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 4 The 10-top-AID/APOBEC signature-linked Canonical Pathways identified by systems biology approach (algorithm I)

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

Canonical 10-top-output_mixed^a				Canonical output_individual^b										Related studies^c
Canonical 10-top-output_mixed^a				APOBEC3G		ESR1		ID2		ID3		PTPRC (CD45)		Related studies^c
Pos.	Canonical pathways	P-value	Molecules	Pos.	Molecules	Pos.	Molecules	Pos.	Molecules	Pos.	Molecules	Pos.	Molecules	Ovarian Cancer	Others
1	Hepatic Fibrosis / Hepatic Stellate Cell Activation	8.32E-08	COL1A1, IGFBP4, CCR5, FN1, CTGF, TIMP1, ACTA2, IL10RA, CCL5, FAS, EGFR					1	COL1A1, IGFBP4, CTGF, TIMP1, ACTA2, FAS, EGFR	5	IGFBP4, FN1	14	CCR5, IL10RA, CCL5	[79, 80, 98]	[81]
2	Altered T Cell and B Cell Signaling in Rheumatoid Arthritis	1.51E-06	HLA-DOA, IL15, TLR8, FCER1G, CD86, TLR3, TNFSF13B, FAS	3	HLA-DOA, IL15, TLR3, TNFSF13B							6	TLR8, FCER1G, CD86		[83]
3	Antigen Presentation Pathway	2.40E-05	PSMB9, HLA-DOA, CIITA, HLA-DPB1, HLA-DPA1	1	PSMB9, HLA-DOA, CIITA, HLA-DPB1, HLA-DPA1									[82, 99]
4	Communication between Innate and Adaptive Immune Cells	2.45E-05	IL15, TLR8, FCER1G, CD86, CCL5, TLR3, TNFSF13B	4	IL15, CCL5, TLR3, TNFSF13B							1	TLR8, FCER1G, CD86, CCL5	[100]
5	Role of Pattern Recognition Receptors in Recognition of Bacteria and Viruses	3.47E-05	IFIH1, CLEC7A, TLR8, CASP1, CCL5, TLR3, C3AR1	2	IFIH1, CLEC7A, CASP1, CCL5, TLR3							9	TLR8, CCL5, C3AR1		[101–103]
6	Allograft Rejection Signaling	1.35E-04	HLA-DOA, FCER1G, CD86, HLA-DPB1, HLA-DPA1, FAS	6	HLA-DOA, HLA-DPB1, HLA-DPA1							25	FCER1G, CD86		[104]
7	Crosstalk between Dendritic Cells and Natural Killer Cells	2.09E-04	CSF2RB, ACTA2, IL15, CD86, TLR3, FAS	21	IL15, TLR3			40	ACTA2,FAS			27	CSF2RB, CD86		[105, 106]
8	CCR5 Signaling in Macrophages	5.25E-04	CCR5, FCER1G, CCL5, GNG12, FAS					27	GNG12, FAS			4	CCR5, FCER1G, CCL5	[107, 108]	[109]
9	CD28 Signaling in T Helper Cells	8.13E-04	PTPRC, HLA-DOA, FCER1G, CD86, ITPR1, LCP2									2	PTPRC, FCER1G, CD86, LCP2		[110, 111]
10	Graft-versus-Host Disease Signaling	9.12E-04	HLA-DOA, FCER1G, CD86, FAS									16	FCER1G, CD86		[112]

^aIPA nomenclature is used for canonical pathways. The 10-top-output_mixed results are shown; the ranking is based on the corresponding IPA-based p-value; the molecules mapped to the pathway are listed
^bPosition of the canonical pathway within the output_individual for each target gene, the corresponding p-value and the molecules mapped to the pathway are indicated. Bold, within the 10-top-output_individual; Italic, outside the 10-top-output_individual. Empty cell: the corresponding pathway was not significant in output_individual
^cLiterature search-based results annotating those canonical pathways in ovarian cancer or other related studies

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ISSN: 1471-2164

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