Skip to main content
. Author manuscript; available in PMC: 2015 Sep 4.
Published in final edited form as: Circ Cardiovasc Genet. 2014 Aug;7(4):548–557. doi: 10.1161/CIRCGENETICS.113.000125

Table 3.

Predicted ceRNAs of PTEN

A: TraceRNA (sequence-based) B:TraceRNA (w/ GBM Gene Expression) C: ceRDB
Symbol SVMicrO
score		 p-value Symbol SVMicrO
score		 p-value Correlation
coefficient		 Symbol Score
QKI 1.199 0.0031 GSPT1 0.9105 0.0065 0.5534 TNRC6B 26
CPEB2 1.099 0.0040 CD2AP 0.8590 0.0074 0.5632 TET3 25
OTUD4 1.079 0.0042 USP15 1.0550 0.0045 0.5167 NFIB 23
PPP6C 1.071 0.0043 PPP6C 1.0706 0.0043 0.4913 ATXN1 21
NOVA1 1.059 0.0044 RAD23B 0.9124 0.0065 0.5167 ANKRD52 20
USP15 1.055 0.0045 NIPBL 0.7567 0.0097 0.6163 tcag7.1228 20
LEMD3 1.031 0.0048 CNOT6 0.8730 0.0072 0.4888 NUFIP2 17
SUZ12 1.027 0.0048 ARF6 0.7706 0.0093 0.5561 CPEB4 16
NARG1 1.022 0.0049 MED14 0.8159 0.0083 0.5100 ZFHX4 16
ZFHX3 1.014 0.0050 KIAA0240 0.9639 0.0057 0.4572 BACH2 15
C18orf25 1.009 0.0050 SOCS5 0.7573 0.0096 0.5438 CLCN5 15
FNDC3B 1.007 0.0051 CSNK1G3 0.7361 0.0102 0.5675 CUGBP2 15
BCL11A 0.967 0.0056 NAB1 0.7867 0.0089 0.4986 ONECUT2 14
ST18 0.967 0.0056 CBFB 0.7516 0.0098 0.5273 AFF1 14
KIAA0240 0.964 0.0057 RPS6KB1 0.7437 0.0100 0.5387 BNC2 14
RSBN1 0.963 0.0057 RPS6KA3 0.7126 0.0108 0.5780 KLF12 14
TET2 0.961 0.0057 TBL1XR1 0.7553 0.0097 0.5019 NFAT5 14
ICK 0.952 0.0058 RBM12 0.8482 0.0076 0.4516 OTUD4 14
SCN2A 0.951 0.0058 ELL2 0.8582 0.0074 0.4472 ZBTB34 14
PAN3 0.925 0.0062 ZFX 0.7595 0.0096 0.4752 ZEB2 14

(a) Best 20 predicted ceRNAs by sequence-pairingof PTEN predicted by SVMicrO based on miRNAs in Table 2 (first column, top 20 predicted miRNAs).

(b) Top 20 predicted ceRNAs by co-expression testof PTEN under the context of GBM. Column “p-value” shows the prediction p-values obtained in (a). Column “Correlation coefficient” lists Pearson correlations between a ceRNA and PTEN calculated using GBM gene expression data (see Materials and Methods). The ranking is based on the Borda merging of the rankings in (a) and that based on the Pearson correlation. ceRNAs shared between Tables 3a and 3b are in b font.

(c)The ceRNAs obtained from ceRDB. ceRNAs that were predicted by both algorithms (within top 50) are in italic. Note: tcag7.1228 is a synonym of UBN2.