Integrated transcriptional profiling and genomic analyses reveal RPN2 and HMGB1 as promising biomarkers in colorectal cancer

Table 1 Comparison of differentially expressed genes with published CRC microarray studies

Gene symbol	Fold change^a	Tumors with prognosis gene signatures^b	Tumors from other microarrays^c
TIMP1	8.34	232	52
AARS^d	4.48		30
PEA15^d	4.23	215	22
CD59	1.61	232
IFITM1	3.03		106
HMGB1^d	2.07	215	496
RPN2^d	1.91		15
IGF2R	1.75	215	107
IGFBP3^d	2.29	232	706
NPM1	2.60	87	679
NQO1^d	3.77	55	200
TGFB1	2.35		531
AKT1	3.33		43
HYOU1^d	2.16		30
STAT1^d	2.83	215	30

^aThe fold changes of differential gene expression between Stage II CRC tumor and normal tissues were extracted from the microarray data presented in Fig. 1
^bPrognosis gene signatures were extracted from the publication of Sanz-Pamplona et al., which surveyed 29 microarray studies with patient’s data of recurrence, metastasis and survival [25]
^cAdditional microarray data from 50 previous publications was extracted from CRC tumor and metastatic specimens (Additional file 1: Table S3). The indicated number stands for tumor specimens with increased gene expression
^dRefers to genes that are involved in transcriptional regulation (Fig. 3; Additional file 1: Table S1) and an overlapping with TCGA data (Additional file 2: Figure S2)