Table 3. Top twenty list of genes significantly over- or under-expressed in SN ONLY.
| Genes | Chr | Expression value A | Expression value B | A/B | p value | q value | Data points A | Data points B | SD% A | SD% B | GO term Process |
|---|---|---|---|---|---|---|---|---|---|---|---|
| OVER-EXPRESSED GENES | |||||||||||
| DEFA3 | chr8 | 103.37 | 20.96 | 4.93 | 0.0250 | 0.0260 | 28 | 27 | 388.81 | 87.01 | innate immune response (GO:0045087) |
| AZGP1 | chr7 | 126.99 | 57.63 | 2.20 | 0.0250 | 0.0260 | 166 | 143 | 109.93 | 108.28 | immune response (GO:0006955) |
| PCDH20 | chr13 | 133.73 | 62.01 | 2.16 | 0.0250 | 0.0260 | 68 | 51 | 99.42 | 95.18 | cell adhesion (GO:0007155) |
| CTSG | chr14 | 42.59 | 19.83 | 2.15 | 0.0250 | 0.0260 | 100 | 88 | 480.67 | 51.89 | angiotensin maturation (GO:0002003) |
| NPTX2 | chr7 | 261.40 | 122.44 | 2.13 | 0.0250 | 0.0260 | 94 | 82 | 87.34 | 102.19 | synaptic transmission (GO:0007268) |
| Hs.291993 | chr13 | 80.19 | 37.69 | 2.13 | 0.0250 | 0.0260 | 56 | 41 | 109.12 | 45.91 | uncharacterized |
| SLC38A2 | chr12 | 1,015.73 | 477.45 | 2.13 | 0.0250 | 0.0260 | 206 | 169 | 114.33 | 118.89 | amino acid transport (GO:0006865) |
| BOK | chr2 | 296.41 | 141.19 | 2.10 | 0.0250 | 0.0260 | 140 | 112 | 153.60 | 133.83 | apoptotic process (GO:0006915) |
| USP54 | chr10 | 675.24 | 327.69 | 2.06 | 0.0250 | 0.0260 | 68 | 51 | 81.51 | 86.91 | protein deubiquitination (GO:0016579) |
| DEFA1 | chr8 | 92.03 | 45.26 | 2.03 | 0.0250 | 0.0260 | 148 | 137 | 378.79 | 368.04 | innate immune response (GO:0045087) |
| USP31 | chr16 | 316.63 | 159.36 | 1.99 | 0.0250 | 0.0260 | 164 | 110 | 91.95 | 83.16 | protein deubiquitination (GO:0016579) |
| LINC00844 | chr10 | 2,425.15 | 1,223.60 | 1.98 | 0.0250 | 0.0260 | 56 | 41 | 85.85 | 97.98 | ncRNA |
| DANCR | chr4 | 305.40 | 160.14 | 1.91 | 0.0250 | 0.0260 | 40 | 26 | 39.04 | 30.96 | uncharacterized |
| LRP2 | chr2 | 130.19 | 68.32 | 1.91 | 0.0250 | 0.0260 | 139 | 113 | 108.13 | 84.02 | Wnt signaling pathway (GO:0060070) |
| DOCK5 | chr8 | 171.88 | 91.12 | 1.89 | 0.0250 | 0.0260 | 310 | 231 | 147.56 | 147.90 | positive regulation of GTPase activity (GO:0043547) |
| PDK4 | chr7 | 347.20 | 184.22 | 1.88 | 0.0250 | 0.0260 | 155 | 122 | 125.33 | 129.28 | cellular metabolic process (GO:0044237) |
| SLC5A11 | chr16 | 352.10 | 188.32 | 1.87 | 0.0250 | 0.0260 | 68 | 51 | 58.45 | 59.75 | apoptotic process (GO:0006915) |
| MAFK | chr7 | 117.65 | 63.73 | 1.85 | 0.0250 | 0.0260 | 139 | 113 | 170.50 | 159.09 | regulation of transcription(GO:0006357) |
| PTGS2 | chr1 | 2,685.97 | 1,479.78 | 1.82 | 0.0250 | 0.0260 | 163 | 133 | 204.02 | 250.58 | NAD metabolic process (GO:0019674) |
| CDK2AP2 | chr11 | 106.81 | 59.57 | 1.79 | 0.0250 | 0.0260 | 99 | 89 | 71.57 | 56.51 | N/A |
| UNDER-EXPRESSED GENES | |||||||||||
