Table 1 Gene ontology analysis by cohort and cluster.
From: The offonome reveals on and off states of gene expression near the detection limit of RNA-seq
Cohort | Cluster name | Ontology | count | p value | fdr |
|---|---|---|---|---|---|
LUAD | Cluster 1 (LaC1) | Developmental process | 538 | 3.01E-12 | 3.93E-09 |
Transmembrane transport | 158 | 2.89E-11 | 3.48E-08 | ||
Nervous system development | 242 | 2.35E-10 | 1.84E-07 | ||
Cluster 2 (LaC2) | Cilium movement | 10 | 3.69E-10 | 5.78E-06 | |
Microtubule-based movement | 13 | 4.99E-10 | 3.91E-06 | ||
Cluster 3 (LaC3) | Ion transport | 117 | 2.69E-11 | 8.44E-08 | |
Anatomical structure development | 349 | 1.19E-10 | 2.34E-07 | ||
Trans-synaptic signaling | 58 | 1.43E-10 | 2.49E-07 | ||
Chemical synaptic transmission | 55 | 5.86E-10 | 5.74E-07 | ||
Cluster 4 (LaC4) | Regulation of transcription by RNA polymerase II | 46 | 2.12E-07 | 1.11E-03 | |
snRNA 3’-end processing | 6 | 5.16E-07 | 8.98E-04 | ||
Cluster 5 (LaC5) | Detection of chemical stimulus involved in sensory perception | 360 | 5.57E-180 | 8.74E-176 | |
G protein-coupled receptor signaling pathway | 463 | 2.53E-145 | 4.41E-142 | ||
Nervous system process | 475 | 5.61E-128 | 8.79E-125 | ||
Keratinization | 36 | 5.64E-13 | 7.30E-11 | ||
Natural killer cell activation involved in immune response | 15 | 1.39E-07 | 8.59E-06 | ||
Type I interferon signaling pathway | 15 | 2.14E-05 | 7.85E-04 | ||
LUSC | Cluster 1 (LsC1) | Positive regulation of cytosolic calcium ion concentration | 21 | 1.21E-06 | 1.11E-03 |
Plasma membrane bounded cell projection organization | 58 | 1.92E-05 | 9.72E-03 | ||
Cell projection organization | 58 | 6.14E-05 | 2.60E-02 | ||
Cluster 2 (LsC2) | Epithelial cell differentiation | 59 | 7.48E-12 | 3.91E-08 | |
Keratinization | 19 | 6.89E-10 | 1.35E-06 | ||
Intermediate filament cytoskeleton organization | 17 | 8.56E-08 | 6.10E-05 | ||
Ion transport | 77 | 2.13E-07 | 1.28E-04 | ||
Cluster 3 (LsC3) | Ion transport | 61 | 1.77E-08 | 9.24E-05 | |
Chemical synaptic transmission | 28 | 8.41E-07 | 1.01E-03 | ||
Regulation of ion transmembrane transport | 30 | 4.99E-06 | 3.13E-03 | ||
Cluster 4 (LsC4) | Cilium movement | 15 | 1.22E-11 | 1.92E-07 | |
Microtubule-based movement | 18 | 1.91E-09 | 1.49E-05 | ||
Cluster 5 (LsC5) | Nervous system process | 310 | 2.34E-37 | 1.23E-33 | |
G protein-coupled receptor signaling pathway | 266 | 1.88E-33 | 4.91E-30 | ||
Detection of stimulus | 165 | 1.27E-24 | 1.42E-21 | ||
Cluster 6 (LsC6) | Detection of chemical stimulus involved in sensory perception of smell | 249 | 5.45E-228 | 8.55E-224 | |
G protein-coupled receptor signaling pathway | 280 | 3.55E-172 | 6.18E-169 | ||
Natural killer cell activation involved in immune response | 9 | 1.90E-07 | 1.64E-05 | ||
Type I interferon signaling pathway | 9 | 7.36E-06 | 4.69E-04 | ||
Lung cancer offonome | Cluster 1 (LasC1) | Cilium movement | 28 | 2.25E-12 | 1.76E-08 |
Microtubule bundle formation | 23 | 3.42E-11 | 1.79E-07 | ||
Axoneme assembly | 20 | 7.19E-11 | 2.82E-07 | ||
Cluster 2 (LasC2) | Epidermis development | 33 | 9.58E-14 | 1.50E-09 | |
Keratinization | 16 | 7.73E-11 | 4.04E-07 | ||
Skin development | 26 | 1.39E-10 | 4.37E-07 | ||
Cluster 3 (LasC3) | Regulation of ion transport | 77 | 1.55E-11 | 8.09E-08 | |
Neuron differentiation | 97 | 2.32E-10 | 6.06E-07 | ||
Cluster 4 (LasC4) | Keratinization | 29 | 5.15E-24 | 8.08E-20 | |
