Table 3. Genes disrupted or deleted entirely in breast cancer cases and involved in TP53 and β-estradiol centered network.

Gene	Aberration type	Involved exonsa	Predicted consequence to transcriptb
BLM	disruption	promoter dup	unknown
EIF2C2	disruption	ex2-ex18,3′UTR dup	unknown
HECW2	disruption	promoter, ex1 dup	unknown
RECQL4	deletion	entire gene	null allele
DAB2IP	disruption	promoter, ex1 del	null allele
LRRC14	deletion	entire gene	null allele
ITGA9	disruption	ex19-ex23 del	in frame deletion
ACSL1	deletion	entire gene	null allele
KLHL1	disruption	promoter, ex1 del	null allele
ESR2	disruption	ex2-ex9, 3′UTR dup	unknown
ARHGAP39	disruption	ex12-ex13, 3′UTR del	premature termination
LRRFIP1	disruption	promoter, ex1 dup	unknown
CASP3	deletion	entire gene	null allele
TRPM3	disruption	promoter, ex1 dup	unknown
KCNIP4	disruption	ex6-ex9, 3′UTR dup	unknown
DCLRE1C	disruption	promoter, ex1-ex4 del	null allele
TRAPPC9	disruption	promoter, ex1-ex3 dup	unknown
STRN	disruption	ex14-ex18, 3′ UTR dup	unknown
PPP1R16A	disruption	ex6-ex10, 3′UTR del	premature termination
SYNE2	disruption	ex50-ex114, 3′UTR dup	unknown
MARCH6	disruption	ex4-ex26, 3′UTR dup	unknown
GPT	deletion	entire gene	null allele
MLF1IP	deletion	entire gene	null allele
SEMA4B	disruption	ex3-ex15, 3′UTR dup	unknown
RBFOX1	disruption	ex11-ex13, 3′UTR dup	unknown
ANKS1B	disruption	promoter, ex1 dup	unknown
NXPH1	disruption	promoter, ex1-ex2 del	null allele
MEP1B	deletion	entire gene	null allele

Disruption = the gene is disrupted by the CNV breakpoints; deletion = the entire gene is deleted. del = partial gene deletion; dup = partial gene duplication.

^aBased on human genome assembly 19 (February 2009).

^bAlthough detailed effects of partial gene duplication to gene transcription are not clear, duplication have potential to disrupt transcription by several mechanisms, such as transcriptional read-through. This can occur by tandem duplication, where gene silencing can be induced by a partially duplicated (3′ deleted) version of the gene itself [54].