Alternative gene regulation during CP differentiation.

Number of genes differentially expressed and alternatively spliced. Gene expression values were calculated for 29,151 Ensembl gene identifiers, of which only 13,583 were examined for AS. Genes examined for AS were required to have constitutive annotated probe sets expressed in both undifferentiated H9 ESCs and derived CPs. Transcriptional activity of genes was determined by using either constitutive probe sets, if present, or all probe sets, when not present. Genes with alternative exons are unique Ensembl genes reported by AltAnalyze with alternatively expressed probe sets. Genes with alternative exons only aligning to AS annotations or only to AP annotations are reported along with genes that associate with both AS and AP (multiple exons or one exon with multiple annotations) and no evidence of AS or AP.

差异表达与可变剪接的基因数目。本研究针对29151个Ensembl基因标识符计算了基因表达值，其中仅13583个被用于可变剪接(Alternative Splicing, AS)分析。用于可变剪接分析的基因需满足：其组成型注释探针集在未分化H9胚胎干细胞(Embryonic Stem Cells, ESCs)及诱导分化得到的CP细胞中均有表达。基因的转录活性通过以下方式判定：若存在组成型探针集则使用该探针集，若不存在则使用全部探针集。带有可变外显子的基因为AltAnalyze软件所鉴定得到的、携带差异表达探针集的唯一Ensembl基因。仅匹配可变剪接注释或仅匹配可变多聚腺苷酸化(Alternative Polyadenylation, AP)注释的基因，与同时关联可变剪接与可变多聚腺苷酸化（含多外显子或单外显子带有多重注释的情况）且无可变剪接或可变多聚腺苷酸化证据的基因，均被纳入本次统计。