MOESM6 of Cellular and molecular characterization of multiplex autism in human induced pluripotent stem cell-derived neurons

Additional file 6: Table S5. (A) Clusters of co-expressed DEGs in cExN and cIN NPCs, with (B-G) associated ToppGene GO-, disease-, and pathway-associated terms. (H-I) DEGs associated with ASD. DEGs specific to the AP (Fig. 5A, E) and DEGs with similar expression in the AP and IS that differed from expression in the UM +/− UC (Fig. 4a, e) were visualized by hierarchical clustering in Fig. 6 and were compared with ASD-associated genes in the SFARI gene database [43], with the Geisinger Developmental Brain Disorder Genes Database [44], and with adult-onset psychiatric disorder-associated genes from PsyGeNET [45, 46]. RPKM values for each gene and sample are shown. The SFARI gene database indicates how each gene is associated with ASD (genetic category, gene score, and number of reports). The Geisinger database indicates the pattern of inheritance of mutations in each gene and the number of reports linking each gene to intellectual disability (ID), ASD, epilepsy (EP), attention-deficit/hyperactivity disorder (ADHD), schizophrenia (SCZ), or bipolar disorder (BD). The PsyGeNET database indicates genes associated with the disorders shown, with ‘unique 4 or 5 abstract’ indicating higher confidence associations.

附加文件6：表S5。(A) 皮质兴奋性神经元（cortical excitatory neurons, cExN）与皮质抑制性神经元（cortical inhibitory neurons, cIN）来源的神经前体细胞（Neural Progenitor Cells, NPCs）内共表达差异表达基因（Differentially Expressed Genes, DEGs）的聚类结果，以及(B-G) 与之关联的ToppGene分析所得基因本体论（Gene Ontology, GO）、疾病及通路相关注释术语。(H-I) 与孤独症谱系障碍（Autism Spectrum Disorder, ASD）相关的差异表达基因。针对AP特异性差异表达基因（图5A、E），以及在AP与IS中表达模式相似但与UM ± UC中表达模式存在差异的差异表达基因（图4a、e），本研究通过层级聚类分析将其可视化于图6，并分别与SFARI基因数据库[43]、盖辛格发育性脑疾病基因数据库[44]以及PsyGeNET数据库[45,46]中的成人起病精神疾病相关基因进行了比对。本数据集提供了所有基因及对应样本的每百万reads外显子片段数（Reads Per Kilobase per Million mapped reads, RPKM）数值。SFARI基因数据库会标注各基因与ASD的关联方式，包括遗传类别、基因评分及相关报道数量。盖辛格发育性脑疾病基因数据库则标注了各基因的突变遗传模式，以及各基因与智力障碍（Intellectual Disability, ID）、ASD、癫痫（Epilepsy, EP）、注意缺陷多动障碍（Attention-Deficit/Hyperactivity Disorder, ADHD）、精神分裂症（Schizophrenia, SCZ）或双相障碍（Bipolar Disorder, BD）相关的报道数量。PsyGeNET数据库标注了与上述疾病相关的基因，其中标注为"unique 4或5篇摘要"的条目代表该基因与疾病的关联可信度更高。