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| Pathway list | Upregulated genes | Downregulated genes |
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| Metabolic pathways (19) | ALOX15B; FPGT; GAA; GART; HPSE; KYNU; PTGES; SQLE | ALDH9A1; FUT4; GAMT; GCLC; GOT2; NDUFV1; PCCB; POLD3; QARS; RPA1; RRM1; UMPS |
| Pathways in cancer (14) | BCL2; BRCA2; CUL2; FGFR1; FOS; STAT1; WNT2 | E2F2; FZD4; HIF1A; JAK1; LAMC1; MLH1; RET |
| MAPK signaling pathway (11) | FGFR1; FOS; NF1; NTRK2; PAK2; RASGRP1; RASGRP4 | CACNG1; MAP2K6; MAP3K5; NTF4 |
| Proteoglycans in cancer (11) | CAV2; FGFR1; HPSE; PXN; WNT2 | CD44; DDX5; ERBB3; FZD4; HIF1A; TIAM1 |
| Spliceosome (11) | DDX42; SNRPB2 | CDC5L; DDX23; DDX5; HNRNPM; ISY1; SF3B1; SF3B2; SFRS3; SR140 |
| Protein processing in endoplasmic reticulum (10) | BAG2; BCL2; CALR; EIF2AK2 | EIF2AK1; MAP3K5; OS9; TXNDC5; UBE2G2; XBP1 |
| Cell cycle (9) | CDKN2D; PCNA | BUB1; BUB1B; CDC45; CDC6; E2F2; MCM3; SMC3 |
| RNA transport (7) | EIF2B4; RNPS1 | EIF2B1; EIF2B5; NMD3; NUP133; NUP85 |
| Cytokine-cytokine receptor interaction (7) | CCL5; CXCL16; IL1RAP | BMP7; CXCL12; EDA; IL4R |
| Regulation of actin cytoskeleton (7) | FGFR1; ITGAL; MYL9; PAK2; PXN | CHRM1; TIAM1 |
| Chemokine signaling pathway (7) | CCL5; CXCL16; PXN; STAT1 | CXCL12; HCK; TIAM1 |
| Ubiquitin mediated proteolysis (7) | CUL2; NEDD4L; UBE2W; WWP2 | PIAS3; TRIP12; UBE2G2 |
| PI3K-Akt signaling pathway (7) | BCL2; FGFR1 | CHRM1; IL4R; JAK1; LAMC1; SGK3 |
| Leukocyte transendothelial migration (6) | ITGAL; MYL9; PXN; SIPA1 | CXCL12; F11R |
| Calcium signaling pathway (6) | ORAI2 | CHRM1; ERBB3; GNA14; GNAS; PPIF |
| Endocytosis (6) | CAV2; NEDD4L | ERBB3; RAB7A; RABEP1; RET |
| Focal adhesion (6) | BCL2; CAV2; MYL9; PAK2; PXN | LAMC1 |
| Cell adhesion molecules (CAMs) (6) | CDH15; ITGAL | ALCAM; CDH3; F11R; LRRC4B |
| Jak-STAT signaling pathway (5) | IRF9; STAT1 | IL4R; JAK1; PIAS3 |
| PPAR signaling pathway (5) | CD36; DBI; SCD; SORBS1 | SLC27A2 |
| RNA degradation (5) | XRN1 | CNOT4; DCP1A; DCP1B; DHX36 |
| Hippo signaling pathway (5) | AREG; BMP5; WNT2 | BMP7; FZD4 |
| ECM-receptor interaction (5) | CD36; CD47 | CD44; HMMR; LAMC1 |
| Purine metabolism (4) | GART | POLD3; RPA1; RRM1 |
| Toll-like receptor signaling pathway (4) | CCL5; FOS; STAT1 | MAP2K6 |
| mRNA surveillance pathway (4) | RNPS1; SMG7 | CSTF3; SMG5 |
| DNA replication (4) | PCNA | MCM3; POLD3; RFC1 |
| Biosynthesis of secondary metabolites (4) | GART; SQLE | ALDH9A1; GOT2 |
| Insulin secretion (4) | PCLO; RIMS2 | GNAS; KCNMB4 |
| Phagosome (4) | CALR; CD36 | CLEC7A; RAB7A |
| Transcriptional misregulation in cancer (4) | TMPRSS2 | DDX5; SIX1; WHSC1 |
| ErbB signaling pathway (4) | AREG; PAK2 | ERBB3; NRG1 |
| Lysosome (4) | GAA | AP4S1; CTSL2; GLA |
| Mismatch repair (4) | PCNA | MLH1; POLD3; RFC1 |
| Nucleotide excision repair (4) | PCNA | ERCC5; POLD3; RFC1 |
| Pyrimidine metabolism (4) | | POLD3; RPA1; RRM1; UMPS |
| Tight junction (3) | CASK; MYL9 | F11R |
| p53 signaling pathway (3) | RPRM | MDM4; PMAIP1 |
| HIF-1 signaling pathway (3) | BCL2; CUL2 | HIF1A |
| NF-kappa B signaling pathway (3) | BCL2; BLNK | CXCL12 |
| Cytosolic DNA-sensing pathway (3) | ADAR; CASP1; CCL5 | |
| T-cell receptor signaling pathway (3) | FOS; PAK2; RASGRP1 | |
| Arginine and proline metabolism (3) | | ALDH9A1; GAMT; GOT2 |
| ABC transporters (3) | ABCG2 | ABCA10; ABCC4 |
| GnRH signaling pathway (3) | CGA | GNAS; MAP2K6 |
| NOD-like receptor signaling pathway (3) | CASP1; CCL5; SUGT1 | |
| Homologous recombination (2) | BRCA2 | POLD3 |
| TGF-beta signaling pathway (2) | BMP5 | BMP7 |
| Adherens junction (2) | FGFR1; SORBS1 | |
| Apoptosis (2) | BCL2; IL1RAP | |
| Wnt signaling pathway (2) | WNT2 | FZD4 |
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