Epithelial cell differentiation | 53 | 3.81E-17 | 1.19E-13 | ||
Intermediate filament organization | 17 | 1.94E-12 | 3.81E-09 | ||
Cluster 5 (LasC5) | Cellular metabolic process | 113 | 3.77E-11 | 2.96E-07 | |
Ion transport | 72 | 1.48E-10 | 1.78E-07 | ||
Inorganic ion transmembrane transport | 43 | 1.23E-09 | 9.17E-07 | ||
Cluster 6 (LasC6) | Detection of chemical stimulus involved in sensory perception | 364 | 1.13E-191 | 1.77E-187 | |
G protein-coupled receptor signaling pathway | 479 | 1.05E-157 | 2.05E-154 | ||
HNSC | Cluster 1 (HNsC1) | Multicellular organismal process | 549 | 1.85E-13 | 4.14E-10 |
Developmental process | 482 | 1.60E-12 | 2.09E-09 | ||
Ion transport | 145 | 2.24E-12 | 2.34E-09 | ||
Cluster 2 (HNsC2) | Muscle contraction | 38 | 4.00E-40 | 3.14E-36 | |
Muscle cell differentiation | 31 | 2.44E-28 | 5.47E-25 | ||
Myofibril assembly | 20 | 2.65E-26 | 5.19E-23 | ||
Actomyosin structure organization | 21 | 3.78E-23 | 5.38E-20 | ||
Skeletal muscle tissue development | 20 | 1.84E-20 | 2.22E-17 | ||
Cluster 3 (HNsC3) | Chemical synaptic transmission | 41 | 9.54E-07 | 3.12E-04 | |
Ion transmembrane transport | 68 | 2.35E-06 | 5.94E-04 | ||
Transmembrane transport | 86 | 3.13E-06 | 7.33E-04 | ||
Nervous system process | 98 | 3.74E-06 | 8.61E-04 | ||
Cluster 4 (HNsC4) | G protein-coupled receptor signaling pathway | 136 | 3.96E-12 | 2.48E-09 | |
Sensory perception | 117 | 6.14E-12 | 3.56E-09 | ||
Neuropeptide signaling pathway | 25 | 1.07E-07 | 3.09E-05 | ||
Cluster 5 (HNsC5) | Detection of chemical stimulus involved in sensory perception | 340 | 2.51E-197 | 3.93E-193 | |
Positive regulation of peptidyl-serine phosphorylation of STAT protein | 12 | 2.36E-07 | 1.50E-05 | ||
Natural killer cell activation involved in immune response | 12 | 1.44E-06 | 8.12E-05 | ||
B cell proliferation | 15 | 1.27E-05 | 5.50E-04 | ||
Type I interferon signaling pathway | 12 | 9.95E-05 | 3.43E-03 | ||
Integrative offonome | Cluster 1 (IC1) | Cell adhesion | 91 | 1.42E-08 | 1.01E-05 |
Microtubule bundle formation | 23 | 4.12E-07 | 2.31E-04 | ||
Inorganic ion transmembrane transport | 67 | 7.61E-07 | 3.73E-04 | ||
Cluster 2 (IC2) | Epidermis development | 65 | 1.08E-24 | 1.70E-20 | |
Keratinization | 33 | 2.28E-20 | 1.19E-16 | ||
Intermediate filament organization | 20 | 1.00E-10 | 9.81E-08 | ||
Cluster 3 (IC3) | Cilium movement | 26 | 2.03E-09 | 1.77E-06 | |
Microtubule-based movement | 37 | 9.35E-08 | 4.58E-05 | ||
Regulation of ion transport | 51 | 2.33E-06 | 7.78E-04 | ||
Cluster 4 (IC4) | Nervous system process | 198 | 2.13E-17 | 3.33E-14 | |
Transmembrane transport | 161 | 3.15E-13 | 3.09E-10 | ||
G protein-coupled receptor signaling pathway | 156 | 5.60E-12 | 3.99E-09 | ||
Chemical synaptic transmission | 74 | 1.00E-11 | 6.30E-09 | ||
Muscle system process | 40 | 8.51E-05 | 6.61E-03 | ||
Striated muscle adaptation | 10 | 1.46E-04 | 1.01E-02 | ||
Cluster 5 (IC5) | Detection of chemical stimulus involved in sensory perception | 340 | 1.80E-202 | 1.41E-198 | |
G protein-coupled receptor signaling pathway | 422 | 2.91E-164 | 5.71E-161 | ||
Regulation of peptidyl-serine phosphorylation of STAT protein | 14 | 1.34E-08 | 1.03E-06 | ||
Natural killer cell activation involved in immune response | 14 | 2.94E-08 | 2.15E-06 | ||
G protein-coupled serotonin receptor signaling pathway | 15 | 1.47E-07 | 9.62E-06 | ||
Type I interferon signaling pathway | 14 | 4.30E-06 | 2.17E-04 |
