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Gene & Protein in Disease Pre-metastatic niche oral cancer: Insights

Table 3. (Continued)
Term % P‑value Genes Fold Bonferroni Benjamini FDR
enrichment
hsa04360: Axon 1.13851992 0.07534992 HRAS, GNAI3, PLXNA1, LIMK2, 1.414120346 0.999999357 0.50977612 61.9675645
guidance PLXNA2, EFNA1, GNAI1, EFNB1,
DPYSL5, EPHB3, EPHB4, EPHA2, PAK6,
NRAS, EPHA4, UNC5B, RAC3, SEMA3F,
RAC1, SEMA4B, SEMA3C, NFATC4,
RHOD, SRGAP1
hsa04916: 0.90132827 0.09220218 HRAS, GNAI3, GNAI1, WNT3A, MITF, 1.458757983 0.999999977 0.567579927 69.6906156
Melanogenesis EDN1, FZD1, TCF7L2, TCF7L1, FZD6,
DVL1, WNT2, NRAS, PLCB3, MC1R,
CALML3, CREB3L1, CALML5, PLCB1
Note: P<0.05 was considered statistically significant.
Abbreviations: ECM: Extracellular matrix; FDR: False discovery rate.
Table 4. Functional annotation analysis of upregulated differentially expressed genes overlapping in non‑metastatic and
metastatic lymph nodes (GSE70604) associated with pre‑metastatic niche‑related genes using the Database for Annotation,
Visualization, and Integrated Discovery tool

Term % P‑value Genes Fold Bonferroni Benjamini FDR
enrichment
hsa04660: T cell 2.22222222 3.75E-14 TNF, CD8A, CD8B, NFKBIE, 3.24474585 6.90E-12 6.90E-12 4.64E-11
receptor signaling CD247, NFKB1, MAP3K7, KRAS,
pathway RASGRP1, ICOS, MAP3K8,
PPP3CB, ZAP70, PIK3CA, CD4,
PIK3R5, NFATC3, AKT3, CD28,
NFATC1, TEC, AKT2, PIK3CG,
PTPN6, ITK, PTPRC, IL5,
CD3G, CD3D, CD3E, PIK3CD,
CTLA4, MALT1, VAV1, CARD11,
MAPK1, LAT, PRKCQ, CBLB,
PLCG1, FYN, CD40LG, LCK,
IKBKG, MAP3K14, GRAP2, LCP2
hsa05340: Primary 1.13475177 1.01E-12 CIITA, PTPRC, CD3D, CD8A, 5.11269376 1.86E-10 9.30E-11 1.25E-09
immunodeficiency CD8B, RFX5, CD3E, CD40, IL7R,
RFXAP, BTK, DCLRE1C, CD19,
CD40LG, ICOS, LCK, IKBKG,
AIRE, ZAP70, CD4, AICDA,
IL2RG, CD79A, BLNK
hsa04662: B cell 1.65484634 1.07E-11 NFKBIE, NFKB1, CD72, BTK, 3.47947214 1.96E-09 6.54E-10 1.32E-08
receptor signaling KRAS, DAPP1, RASGRP3, RAC2,
pathway PPP3CB, PIK3CA, CD22, PIK3R5,
INPP5D, NFATC3, AKT3, AKT2,
NFATC1, BLNK, SYK, PIK3CG,
PTPN6, CR2, LYN, PIK3CD,
MALT1, VAV1, PRKCB, CARD11,
MAPK1, CD19, FCGR2B, PLCG2,
IKBKG, CD79B, CD79A
hsa04640: 1.74940898 4.52E-11 CSF3, TNF, HLA‑DRB1, CD8A, 3.207819 8.31E-09 2.08E-09 5.58E-08
Hematopoietic cell CD8B, FCER2, HLA‑DRB3,
lineage KIT, IL7R, IL11, FLT3LG, IL4R,
MS4A1, CD2, CD22, CD4,
GP1BA, CD5, CSF2RA, CD7,
CR2, IL5, CD3G, CD3D, IL7,
CD3E, FLT3, CD1C, CD1B,
ITGA4, IL6R, CD1E, CD1D,
CD37, CD19, IL3RA, HLA‑DRA
(Cont’d...)

Volume 3 Issue 4 (2024) 10 doi: 10.36922/gpd.2971