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Table 5 GPEA analysis of gene family gene sets for the UC RNAseq, Bead and Oligo GRN

From: Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data

Tag Name RNAseq Bead Oligo
CD CD molecules 380/591/0 365/319/1.1e-140 351/319/8.9e-106
ZKRAB Zinc fingers, C2H2-type with KRAB domain 338/764/0 306/289/5.3e-155 143/108/5.6e-64
RPL L ribosomal proteins 59/119/1.2e-175 55/49/2.2e-59 44/72/3.4e-102
ZNF Zinc fingers, C2H2-type 697/1307/0 641/515/4e-114 362/242/2.3e-53
HIST Histones/Replication-dependent 67/236/0 61/154/5.7e-252 26/32/1.3e-48
HLA Histocompatibility complex 24/46/1.1e-85 25/33/2.9e-57 19/22/9.1e-36
C1SET Immunoglobulin superfamily/C1-set domain containing 38/51/1e-75 38/34/1.5e-46 37/26/1.1e-28
KLK Kallikreins 17/26/1.2e-49 16/15/2.8e-26 14/14/1.7e-23
MT Metallothioneins 14/12/3.5e-20 12/12/7.1e-23 10/10/3.5e-18
PCDHC Cadherins/Protocadherins : Clustered 57/150/7.8e-242 56/24/6.6e-21 22/14/1.3e-17
IGD Immunoglobulin superfamily/Immunoglobulin-like domain containing 233/175/3.6e-85 221/77/5.1e-22 177/67/2.6e-17
KRT Keratins 55/87/1.4e-121 51/20/2.8e-17 35/20/1.5e-20
HOXL Homeoboxes/ANTP class : HOXL subclass 52/54/1.6e-66 50/39/1.8e-46 43/20/5.2e-17
COLLAGEN Collagens 46/37/3.4e-43 43/21/1.1e-21 33/17/5.5e-17
RPS S ribosomal proteins 34/40/7.2e-59 32/14/3.1e-15 29/28/6.1e-38
PSM Proteasome (prosome, macropain) subunits 45/25/4.1e-25 43/15/5e-13 42/26/7.7e-26
RBM RNA binding motif (RRM) containing 209/114/2.6e-46 186/50/1.6e-12 151/72/2.3e-28
ENDOLIG Endogenous ligands 230/77/7.9e-16 221/62/3.3e-13 192/62/2.8e-11
VSET Immunoglobulin superfamily/V-set domain containing 161/95/1.4e-50 150/42/5.2e-14 110/33/9e-11
comI Mitochondrial respiratory chain complex/Complex I 38/14/3.9e-12 38/12/2.6e-10 31/15/7.3e-15
UGT UDP glucuronosyltransferases 20/15/4.8e-22 20/17/2.3e-27 7/5/1.4e-08
IFF2 Intermediate filaments type II, keratins (basic) 26/23/2.6e-33 24/8/3e-08 15/7/1.8e-08
comIV Mitochondrial respiratory chain complex/Complex IV 16/13/8.5e-21 15/6/1.3e-07 12/7/6.3e-10
S100 S100 calcium binding proteins 21/12/1.1e-15 21/7/1.8e-07 17/7/1.1e-07
LNCRNA Long non-coding RNAs 548/407/1.2e-78 468/168/2e-14 107/25/5.4e-06
complement Complement system 35/18/3.8e-19 33/7/1e-04 30/9/9.6e-07
CYP Cytochrome P450s 62/37/1.1e-33 56/10/0.00019 48/22/1.2e-17
SERPIN Serine (or cysteine) peptidase inhibitors 36/21/2.1e-23 35/8/1.2e-05 30/7/0.00031
  1. Shown are the commonly significant gene family subnetworks of the RNAseq, Bead and Oligo UC GRN, number of genes of the gene family subnetwork, the number of interactions and the Bonferroni adjusted P-value (Genes/Interactions/P-value).