Table 3.

Pathways targeted by the miRNAs found (A) more expressed in GII + GIII vs GI cases and (B) less expressed in GII + GIII vs GI cases.

Pathway name	Entities found	Entities total	p-Value	FDR	Genes
A
Antigen presentation: Folding, assembly and peptide loading of class I MHC	62	102	1.11E−16	3.06E−14	CALR, ERAP1, ERGIC2, HLA-A, HLA-B, MAP2, SAR1B, TWF1
Interferon signaling	77	250	1.11E−16	3.06E−14	CIITA, HLA-A, HLA-B, ICAM1, IFNG, IRF1, IRF2, IRF6, JAK1, PTPN1, SOCS3, SUMO1, TRIM2, TRIM29, KPNA5, KPNB1, NUP160, PLCG1, PPM1B
ER-phagosome pathway	59	165	1.11E−16	3.06E−14	CALR, HLA-A, HLA-B, SEC61B, SNAP25
Immunoregulatory interactions between a lymphoid and a non-lymphoid cell	62	316	5.89E−10	1.08E−07	COL1A1, HLA-A, HLA-B, ICAM1, PDCL, PRKAA2, SLAMF6, VKORC1L1
Apoptotic execution phase	13	54	6.41E−04	8.14E−02	CAD, CSRP1, KPNB1, MAP2, PAK2, PARP1, PPP2R2A, SATB1, SERP1, SH3BP2, SH3PXD2A, TJP1
Syndecan interactions	8	29	3.01E−03	3.32E−01	ACTN1, COL1A1, COL5A1, COL5A2, ITGA2, PRKAA2, SDC4, THBS1
RUNX1 regulates expression of components of tight junctions	4	8	4.00E−03	4.19E−01	CBFB, PPP2R2A, TJP1

B
Neddylation	43	241	2.02E−04	1.22E−01	ANKRD52, ASB1, ATP6V1A, CAND1, CD2AP, CHD9, COPS2, CUL1, CUL3, CUL5, DCAF10, DCAF8, DCUN1D1, DHTKD1, DTL, EPAS1, FBXL3, FBXO30, FEM1B, FEM1C, GBF1, GLS, KBTBD6, KLHL20, KLHL42, LZIC, MED13, MSMO1, PRICKLE2, PSMF1, RBBP7, RBX1, RPN2, SOCS4, SOCS6, TCERG1, TULP4, UBE2Q2, UBXN7, VHL, VLDLR, XRN1
Cyclin D associated events in G1	14	48	3.90E−04	1.22E−01	CCND1, CCND2, CCNH, CDK6, CDKN1A, CDKN1B, CUL1, E2F3, RB1, RBL1, RBL2
FOXO-mediated transcription of cell cycle genes	10	27	4.33E−04	1.22E−01	CCNG2, CDKN1A, CDKN1B, RBL2, SMAD3, CCNG2, CDKN1A, CDKN1B, RBL2
Nuclear Receptor transcription pathway	20	86	4.80E−04	1.22E−01	ATL3, CCNI, CEP55, CIT, NR3C1, NR6A1, NRBP1, RORA
Amino acids regulate mTORC1	16	61	4.90E−04	1.22E−01	ATP6V0E1, ATP6V1A, ATP6V1C1, ATP6V1G1, FNIP2, GPD2, KLHL20, LAMTOR1, MIOS, MORF4L1, MYO1C, NLGN1, RPN2, RRAGD, SEC23A, SEH1L, SERINC1, VAPA
RUNX3 regulates WNT signaling	6	10	5.40E−04	1.22E−01	CCND1, CTNNB1, RUNX3, TCF4, TCF7L1, ZFYVE16
Signaling by PDGFRA extracellular domain mutants	8	19	7.04E−04	1.27E−01	KRAS, NRAS, PDGFRA, PIK3R1, SOS1, STAT1, STAT3
Antigen processing: Ubiquitination & proteasome degradation	50	315	8.83E−04	1.45E−01	AFF4, ANKRD52, ASB1, ATP6V1A, BIRC6, CD2AP, CDC23, CHD9, CUL1, CUL3, CUL5, DHTKD1, FBXL3, FBXO30, GBF1, GLS, HERC1, ITCH, KBTBD6, KDM6B, KLHL20, KLHL42, LNPEP, LZIC, MKRN1, MSN, MYLIP, PABPN1, PPTC7, PRICKLE2, PSMF1, RBX1, RLIM, RNF138, RNF19A, RPN2, SH3RF1, SIAH2, UBE2B, UBE2G1, UBE2J1, UBE2K, UBE2Q2, UBE2W, UBE2Z, UBE3C, UBE4A, VHL, WWP1
Signaling to ERKs	12	42	1.17E−03	1.76E−01	CRKL, CWC22, E2F3, FRS2, GM2A, KRAS, MAPK1, NRAS, RIT1, SNRNP27, SOS1, YWHAB
Signaling by FGFR3 fusions in cancer	7	17	1.69E−03	1.94E−01	FRS2, GAB1, KRAS, NRAS, PIK3R1, SOS1
Signaling by insulin receptor	20	97	1.97E−03	1.97E−01	ATP11B, ATP6V0E1, ATP6V1A, ATP6V1C1, ATP6V1G1, FRS2, GAB1, GPD2, KRAS, MAPK1, NRAS, PIK3C3, PIK3R1, RPN2, SERINC1, SOS1, THBS2, TNPO1, VAPA
Signaling by NTRKs	29	166	2.72E−03	2.45E−01	CRKL, CWC22, DHTKD1, E2F3, EP300, F3, FRS2, GAB1, GM2A, KRAS, MAPK1, MEF2A, NRAS, PIK3R1, PPP2CB, RAB11FIP5, REST, RHOA, RIT1, RPS6KA3, SLC30A7, SNRNP27, SOS1, STAT3, TRIB1, YTHDF1, YWHAB
TFAP2 (AP-2) family regulates transcription of cell cycle factors	4	6	3.15E−03	2.59E−01	CDKN1A, DHTKD1, KDM5B, TFAP2C
Downstream signaling of activated FGFR4	10	36	3.53E−03	2.76E−01	ATP11B, FRS2, GAB1, KRAS, NRAS, PIK3R1, SOS1, THBS2, TNPO1