Table 3 A summary of overlaps that were discussed in details in this paper

Chang_Serum_Response_up & Schumacher_MYC_up

The c-Myc oncogene mediates response to serum stimulation and triggers proliferative growth [18, 19].

Sana_IFNG_Endothelial_Dn & Zeller_MYC_Up, MYC_Targets

Interferon γ (IFNG) inhibits cell growth through suppression of c-MYC expression [2].

Yes

Taketa_NUP9_HOXA9_3d_Up and interferon α and β gene sets

Transduction of fusion protein NUP98-HOXA9 induces "up-regulation of IFNβ1 and is accompanied by marked up-regulation of IFN-induced genes" [20].

CMV (cytomegalovirus) infection & Various cytokine regulated gene sets

Host cell response to CMV infection might be mediated by these cytokines.

StemCell_Embryonic_up & BRCA_Prognosis_Neg

Aggressive tumors share some expression signature of embryonic stem cells [5].

P53_Genes_All & Zeller_MYC_Dn

p53 represses the oncogene MYC possibly through miRNA-145 [45].

Yes

Gay_YY1_up & P53_Genes_All

YY1 inhibits the activation of p53 [36].

Yes

Cancer_undifferentiated_Meta_up & IDX_TSA_UP_Cluster3

Genes involved in TSA-induced differentiation of fibroblasts into adipocytes are also upregulated in undifferentiated tumors.

Peng_Glutamine_Dn & several MYC upregulated gene sets

Glutamine starvation might suppress cell growth by repression of MYC pathway.

Yes

Manalo_hypoxia_Dn, StemCell_Embryonic_up, Le_Myelin_up

Cell cycle genes are regulated by hypoxia, stem cells, and growth after wounding.

Partly