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Table 2 Overlap of PMS differentially expressed genes (FDR < 5%) with other ASD iPSC transcriptome studies

From: Transcriptional signatures of participant-derived neural progenitor cells and neurons implicate altered Wnt signaling in Phelan-McDermid syndrome and autism

Study descriptionhiPSC-NPCshiPSC-neuronsEnriched GO terms
Author and yearTarget geneApproachCellular modelFET P-valueOdds ratioIntersectExample genesFET P-valueOdds ratioIntersectExample genes
Huang et. 2019SHANK3shRNA KDhiPSC-derived neurons3.3E-041.9344COL5A2, COL18A1NDP, ADAMTS18, CRTAP, NFATC12.4E-074.6420WNT3A, BCAN, FRZB, SPO3, APCDD1, WNT7BCanonical Wnt signaling, perinuclear endoplasmic reticulum lumen
Wang et. 2015CHD8CRISPR/Cas9 heterozygous KOhiPSC-derived NPCs4.0E-031.7133CCCND1, VCAN, NFATC1, SMAD9, LRRC8B, HOXB51.8E-054.1415FRZB, FREM1, RSPO3, ROR2, MMP15, WNT3ACanonical Wnt signaling, golgi lumen, perinuclear endoplasmic reticulum lumen
CHD8CRISPR/Cas9 heterozygous KOhiPSC-derived neurons1.3E-071.9591NKD2, COL5A2, COL18A1, NCAN, COL14A1, INHBE5.7E-073.4829BCAN, FRZB, FREM1, RSPO3, ID1-3, WNT7BNon-canonical Wnt signaling pathway, ECM, Glypican pathway
Chen et. 2014TCF4shRNA KDhiPSC-derived NPCs6.2E-010.935ABCB4, FBXL15, SHF, NELL2, ADAMTSL16.8E-010.891PLEKHA5NA
EHMT1shRNA KDhiPSC-derived NPCs1.8E-032.0523NKD2, CAMK2A, COL18A1, VCAN, NCAN, HOXB61.8E-044.5210BCAN, ID2, ID1, WNT7B, ST6GALNAC3, CORO2BGolgi lumen, ECM, neuron differentiation
Gigek et al. 2015MBD5shRNA KDHuman neural stem cells8.8E-010.676NCAN, SMAD9, E2F7, MARCKSL1, IFITM3, TOP1MT5.6E-011.072ID1, KCNJ10Perineuronal net, ALK1 signaling
SATB2shRNA KDHuman neural stem cells1.7E-011.4111NCAN, HMGA2, KCND3, SIGMAR1, DDB2, GAD12.6E-045.308BCAN, ID1, KCNIP1, KLF10, CORO2B, MPC1ECM proteoglycans, GABA synthesis, p53 signaling, Ras mediated sigaling
Zeng et al. 2013NRXN1shRNA KDHuman neural stem cells1.3E-034.068ZFHX3, NCAN, GFRA1, LRRC8B, DDB2, TMEM151B4.2E-024.684HSPA2, NKD2, COL5A2, KCNIP1Wnt signaling, golgi lumen, L-glutamate import, ion channel complex
Deneault et al. 2018ATRXCRISPR/Cas9 heterozygous KOiPSCs4.0E-021.4332SHANK3, CAMK2N1, INHBE, IGFBP3, SOCS2, GNB42.4E-022.2010BCAN, ID2, SHANK3, CAMK2N1, ST6GALNAC3, RHOUNA
CHD8CRISPR/Cas9 heterozygous KO1.0E+000.000-2.4E-013.721OLIG3NA
AFF2CRISPR/Cas9 heterozygous KO8.8E-010.552CRHBP, GRHL35.4E-011.311HSPA2NA
CACNA1CCRISPR/Cas9 homozygous KO1.5E-011.726INHBE, GRID2, GPC6, SLC7A2, ADM2, CHMP61.7E-012.712KLF10, ID2NA
KCNQ2CRISPR/Cas9 homozygous KO6.3E-011.011MDGA21.0E+000.000-NA
SCN2ACRISPR/Cas9 homozygous KO2.0E-042.0655CCND1, NKD2, COL5A2, VCAN, CRTAP, CAMK2A1.7E-032.5616FRZB, ID1-3, HSPA2, SMOX, ST6GALNAC3, CORO2BVoltage gated sodium channel activity, neuronal precursor differentiation
ASTN2CRISPR/Cas9 homozygous KO3.3E-011.335INHBE, FOXI3, STK32B, SEMA6D, MANEAL5.5E-011.251FOXB1Glycoproteins, ECM, Axon guidance
DLGAP2CRISPR/Cas9 homozygous KO9.3E-010.381IGFBP31.0E-013.762ST6GALNAC3, RHOUNA
TENM1CRISPR/Cas9 heterozygous KO1.8E-011.4011CAMK2N1, SULT1C4, IGFBP3, CELSR1, MOCOS, FBXO258.2E-010.591CAMK2N1NA
ANOS1CRISPR/Cas9 heterozygous KO4.0E-011.462MDGA2, SHISA31.0E+000.000-NA
ATRXCRISPR/Cas9 heterozygous KOiPSC-derived neurons6.7E-072.3647CAMK2A, COL14A1, NCAN, GPC3, SHANK3, TSHZ22.1E-032.8812WNT3A, FRZB, GPC3, SHANK3, TSHZ2, ARHGAP20Cell migration, positive regulation of Wnt, glutamate receptor activity
CHD8CRISPR/Cas9 heterozygous KO1.0E+000.000 2.7E-028.272PCDHGA3, PCDHGA7NA
AFF2CRISPR/Cas9 heterozygous KO3.9E-011.492IGFBP3, COL14A13.4E-027.272SLITRK2, PIEZO2NA
CACNA1CCRISPR/Cas9 homozygous KO6.6E-010.941RASGRP11.0E+000.000-NA
KCNQ2CRISPR/Cas9 homozygous KO1.0E+000.000-1.3E-0417.194WNT3A, MSX2, PIEZO2, PCDHGA3NA
SCN2ACRISPR/Cas9 homozygous KO1.0E+000.000-4.2E-026.422PCDHGA3, PCDHGA7NA
ASTN2CRISPR/Cas9 homozygous KO1.0E+000.000-3.3E-0515.205WNT3A, ID1, MSX2, PIEZO2, PCDHGA3NA
DLGAP2CRISPR/Cas9 homozygous KO1.0E+000.000-1.0E+000.000-NA
TENM1CRISPR/Cas9 heterozygous KO2.9E-011.2312GPC3, ARHGAP20, COL14A1, VCAN, SLC10A4, CAMSAP35.0E-033.607WNT3A, ID1, MSX2, DPPA4, GPC3, ARHGAP20ECM, Glypican pathway, Wnt signaling, signaling patways regulating stem cell pluripotency
ANOS1CRISPR/Cas9 heterozygous KO1.0E+000.000-6.6E-0317.772WNT3A, PCDHGA3NA
  1. A Fisher’s exact test (FET) and an estimated odds-ratio were used to compute significance of each overlap. When the intersection is greater than six, only six intersecting example genes are displayed for brevity. All overlapping genes found in common with the current study were pooled and subjected to pathway analyses using FET and a genome background set to 17353 genes
  2. KD knockdown, KO knockout