Table 2 Overlap of PMS differentially expressed genes (FDR < 5%) with other ASD iPSC transcriptome studies
Study description | hiPSC-NPCs | hiPSC-neurons | Enriched GO terms | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
Author and year | Target gene | Approach | Cellular model | FET P-value | Odds ratio | Intersect | Example genes | FET P-value | Odds ratio | Intersect | Example genes | |
Huang et. 2019 | SHANK3 | shRNA KD | hiPSC-derived neurons | 3.3E-04 | 1.93 | 44 | COL5A2, COL18A1NDP, ADAMTS18, CRTAP, NFATC1 | 2.4E-07 | 4.64 | 20 | WNT3A, BCAN, FRZB, SPO3, APCDD1, WNT7B | Canonical Wnt signaling, perinuclear endoplasmic reticulum lumen |
Wang et. 2015 | CHD8 | CRISPR/Cas9 heterozygous KO | hiPSC-derived NPCs | 4.0E-03 | 1.71 | 33 | CCCND1, VCAN, NFATC1, SMAD9, LRRC8B, HOXB5 | 1.8E-05 | 4.14 | 15 | FRZB, FREM1, RSPO3, ROR2, MMP15, WNT3A | Canonical Wnt signaling, golgi lumen, perinuclear endoplasmic reticulum lumen |
CHD8 | CRISPR/Cas9 heterozygous KO | hiPSC-derived neurons | 1.3E-07 | 1.95 | 91 | NKD2, COL5A2, COL18A1, NCAN, COL14A1, INHBE | 5.7E-07 | 3.48 | 29 | BCAN, FRZB, FREM1, RSPO3, ID1-3, WNT7B | Non-canonical Wnt signaling pathway, ECM, Glypican pathway | |
Chen et. 2014 | TCF4 | shRNA KD | hiPSC-derived NPCs | 6.2E-01 | 0.93 | 5 | ABCB4, FBXL15, SHF, NELL2, ADAMTSL1 | 6.8E-01 | 0.89 | 1 | PLEKHA5 | NA |
EHMT1 | shRNA KD | hiPSC-derived NPCs | 1.8E-03 | 2.05 | 23 | NKD2, CAMK2A, COL18A1, VCAN, NCAN, HOXB6 | 1.8E-04 | 4.52 | 10 | BCAN, ID2, ID1, WNT7B, ST6GALNAC3, CORO2B | Golgi lumen, ECM, neuron differentiation | |
Gigek et al. 2015 | MBD5 | shRNA KD | Human neural stem cells | 8.8E-01 | 0.67 | 6 | NCAN, SMAD9, E2F7, MARCKSL1, IFITM3, TOP1MT | 5.6E-01 | 1.07 | 2 | ID1, KCNJ10 | Perineuronal net, ALK1 signaling |
SATB2 | shRNA KD | Human neural stem cells | 1.7E-01 | 1.41 | 11 | NCAN, HMGA2, KCND3, SIGMAR1, DDB2, GAD1 | 2.6E-04 | 5.30 | 8 | BCAN, ID1, KCNIP1, KLF10, CORO2B, MPC1 | ECM proteoglycans, GABA synthesis, p53 signaling, Ras mediated sigaling | |
Zeng et al. 2013 | NRXN1 | shRNA KD | Human neural stem cells | 1.3E-03 | 4.06 | 8 | ZFHX3, NCAN, GFRA1, LRRC8B, DDB2, TMEM151B | 4.2E-02 | 4.68 | 4 | HSPA2, NKD2, COL5A2, KCNIP1 | Wnt signaling, golgi lumen, L-glutamate import, ion channel complex |
Deneault et al. 2018 | ATRX | CRISPR/Cas9 heterozygous KO | iPSCs | 4.0E-02 | 1.43 | 32 | SHANK3, CAMK2N1, INHBE, IGFBP3, SOCS2, GNB4 | 2.4E-02 | 2.20 | 10 | BCAN, ID2, SHANK3, CAMK2N1, ST6GALNAC3, RHOU | NA |
CHD8 | CRISPR/Cas9 heterozygous KO | 1.0E+00 | 0.00 | 0 | - | 2.4E-01 | 3.72 | 1 | OLIG3 | NA | ||
