PTMoreR: a motif-centric analysis enabling cross-species PTM mapping and comparative phosphoproteomics across mammals
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Supplementary Table S2-S7 for PTMoreR Table S2. The 115,179 and 42,997 phosphorylation sites (P-sites) for human and mouse phosphoproteomes obtained from two recent large-scale studies 1,2. Two sheet names here are marked as “Human.identified” and “Mouse.identified” respectively. Table S3. The information and organism identifies for the 129 mammalian species downloaded from UniProt (http://www.uniprot.org/) 3. Table S4. The features and the detectability matrix of P-sites in the Human.identified phosphoproteome data across species. Column 1 to 3 are UniProt ID, residue, and P-site position, respectively. Column 4 to 17 are the annotated phosphoproteome features that used in the Figure 2C, Figure 4B, 4E, 4F, Supplementary Figure S4 and S7B-S7C. Column 18 to 146 are the detectability matrix, in which the values are 0 for those sites not mapped in corresponding species and 1 for those mapped. The window similarity scores are >= 8. Table S5. The GO terms with the BH adjusted P value < 0.01 in one of Q1-Q5 segments and > 0.05 in the other four from the GO enrichment analysis based on corresponding phosphoproteins. Table S6. The results with BH adjusted P value < 0.01 from the kinase enrichment analysis in each of Q1-Q5 segments. Table S7. The phosphorylation expression data and statistical results from 10 common mammalian species (Euarchontoglires (i.e., Human, Rat, Rabbit, Monkey) and Laurasiatheria (i.e., Cow, Horse, Pig, Dog, Cat, Sheep)) 4. References 1. Giansanti, P., Samaras, P., Bian, Y., Meng, C., Coluccio, A., Frejno, M., Jakubowsky, H., Dobiasch, S., Hazarika, R.R., Rechenberger, J. et al. (2022) Mass spectrometry-based draft of the mouse proteome. Nat Methods, 19, 803-811. 2. Ochoa, D., Jarnuczak, A.F., Vieitez, C., Gehre, M., Soucheray, M., Mateus, A., Kleefeldt, A.A., Hill, A., Garcia-Alonso, L., Stein, F. et al. (2020) The functional landscape of the human phosphoproteome. Nat Biotechnol, 38, 365-373. 3. UniProt, C. (2021) UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res, 49, D480-D489. 4. Ba, Q., Hei, Y., Dighe, A., Li, W., Maziarz, J., Pak, I., Wang, S., Wagner, G.P. and Liu, Y. (2022) Proteotype coevolution and quantitative diversity across 11 mammalian species. Sci Adv, 8, eabn0756.
PTMoreR 补充表 S2 至 S7 表S2：取自两项近期大规模研究[1,2]的人类与小鼠磷酸化组学对应的115179个和42997个磷酸化位点（P-sites）。本表包含两个工作表，分别命名为"Human.identified"与"Mouse.identified"。 表S3：从UniProt（http://www.uniprot.org/）[3]下载的129种哺乳动物的相关信息及物种标识。 表S4：跨物种的Human.identified磷酸化组学数据中磷酸化位点的特征及可检测性矩阵。第1至3列依次为UniProt编号（UniProt ID）、氨基酸残基及磷酸化位点位置；第4至17列为注释后的磷酸化组学特征，用于图2C、图4B、4E、4F以及补充图S4、S7B~S7C的分析；第18至146列为可检测性矩阵，其中值为0代表该位点未在对应物种中比对上，值为1代表已比对上。此处窗口相似度得分≥8。 表S5：基于对应磷酸化蛋白进行GO富集分析所得的GO条目，其BH校正P值在Q1~Q5五个分段中的一个分段内小于0.01，且在其余四个分段内大于0.05。 表S6：在Q1~Q5每个分段中进行激酶富集分析所得的结果，其BH校正P值均小于0.01。 表S7：取自10种常见哺乳动物的磷酸化表达数据及统计结果，这10种动物分属真灵长总目（Euarchontoglires，即人类、大鼠、兔、猴）与劳亚兽总目（Laurasiatheria，即牛、马、猪、犬、猫、羊）[4]。 参考文献 1. Giansanti, P., Samaras, P., Bian, Y., Meng, C., Coluccio, A., Frejno, M., Jakubowsky, H., Dobiasch, S., Hazarika, R.R., Rechenberger, J. 等. (2022) 基于质谱的小鼠蛋白质组草图. 《Nature Methods》, 19, 803-811. 2. Ochoa, D., Jarnuczak, A.F., Vieitez, C., Gehre, M., Soucheray, M., Mateus, A., Kleefeldt, A.A., Hill, A., Garcia-Alonso, L., Stein, F. 等. (2020) 人类磷酸化组学的功能图谱. 《Nature Biotechnology》, 38, 365-373. 3. UniProt 联盟. (2021) UniProt：2021年通用蛋白质知识库. 《Nucleic Acids Research》, 49, D480-D489. 4. Ba, Q., Hei, Y., Dighe, A., Li, W., Maziarz, J., Pak, I., Wang, S., Wagner, G.P. 与 Liu, Y. (2022) 11种哺乳动物的蛋白质型共进化与定量多样性. 《Science Advances》, 8, eabn0756.
