A novel analysis strategy for integrating methylation and expression data reveals core pathways for thyroid cancer aetiology

Table 3 Rankings of functional enrichment results - Part 2.

	Model 5 (>15% Methylation Change and Inversely Correlated)				Model 6 (>15% .Methylation Change)				Model 7 (>15% Methylation Change, Significances Combined)				Model 8 (>15% Methylation Change, Inverse Correlated,Significances Combined)
KEGG TERMs	A	B	C	D	A	B	C	D	A	B	C	D	A	B	C	D
MAPK Signalling	-	-	-	45	16	3	2	2	29	4	8	6	-	-	-	59
ECM Receptor	14	-	28	6	8	-	35	3	3	10	3	3	18	-	34	7
ErbB Signalling	-	15	13	5	26	6	7	7	28	8	13	10	31	3	4	4
NF-KB Signalling	22	-	35	29	18	-	41	31	20	-	39	22	5	-	19	11
Wnt-β-Catenin Signalling	21	-	34	72	64	28	40	46	51	-	62	72	-	-	-	-
VEGF Signalling	25	24	17	51	44	34	36	37	50	30	33	30	34	21	17	60
Thyroid Cancer	28	14	15	88	32	27	22	106	39	20	22	45	28	17	13	65
Adherens Junction	9	8	5	7	25	24	15	6	26	7	9	14	8	-	24	10
p53 Signalling	-	-	-	26	-	-	-	80	40	-	50	54	-	-	-	25
TGF-beta Signalling	-	-	-	12	41	32	32	9	10	3	4	13	-	-	-	-
Notch Signalling	5	9	2	49	-	4	26	24	54	18	28	12	-	22	50	55
GnRH Signalling	-	6	23	21	19	33	21	40	-	41	78	56	2	-	8	37
Neurotrophin Signalling	7	2	3	15	15	14	8	12	13	13	7	17	20	-	36	21
Focal Adhesion	4	-	16	1	3	17	4	1	1	6	2	2	7	-	23	2
Transcr. Misregulation	-	-	-	40	30	-	48	77	58	-	68	51	-	-	-	65
Apoptosis	2	-	7	8	20	-	42	20	6	-	27	4	25	-	38	1
Pathways in Cancer	3	-	8	3	1	1	1	8	2	1	1	1	3	-	11	3
Toll-like receptor signalling pathway	-	-	-	75	-	-	-	-	-	-	-	8	-	-	-	5
Pentose-phosphate pathway	18	12	10	25	-	30	64	-	34	31	29	18	4	-	14	17

Rankings of previously identified thyroid-cancer associated pathways in PANOGA functional enrichment results - Part2. For each analysis strategy four different results are obtained in order to understand differences between different data selection strategies; A) Batch230 Results B) Batch250 Results C) Functional Enrichment Results of different Batches combined D) Batch230+Batch250 (Pooled) results. Model 5 represents, genes having more than 15% methylation change and are inversely correlated with expression values, Model 6 represents genes having more than 15% methylation change, Model 7 represents genes having more than 15% methylation change and having FDR<0.01 after significance values of methylation and expression are combined and finally Model 8 represents, genes having more than 15% methylation change, inversely correlated with expression values and having FDR<0.01 after significance values of methylation and expression are combined.

ISSN: 1471-2164