AFF2 | CRISPR/Cas9 heterozygous KO | 8.8E-01 | 0.55 | 2 | CRHBP, GRHL3 | 5.4E-01 | 1.31 | 1 | HSPA2 | NA | ||
CACNA1C | CRISPR/Cas9 homozygous KO | 1.5E-01 | 1.72 | 6 | INHBE, GRID2, GPC6, SLC7A2, ADM2, CHMP6 | 1.7E-01 | 2.71 | 2 | KLF10, ID2 | NA | ||
KCNQ2 | CRISPR/Cas9 homozygous KO | 6.3E-01 | 1.01 | 1 | MDGA2 | 1.0E+00 | 0.00 | 0 | - | NA | ||
SCN2A | CRISPR/Cas9 homozygous KO | 2.0E-04 | 2.06 | 55 | CCND1, NKD2, COL5A2, VCAN, CRTAP, CAMK2A | 1.7E-03 | 2.56 | 16 | FRZB, ID1-3, HSPA2, SMOX, ST6GALNAC3, CORO2B | Voltage gated sodium channel activity, neuronal precursor differentiation | ||
ASTN2 | CRISPR/Cas9 homozygous KO | 3.3E-01 | 1.33 | 5 | INHBE, FOXI3, STK32B, SEMA6D, MANEAL | 5.5E-01 | 1.25 | 1 | FOXB1 | Glycoproteins, ECM, Axon guidance | ||
DLGAP2 | CRISPR/Cas9 homozygous KO | 9.3E-01 | 0.38 | 1 | IGFBP3 | 1.0E-01 | 3.76 | 2 | ST6GALNAC3, RHOU | NA | ||
TENM1 | CRISPR/Cas9 heterozygous KO | 1.8E-01 | 1.40 | 11 | CAMK2N1, SULT1C4, IGFBP3, CELSR1, MOCOS, FBXO25 | 8.2E-01 | 0.59 | 1 | CAMK2N1 | NA | ||
ANOS1 | CRISPR/Cas9 heterozygous KO | 4.0E-01 | 1.46 | 2 | MDGA2, SHISA3 | 1.0E+00 | 0.00 | 0 | - | NA | ||
ATRX | CRISPR/Cas9 heterozygous KO | iPSC-derived neurons | 6.7E-07 | 2.36 | 47 | CAMK2A, COL14A1, NCAN, GPC3, SHANK3, TSHZ2 | 2.1E-03 | 2.88 | 12 | WNT3A, FRZB, GPC3, SHANK3, TSHZ2, ARHGAP20 | Cell migration, positive regulation of Wnt, glutamate receptor activity | |
CHD8 | CRISPR/Cas9 heterozygous KO | 1.0E+00 | 0.00 | 0 | Â | 2.7E-02 | 8.27 | 2 | PCDHGA3, PCDHGA7 | NA | ||
AFF2 | CRISPR/Cas9 heterozygous KO | 3.9E-01 | 1.49 | 2 | IGFBP3, COL14A1 | 3.4E-02 | 7.27 | 2 | SLITRK2, PIEZO2 | NA | ||
CACNA1C | CRISPR/Cas9 homozygous KO | 6.6E-01 | 0.94 | 1 | RASGRP1 | 1.0E+00 | 0.00 | 0 | - | NA | ||
KCNQ2 | CRISPR/Cas9 homozygous KO | 1.0E+00 | 0.00 | 0 | - | 1.3E-04 | 17.19 | 4 | WNT3A, MSX2, PIEZO2, PCDHGA3 | NA | ||
SCN2A | CRISPR/Cas9 homozygous KO | 1.0E+00 | 0.00 | 0 | - | 4.2E-02 | 6.42 | 2 | PCDHGA3, PCDHGA7 | NA | ||
ASTN2 | CRISPR/Cas9 homozygous KO | 1.0E+00 | 0.00 | 0 | - | 3.3E-05 | 15.20 | 5 | WNT3A, ID1, MSX2, PIEZO2, PCDHGA3 | NA | ||
DLGAP2 | CRISPR/Cas9 homozygous KO | 1.0E+00 | 0.00 | 0 | - | 1.0E+00 | 0.00 | 0 | - | NA | ||
TENM1 | CRISPR/Cas9 heterozygous KO | 2.9E-01 | 1.23 | 12 | GPC3, ARHGAP20, COL14A1, VCAN, SLC10A4, CAMSAP3 | 5.0E-03 | 3.60 | 7 | WNT3A, ID1, MSX2, DPPA4, GPC3, ARHGAP20 | ECM, Glypican pathway, Wnt signaling, signaling patways regulating stem cell pluripotency | ||
ANOS1 | CRISPR/Cas9 heterozygous KO | 1.0E+00 | 0.00 | 0 | - | 6.6E-03 | 17.77 | 2 | WNT3A, PCDHGA3 | NA | ||