Pre-implantation embryo

The source of this pathway is RNA-Seq data from single-cell pre-implantation embryos, Supplemental Table 1 from [http://www.nature.com/nsmb/journal/v20/n9/full/nsmb.2660.html Yan et al.] Analysis options for running the single-cell analysis workflow in AltAnalyze (ICGS): * For optimal filtering (not too restrictive), change the Fold change filter cutoff from 10 to 100 and the Minimum number of samples differing from 3 to 2. * Change the Select the column clustering method to hopach. * The final ICGS cell cluster groups (hopach) were further analyzed to identify genes with restricted expression in one of the identified sub-populations using the MarkerFinder algorithm in AltAnalyze (RPKM>1). * MarkerFinder identified genes for each sub-population (e.g., 8-cell pattern 1) were further filtered for DNA-binding and RNA-binding factors, that are reported in this pathway. Proteins on this pathway have targeted assays available via the [https://assays.cancer.gov/available_assays?wp_id=WP3527 CPTAC Assay Portal]

本路径的来源为单细胞早期胚胎的RNA-Seq数据，详见[http://www.nature.com/nsmb/journal/v20/n9/full/nsmb.2660.html Yan et al.]的补充表格1。在AltAnalyze（ICGS）中运行单细胞分析工作流程的选项分析：* 为实现最佳过滤（不过于严格），将倍数变化过滤阈值从10调整为100，并将最小差异样本数从3调整为2。* 更改选择列聚类方法为hopach。* 对最终的ICGS细胞聚类组（hopach）进行进一步分析，以识别在所识别的亚群中表达受限的基因，采用AltAnalyze（RPKM>1）中的MarkerFinder算法。* MarkerFinder针对每个亚群（例如，8细胞模式1）识别的基因进一步筛选DNA结合和RNA结合因子，这些因子在本路径中有所报道。* 本路径上的蛋白质具有通过[https://assays.cancer.gov/available_assays?wp_id=WP3527 CPTAC检测门户]可用的靶向检测方法。