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Table 2 The list of transcription factors removed by standard NCA algorithm but retained by ISNCA in the EGF data set and its involvement in previous breast cancer studies

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

TF symbol

Description

Breast cancer related?

% removed

PMIDs

ATF2

Activating transcription factor 2

Yes

92

19331149, 18677098,

    

17079470, 17258390

FOXA1

Forkhead box A1

Yes

84

19261198, 24528009,

    

25155268, 17373880

SMAD5

SMAD family member 5

Yes

91

23334326, 19096363

    

17786313

RARG

Retinoic acid receptor-gamma

Yes

91

21482774, 15375546

    

10928067

REL

v-rel avian reticuloendotheliosis viral oncogene

Yes

13

21482774, 15375546

ATF3

Activating transcription factor 3

Yes

91

23921126, 24494067,

    

20930144, 17952119

ETV4

ETS translocation variant 4

Yes

89

17467662, 22075993

FOS

FBJ murine osteosarcoma viral

Yes

84

15319566, 19925682

 

oncogene homolog

   

FOSL1

Fos-related antigen 1

Yes

93

19925682, 21570421

JUNB

jun B proto-oncogene

Yes

94

24073962, 8417822

MYBL2

Myb-related protein B

Yes

83

25337223, 25502082,

    

22037783

NFIA

Nuclear factor 1 A-type

Yes

90

24393253, 20525248

NOTCH1

Notch homolog 1,

Yes

81

25287362, 25544568,

 

translocation associated

  

24970818

PAX3

Paired box 3

Yes

89

24438019, 20525248

SMAD7

SMAD family member 7

Yes

82

22841502, 22033246

FLI1

Fli-1 proto-oncogene,

Yes

79

25379017, 17727680,

 

ETS transcription factor

  

17172821

  1. % 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