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Table 2 DbTFtarget gene categorisation

From: Finding gene regulatory network candidates using the gene expression knowledge base

Novel DbTF

Function

CCK2RDbTF

TGs

AR42J expressed

Gastrin responsive

CREM

Activator

CREB1

JUN

Yes

Yes

FOXP3

Repressor

CREB1

IFNG

No

No

 

Repressor

CREB1

IL10

No

No

 

Repressor

CREB1

BCL2

No

No

 

Repressor

CREB1

MALAT1

No

No

TCF7L2

Repressor

CREB1

MYOD1

No

No

FOXP3

Repressor

NFkB1

PIGR

No

No

 

Repressor

NFkB1

CXCL5

No

No

 

Repressor

NFkB1

VCAM1

No

No

 

Repressor

NFkB1

VWF

No

No

 

Repressor

NFkB1

IFNG

No

No

 

Repressor

NFkB1

IL8

No

No

 

Repressor

NFkB1

BCL2A1

No

No

 

Repressor

NFkB1

NFKB1

Yes

Yes

 

Repressor

NFkB1

IER3

Yes

Yes

 

Repressor

NFkB1

CD40LG

No

No

 

Repressor

NFkB1

SELE

No

No

 

Repressor

NFkB1

ALOX5AP

Yes

Yes

SMAD3

Repressor

NFkB1

MMP9

No

No

PARP1

Activator

NFkB1

BRCA2

Yes

Yes

  1. The table lists shared target genes of the novel DbTFs and CCK2R core DbTFs, retrieved through use case I-III. Key for columns (left to right): Novel DbTFs: Proteins that transcriptionally regulate the core CCK2R-DbTFs (CREB1, NFkB1 and TCF7L2); Function: Role of the regulators; CCK2R-DbTF: core CCK2R-DbTF that is regulated by the Novel DbTF indicated in column one; TGs: Target genes retrieved from GeXKB that are found to be common between the novel DbTFs and the CCK2R core DbTF(s); AR42J expressed: known status of target genes expression in AR42J cells [19]; Gastrin responsive: known responsiveness of target genes to gastrin treatment [19].