Supplemental data for thesis

Supplemental data for thesis submitted to Cardiff University School of Biosciences:
Cepraga, A.A. (2020) "An investigation into Mef2-interacting proteins during embryonic muscle development of Drosophila"
Each file is provided twice: in a plain-text format such as .tsv , and as an Excel file. Note that .tsv files are tab-delimited. Make sure
that they are not treated as space-delimited when imported in
spreadsheet software to display them properly.
This repository contains:- Table S1: Raw spectral counts and hit ranking of all proteins identified by TAP/MS (total spectral counts for each protein identified by MS in tandem affinity purification from Drosophila embryos with Mef2 as the tagged bait)- Table S2: Mef2 GO biological process terms- Table S3: High-interest candidates identified by each analysis
- Table S4: Overlap of TAP datasets with muscleRNAi screen by Schnorrer et al 2010
- Data supplementals for individual figures. The file names indicate which figure the file corresponds to. Most of these report the IDs of genes in the different overlap fields of Venn diagrams. The dataset for Fig4.12 contains the functional similarity network including the pairwise functional similarity scores between the candidates.
- The file for Fig4.8 contains pmax for all candidates across embryonic stagings. The file for Fig4.10 contains GO enrichment for all Mef2 GO terms in each dataset and subset. These two files are in the appropriate format for use in the Morpheus matrix visualisation tool at https://software.broadinstitute.org/morpheus/ (Download the .gct files from here, open the Morpheus page, click "select file" and select the .gct file from your Downloads folder.)

- a Morpheus color scheme file to be used in conjunction with Fig4-10GOenrichment[...].gct. To apply the colour scheme, first download both the Fig4-10.gct and the color-scheme.json files. Open the Fig4-10.gct in Morpheus as described above. Click the Options button in the top-right corner (cogwheel symbol), which opens the Color scheme dialog. Scroll down to find the field "Saved color scheme" and select "My computer" from the dropdown box. Finally, click "Load color scheme" and select the downloaded .json file from your Downloads folder.

本数据集为提交至卡迪夫大学生物科学学院的学位论文补充数据：Cepraga, A.A.（2020）《果蝇胚胎肌肉发育过程中Mef2互作蛋白的研究》

所有文件均提供两种格式：纯文本格式（如.tsv格式）与Excel文件。请注意，.tsv文件采用制表符分隔，在电子表格软件中导入时，请确保其不会被识别为空格分隔格式，以保证正确显示。

本数据集仓库包含以下内容：
- 表S1：通过TAP/MS鉴定的所有蛋白质的原始光谱计数与命中排名（即以Mef2为标记诱饵，从果蝇胚胎中开展串联亲和纯化后经质谱鉴定得到的每种蛋白质的总光谱计数）
- 表S2：Mef2的基因本体（Gene Ontology, GO）生物过程术语
- 表S3：各分析所鉴定的高关注度候选蛋白
- 表S4：TAP/MS数据集与Schnorrer等人2010年开展的肌肉RNAi筛选数据集的重叠情况

- 各独立图表的补充数据。文件名标注了其对应的图表编号。此类文件大多用于标注维恩图不同重叠区域的基因ID。图4.12对应的数据集包含功能相似性网络，其中包含候选蛋白间的成对功能相似性得分。

- 图4.8对应的文件包含所有候选蛋白在各胚胎发育分期阶段的pmax值。图4.10对应的文件包含各数据集及子集下所有Mef2相关GO术语的基因本体富集分析结果。这两个文件的格式适配https://software.broadinstitute.org/morpheus/ 提供的Morpheus矩阵可视化工具：可从该链接下载.gct格式文件，打开Morpheus页面后，点击"select file"并选择下载文件夹中的.gct文件即可。

- 配套用于Fig4-10GOenrichment[...].gct的Morpheus配色方案文件。如需应用该配色方案，请先同时下载Fig4-10.gct与color-scheme.json两个文件。按前述步骤在Morpheus中打开Fig4-10.gct后，点击右上角的选项按钮（齿轮图标）打开配色方案对话框，下拉至"Saved color scheme"字段，从下拉菜单中选择"My computer"，最后点击"Load color scheme"并选择下载文件夹中的.json配色文件即可。