TABLE 2

Gene set enrichment analysis was carried out to identify differentially regulated pathways between P2 N-HBECs and P5 B-HBECs

NAMEDirectionSIZEESNESFDR q-valueLeading edge
KOBAYASHI EGFR SIGNALING_24HR_DNUpregulated2440.742.230tags: 74%, list: 16%, signal: 88%
ROSTY CERVICAL CANCER PROLIFERATION CLUSTERUpregulated1370.742.130tags: 84%, list: 18%, signal: 102%
SOTIRIOU BREAST CANCER GRADE 1_VS_ 3 UPUpregulated1460.742.130tags: 85%, list: 18%, signal: 103%
MANALO HYPOXIA DNUpregulated2820.692.110tags: 65%, list: 15%, signal: 75%
DUTERTRE ESTRADIOL_RESPONSE_24HR UPUpregulated3160.682.100tags: 68%, list: 15%, signal: 80%
BLUM RESPONSE TO_SALIRASIB_DNUpregulated3400.662.060tags: 70%, list: 18%, signal: 85%
ZHOU CELL CYCLE GENES IN IR RESPONSE 6HRUpregulated820.772.060tags: 78%, list: 14%, signal: 91%
ZHOU CELL CYCLE GENES IN IR RESPONSE 24HRUpregulated1230.732.040tags: 77%, list: 17%, signal: 93%
SARRIO EPITHELIAL MESENCHYMAL TRANSITION UPUpregulated1730.692.020tags: 73%, list: 18%, signal: 88%
FOURNIER ACINAR_DEVELOPMENT_LATE_2Upregulated2700.662.010tags: 64%, list: 16%, signal: 76%
TIEN INTESTINE PROBIOTICS_24HR_DNDownregulated213−0.69−2.110tags: 82%, list: 21%, signal: 103%
BOSCO EPITHELIAL DIFFERENTIATION MODULEDownregulated69−0.75−2.012.57×10−4tags: 74%, list: 18%, signal: 90%
KEGG RIBOSOMEDownregulated88−0.73−2.033.85×10−4tags: 88%, list: 23%, signal: 114%
REACTOME SRP_DEPENDENT_COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANEDownregulated126−0.68−1.984.69×10−4tags: 83%, list: 23%, signal: 107%
REACTOME PEPTIDE_CHAIN_ELONGATIONDownregulated102−0.72−1.985.86×10−4tags: 87%, list: 23%, signal: 113%
RICKMAN HEAD_AND_NECK_CANCER_EDownregulated87−0.71−1.940.00184tags: 71%, list: 17%, signal: 85%
REACTOME 3_UTR_MEDIATED_TRANSLATIONAL REGULATIONDownregulated123−0.66−1.930.00203tags: 71%, list: 19%, signal: 87%
REACTOME TRANSLATIONDownregulated165−0.63−1.880.00587tags: 66%, list: 19%, signal: 82%
REACTOME NONSENSE MEDIATED DECAY ENHANCED BY THE_EXON JUNCTION_COMPLEXDownregulated123−0.64−1.870.00609tags: 80%, list: 23%, signal: 103%
HOLLERN EMT_BREAST_TUMOR_DNDownregulated95−0.65−1.820.01532tags: 51%, list: 12%, signal: 57%

143 pathways were significantly (q<0.05) enriched in B-HBECs and 20 were enriched in the N-HBECs (top 10 shown ranked on q-value and then ES). Size indicates the number of genes in the gene set after filtering out those not in the expression dataset.

N-HBEC: normal human bronchial epithelial cell; B-HBEC: BMI-1-expressing human bronchial epithelial cells; ES: enrichment score for the gene set, which is the degree that the gene set is over-represented at the top or bottom of the ranked list of genes in the expression dataset; NES: normalised enrichment score; FDR q-value: false discovery rate adjusted p-value, which is the estimated probability that the NES represents a false positive; leading edge subset: subset of members that contribute the most to the ES; tags: percentage of genes contributing to the ES.