Iterative sub-network component analysis enables reconstruction of large scale genetic networks

BMC Bioinformatics

Table 3 The list of transcription factors removed by standard NCA algorithm but retained by ISNCA in the HRG data set and its involvement in previous breast cancer studies

TF symbol	Description	Breast cancer related?	% removed	PMIDs
ATF2	Activating transcription factor 2	Yes	81	19331149, 18677098,
				17079470, 17258390
FOXA1	Forkhead box A1	Yes	85	19261198, 24528009,
				25155268, 17373880
SMAD5	SMAD family member 5	Yes	86	23334326, 19096363
				17786313
RARG	Retinoic acid receptor-gamma	Yes	81	21482774, 15375546
				10928067
REL	v-rel avian reticuloendotheliosis viral oncogene homolog	Yes	71	21482774, 15375546
E2F2	E2F transcription factor 2	Yes	92	25028721, 24934442,
				24362522
NFkB2	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2	Yes	89	12835724, 7478612
TCF7	transcription factor 7	Yes	91	26079538, 24401947
SP2	Sp2 transcription factor	Yes	93	20382698
PAX6	Paired box 6	Yes	86	21944253, 25323813
PGR	Progesterone receptor	Yes	91	26277479, 26153859

% removed indicates that number of times standard NCA failed to retain the particular transcription factor on 100 tested networks. PMID is the PubMed database identification number

ISSN: 1471-2105