB10, PSMB9, RARRES3, TLR3, TNFSF13B, TRIM22							7	AIF1, CCL5, CCR5, CD2, CD86, CYBB, FCER1G
4	TGFB1	8.38E-18	ACTA2, ALOX5, BGN, CASP1, CCL5, CCR5, CD86, CDH11, CDKN1A, CIITA, COL1A1, COL5A1, COL6A1, COL6A2, CTGF, CTSS, CYBB, DKK3, DOCK2, EMILIN1, ENG, FAS, FBN1, FCER1G, FN1, GMPR, GZMA, HEXB, ID1, ID2, ID3, IFIH1, IGFBP4, IGFBP7, IL10RA, IL15, IRF1, ITGAM, ITPR1, PDLIM5, PLOD1, PMEPA1, PTPRC, RAB31, RHOB, SNAI2, SPOCK1, TIMP1, TNFRSF14, TNFSF13B, VCAN, ZFP36	161	ALOX5, CCL5, IRF1, ITGAM			3	ACTA2, CDH11, CDKN1A, COL1A1, CTGF, ENG, FAS, HEXB, ID1, RAB31, RHOB, SNAI2, TIMP1, ZFP36	3	BGN, CDH11, COL5A1, FBN1, FN1, ID1, PMEPA1, RHOB, SNAI2, SPOCK1
5	TNF	1.25E-16	ABR, AEBP1, ALOX5, AR, BGN, CARD16, CARD6, CASP1, CCL5, CCR5, CD47, CD86, CDH11, CDKN1A, CIITA, COL1A1, CSF2RB, CTGF, CTSS, CYBB, EGFR, ENG, ESR1, FAS, FCER1G, FCGRT, FN1, GBP2, HEXB, ID1, ID3, IFIH1, IGFBP4, IL10RA, IL15, IRF1, ITGAM, ITPR1, NID1, PPAP2A, PSMB10, PSMB9, RARRES3, SDC2, TIMP1, TLR3, TLR8, TNFSF13B, ZFP36	7	CASP1, CCL5, CTSS, GBP2, IL15, IRF1, ITGAM, PSMB10, PSMB9, RARRES3, TLR3, TNFSF13B			69	CDH11, CDKN1A, EGFR, FAS, HEXB, NID1, PPAP2A, TIMP1	52	AEBP1, CDH11, FN1, ITPR1, NID1, PPAP2A	181	CCL5, CCR5, CD86, CYBB
6	IL10	1.91E-15	ACTA2, CCL5, CCR5, CD2, CD86, CDKN1A, CIITA, CLEC7A, COL1A1, CSF2RB, CTSS, FAS, FCER1G, GZMA, IGFBP4, IL10RA, IRF1, PSMB9, TIMP1, TLR3, TLR8, TNFSF13B, VCAN, ZFP36	87	CCL5, CIITA, TLR3			97	ACTA2, CDKN1A, TIMP1, ZFP36			45	CCL5, CD2, CD86
7	STAT3	5.98E-15	CASP1, CCL5, CCR5, CD86, CDKN1A, CIITA, COL5A1, ESR1, FAS, FCER1G, FN1, GBP2, ID2, IFIH1, IRF1, ITGAM, PSMB9, SMAD9, TIMP1, TLR3, TRIM14, TRIM22, VCAN, XAF1, ZFP36	9	CASP1, CIITA, GBP2, IRF1, ITGAM, PSMB9, TLR3, XAF1			461	CDKN1A, TIMP1, ZFP36	106	FN1, SMAD9, VCAN
8	IL6	2.87E-14	BGN, CASP1, CCL5, CCR5, CD48, CD53, CD86, CDKN1A, CIITA, CSF2RB, CTGF, CYBB, EGFR, FAS, FCGRT, FN1, GBP2, ID1, ID2, IGFBP4, IL15, IRF1, ITGAM, PSMB10, PSMB9, PTPRC, RNASE6, TIMP1, TLR3, TLR8	13	CASP1, CIITA, GBP2, IRF1, ITGAM, PSMB9, TLR3			211	CDKN1A, ID1, ID2, TIMP1
9	IL13	7.28E-14	C3AR1, CASP1, CCL5, CCR5, CD48, CD86, CLEC7A, COL1A1, COL6A2, CTGF, CTSS, CYBB, EGFR, FAS, FGD2, HOMER2, NID1, SAMSN1, SLA, SNAI2, TFEC, TIMP1, TNFSF13B	70	CASP1, CCL5, CTSS, FGD2			512	FAS, NID1, TIMP1			1	C3AR1, CCL5, CCR5, CD48, CD86, CYBB, SAMSN1, SLA
10	tretinoin	1.15E-13	C3AR1, CASP1, CCR5, CD53, CD86, CDKN1A, COL1A1, CTGF, CYBB, DDX60L, DLC1, EGFR, EYA2, FCER1G, FN1, GZMA, HS3ST1, ID1, ID2, ID3, IFIH1, IGFBP4, IGFBP7, IL10RA, IRF1, ITGAM, LAMB1, MEIS1, MNDA, NID2, PLEK, PSMB9, RARRES3, SAMD9L, SLA, SMAD9, SOX17, THSD4, TIMP1, TLR3, TRIM22, XAF1

^aThe 10-top-output_mixed results are shown; the ranking is based on the corresponding IPA-based p-value; the molecules associated with the corresponding Upstream Regulator are listed
^bPosition of the Upstream Regulator within the output_individual for each target gene, the molecules associated with the Upstream Regulator are indicated. Color code: grey, within the 10-top-output_individual; white, outside the 10-top-output_individual. Empty cell: the corresponding Upstream Regulator was not significant in output_individual

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