A systems approach to mapping transcriptional networks controlling surfactant homeostasis

Xu, Yan; Zhang, Minlu; Wang, Yanhua; Kadambi, Pooja; Dave, Vrushank; Lu, Long J; Whitsett, Jeffrey A

doi:10.1186/1471-2164-11-451

BMC Genomics

Table 4 TF-TG functional similarity and expression correlation (CEBPA and SREBP)

From: A systems approach to mapping transcriptional networks controlling surfactant homeostasis

CEBPA				SREBP
Rank by Kappa Similarity	Known Targets	Rank by correlation	Known Targets	Rank by Kappa Similarity	known Targets	Rank by Correlation	Known Targets
Cebpa	Kyrmizi et al. 2006	Cebpa	Kyrmizi et al. 2006	Srebf1	She et al. 2005	Srebf1	She et al. 2005
Foxf1a	Kim et al, 2005	S100 g		Mtdh		Lipg	Reed et al. 2008
Foxa1		Lpcat1		Supt16h		Wdr81
Ets1	Lefterova et al. 2008	Sftpb	Martis et al. 2006	Id2		6330416G13Rik
Sox7		Dlk1	Shimomura et al. 1998	Ebf1		Abca3
Foxa2	Martis et al 2006	Serpinb6b		Elf5		Wars	Reed et al. 2008
Wwtr1		Timp3	Lefterova et al. 2008	Ankib1		Lyzs
Elf5		Edil3		Fah		Serpinf1
Smad5		Abca3		Fli1		Dhcr7	Reed et al. 2008
Tbx4		3110001I20Rik		Soat1	Farrell, et al. 2005	Siva1
Fli1		Bex2		Ahr	Iwano et al. 2005	Ndst1
Ahr		Tspan11		Cdkn2b		Cds2
Etv5		Vsnl1		Foxo3		Bcl6b
Id2	Tavor et al. 2003	Cd38		Sox7		Matn4
Runx1t1	Rochford et al 2004	1190002N15Rik		Mid1ip1		Ier3
Mef2c		Pard6b		Cbfa2t3		Scd1	Horton et al. 2002
Ebf1	Jimenez, et al. 2007	Emp2		Mef2c		Hck
Klf7		Id2	Tavor et al. 2003	Myb		Dag1
Prdm1		Kit		Zfx		Bcl2a1a
Jun	Rangatia et al. 2002	Mme		Acsl4		Sox7
Utp11l		B3gnt2		Cebpa	Pedersen et al. 2007	Ahr	Iwano et al. 2005
Tcfcp2l1		Ndst1		Dhcr7		Rab6b
Cbfa2t3		Lyz1	Lefterova et al. 2008	Etv5		Slc1a5
Fos	Cammenga et al. 2003	Lyz	Lefterova et al. 2008	Foxa1		Slc34a2
Stat3	Numata et al. 2005	Syne2		Foxa2		Enpp2
Sox2		Tgoln1		Rab2		Hdc	Ai et al. 2006
Myb	Verbeek, et al. 1999	Klf7		Runx1t1		Sftpb
Srebf1	Le et al. 2002	Atp6v1b2		Tbx4		Kdr
Klf9		Me1	Lefterova et al. 2008	Tcfcp2l1		Tsn
Foxo3a		Tcfcp2l1		Upk3b		Rtkn2
Cdkn2b		Rtkn2		Foxf1a		Zdhhc14
Ankib1		Krt19		Sox2		Dtna
Fah		Slc34a2		Stat3		Lphn3
Mapk14	Kumar et al. 2003	Prdx6		Aytl2		Lpcat1
Cyp4v3		Fabp5		Ets1		Scd2	Tabor et al. 1999
Elovl1		Ier3		Exosc7		Emp2
Qk	Lefterova et al. 2008	Scd1	Christy et al. 1989	Elovl1		Hc
Rcan1		Cd55		Fos		Cyp4v3
Exosc7		Exosc7		Ggcx		Mid1ip1
Gadd45g		Kdr		Klf9		Lyz

Correlation: the expression profile similarities between TF and genes in the same cluster were calculated using Pearson Correlation and ranked accordingly from high to low based on the correlation coefficient. The top 40 genes with the highest correlation with Cebpa and Srebf1 are listed in Table 4.
Kappa similarity was calculated to estimate functional similarity between TF and genes based on the shared annotation terms. TF-TG functional association were ranked from high to low based on the Kappa value. The top 40 genes sharing the highest functional annotations with Cebpa and Srebf1 are listed in Table 4.
We collected the positive TF-TG relationships from Ingenuity knowledge base (Ingenuity), Transfac 11.3 (Biobase), Eldorado (Genomatix) and PubMed. References for the known TF-TG relationships are listed in the table.

Back to article page

ISSN: 1471-2164

Contact us

Submission enquiries: bmcgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com