| NHLRC1 | chr6 | 12.33 | 84.44 | 0.15 | 0.0250 | 0.0252 | 28 | 27 | 21.35 | 397.11 | protein polyubiquitination (GO:0000209) |
| C12orf50 | chr12 | 14.49 | 102.57 | 0.14 | 0.0250 | 0.0252 | 84 | 70 | 70.81 | 685.40 | nucleic acid binding (GO:0003676) |
| SIRPD | chr20 | 25.92 | 185.50 | 0.14 | 0.0250 | 0.0252 | 68 | 53 | 35.55 | 623.70 | N/A |
| WNT9B | chr17 | 15.56 | 112.31 | 0.14 | 0.0250 | 0.0252 | 44 | 36 | 64.63 | 495.38 | Wnt signaling pathway (GO:0060070) |
| REG4 | chr1 | 13.16 | 101.70 | 0.13 | 0.0250 | 0.0252 | 84 | 62 | 40.77 | 669.15 | carbohydrate binding (GO:0030246) |
| OR51G1 | chr11 | 13.23 | 104.38 | 0.13 | 0.0250 | 0.0252 | 28 | 27 | 28.50 | 312.26 | signal trasduction (GO:0007165) |
| IQCF6 | chr3 | 12.95 | 105.92 | 0.12 | 0.0250 | 0.0252 | 40 | 26 | 35.21 | 441.65 | N/A |
| CFAP54 | chr12 | 15.62 | 128.26 | 0.12 | 0.0250 | 0.0252 | 44 | 40 | 45.56 | 532.52 | integral component of membrane |
| KDF1 | chr1 | 13.87 | 121.06 | 0.11 | 0.0250 | 0.0252 | 68 | 53 | 55.21 | 619.20 | developmental growth (GO:0048589) |
| KIAA0087 | chr7 | 10.14 | 89.23 | 0.11 | 0.0250 | 0.0252 | 65 | 62 | 38.06 | 679.79 | ncRNA |
| CLC | chr19 | 16.14 | 153.92 | 0.10 | 0.0250 | 0.0252 | 100 | 88 | 87.05 | 825.34 | apoptotic process (GO:0006915) |
| CDY2A | chrY | 18.56 | 177.17 | 0.10 | 0.0250 | 0.0252 | 28 | 27 | 46.12 | 460.82 | histone acetylation (GO:0016573) |
| MAGEA2B | chrX | 12.85 | 134.08 | 0.10 | 0.0250 | 0.0252 | 28 | 29 | 37.22 | 459.70 | negative regulation of protein acetylation (GO:1901984) |
| COLCA2 | chr11 | 48.63 | 537.78 | 0.09 | 0.0250 | 0.0252 | 40 | 26 | 32.55 | 456.61 | N/A |
| FOXB2 | chr9 | 14.85 | 169.39 | 0.09 | 0.0250 | 0.0252 | 28 | 27 | 53.82 | 453.21 | cell differentiation (GO:0030154) |
| ANGPTL5 | chr11 | 14.78 | 231.16 | 0.06 | 0.0250 | 0.0252 | 28 | 27 | 32.65 | 463.92 | N/A |
| ARSH | chrX | 16.93 | 267.32 | 0.06 | 0.0250 | 0.0252 | 28 | 27 | 62.76 | 473.06 | metabolic process (GO:0008152) |
| PSMG3-AS1 | chr7 | 32.90 | 625.84 | 0.05 | 0.0250 | 0.0252 | 16 | 13 | 34.45 | 334.15 | ncRNA |
| TEX22 | chr14 | 19.35 | 428.53 | 0.05 | 0.0250 | 0.0252 | 16 | 11 | 32.01 | 313.27 | N/A |
| OR8H3 | chr11 | 32.63 | 813.20 | 0.04 | 0.0250 | 0.0252 | 28 | 27 | 74.87 | 495.50 | signal trasduction (GO:0007165) |
The twenty most over- and under-expressed genes resulted in SN ONLY (pool A vs. pool B) "Map" mode analysis with a segment window of 12,500 bp, considering genome median analysis (see full results in Supplementary Information section). Data points: number of spots related to an expression value for the locus. SD: standard deviation of the expression value indicated as percentage of the mean. GO term Process: description and accession number of the main biological process associated to the gene according to Gene Ontology Consortium. N/A: not available in the Gene Ontology database.