Bioinformatics notebook for Plot.ly

FANTOM5 provides high precision data of thousands of human and mouse samples. The vastness of this data can be overwhelming and operating it locally is challenging. Luckily, there are many tools out there to make our life easier. For creating a small data subset we can work with in this tutorial, I used TET: Fantom 5 Table Extraction tool. I picked a few human samples, mostly brain tissues with a few outliers, like uterus and downloaded a tab-separated file from the website. For more advanced data extraction, it's good to have a look atTET's API. I have picked normalized tpm(tags per million) and annotated data, so we can focus only on processed data for protein coding genes.

FANTOM5 提供了涵盖数千份人类与小鼠样本的高精度数据。该数据集体量庞大，易使人应接不暇，且本地操作颇具挑战。所幸目前已有多款工具可简化相关工作。为制作本教程所需的小型数据子集，我使用了TET（FANTOM5表格提取工具，Fantom 5 Table Extraction tool）。我选取了多份人类样本，以脑组织为主，同时纳入了子宫等少量非典型样本，并从官网下载了制表符分隔格式的数据文件。若需开展更高级的数据提取工作，可参考TET的应用程序编程接口（API）。我选取了标准化后的TPM（每百万标签计数，tags per million）数据与注释后的数据，因此我们可仅聚焦于蛋白编码基因的预处理后数据。