Context-specific gene regulatory networks subdivide intrinsic subtypes of breast cancer

BMC Bioinformatics

Table 2 Contexts summary

Contexts	Samples	Genes	ER +/ ER-	PgR+/PgR-	LN+/LN-	Grade	Subtypes
C 89	1418	2	ER+	PgR+		Low	Normal, LumA
C 16	1330	16	ER+	PgR+		Low	Normal, Her2, LumB, LumA
C 75	1200	4
C 34	1186	23			LN+
C 68	1068	4
C 40	1044	6			LN+	Low	LumA
C 57	824	7			LN+	High	Basal
C 73	805	3		PgR+	LN-	High	LumB
C 51	788	6	ER+	PgR+		Low	Normal, LumA
C 18	738	10	ER-	PgR-	LN+	High	Normal, Basal
C 67	731	4
C 79	658	2	ER+	PgR+		Low	Normal, LumB, LumA
C 55	551	6			LN-	High
C 49	549	6			LN-
C 150	395	5	ER-	PgR-	LN+	High	Basal, Her2
C 126	336	2			LN-	Low	LumA
C 162	248	2	ER-	PgR-		High	Basal, Her2
C 134	234	4	ER-	PgR-		High	Basal, Her2
C 160	202	2	ER-	PgR-		High	Basal
C 48	188	27	ER-	PgR-		High	Basal
C 121	186	2					Normal
C 143	185	4	ER+		LN-	High
C 147	175	3			LN-	High	LumB
C 168	154	5	ER-	PgR-	LN-	High	Basal
C 146	153	2			LN-	High
C 110	152	5	ER-	PgR-		High	Basal
C 145	150	9	ER-		LN-	High	Basal
C 159	150	3	ER-				Basal
C 130	129	2	ER-	PgR-		High	Basal
C 124	128	2			LN-	High	LumB
C 131	126	2	ER+	PgR+		Low	Normal, LumA
C 28	121	10			LN+	Low	Normal
C 155	119	3	ER-			High	Basal
C 50	118	42	ER+				LumA
C 153	115	5					Normal
C 139	111	2
C 104	95	5
C 144	90	7			LN-	High
C 22	86	31	ER-	PgR-	LN+	High	Basal, Her2
C 115	86	2	ER+	PgR+	LN+	Low	Normal, LumA
C 111	84	4	ER-	PgR-		High	Basal,

Results show contexts (ordered by number of samples) obtained after context-motif mining and MCL in column 1; contexts samples associated with a threshold 0.7 and specificity of 2 in column 2 and context genes in column 3. Context enrichments with clinical and molecular features (ER Status, PgR Status, Grade and LN Status) are shown in columns 4-7, selected after a statistical significance of < 0.05 (Low Grade =Grades 1 and 2; High Grade = Grade 3). Last column shows intrinsic subtype enrichments with LumA=Luminal A, LumB= Luminal B, Basal = Basal-like , Her2 and normal Tumors.

ISSN: 1471-2105