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. 2023 Jan 6;51(D1):D460-D465.
doi: 10.1093/nar/gkac783.

PhaSepDB in 2022: annotating phase separation-related proteins with droplet states, co-phase separation partners and other experimental information

Chao Hou  1   2 , Xinxin Wang  1   2 , Haotai Xie  3 , Taoyu Chen  1   2 , Peiyu Zhu  1   2 , Xiaofeng Xu  1   2 , Kaiqiang You  1   2 , Tingting Li  1   2
Affiliations

PhaSepDB in 2022: annotating phase separation-related proteins with droplet states, co-phase separation partners and other experimental information

Chao Hou et al. Nucleic Acids Res. .

Abstract

Phase separation (PS) proteins form droplets to regulate myriad membraneless organelles (MLOs) and cellular pathways such as transcription, signaling transduction and protein degeneration. PS droplets are usually liquid-like and can convert to hydrogel/solid-like under certain conditions. The PS behavior of proteins is regulated by co-PS partners and mutations, modifications, oligomerizations, repeat regions and alternative splicing of the proteins. With growing interest in PS condensates and associated proteins, we established PhaSepDB 1.0, which provided experimentally verified PS proteins and MLO-related proteins. The past few years witnessed a surge in PS-related research works; thus, we kept updating PhaSepDB. The current PhaSepDB contains 1419 PS entries, 770 low-throughput MLO-related entries and 7303 high-throughput MLO-related entries. We provided more detailed annotations of PS proteins, including PS verification experiments, regions used in experiments, phase diagrams of different experimental conditions, droplet states, co-PS partners and PS regulatory information. We believe that researchers can go further in studying PS proteins with the updated PhaSepDB (http://db.phasep.pro/).

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Figures

Figure 1.
Figure 1.
Statistical analysis of PS and MLO entries in PhaSepDB. (A) Organism distribution of PS entries. (B) Proteins with many PS entries. (C) MLOs with many PS entries. (D) Counts and overlaps of PS entries with different PS verification experiments. (E) Counts and overlaps of PS entries with different droplet states. (F) MLOs with many MLO entries.
Figure 2.
Figure 2.
The interfaces of PhaSepDB. (A) Home page: users can search according to gene name, UniProt entry and MLOs. (B) Browse page: users can browse all PS entries via combinatorial search. (C) Query result page: two tables of PS entries and MLO entries. (D) MLO Browse page: all MLOs are displayed in graphical navigation and a table. (E) MLO detail page: basic information and related entries of the MLO. (F) Detailed page: detailed information for each entry.
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References

    1. Zhang H., Ji X., Li P., Liu C., Lou J., Wang Z., Wen W., Xiao Y., Zhang M., Zhu X.. Liquid–liquid phase separation in biology: mechanisms, physiological functions and human diseases. Sci. China Life Sci. 2020; 63:953–985. - PubMed
    1. Hnisz D., Shrinivas K., Young R.A., Chakraborty A.K., Sharp P.A.. A phase separation model for transcriptional control. Cell. 2017; 169:13–23. - PMC - PubMed
    1. Feric M., Misteli T.. Phase separation in genome organization across evolution. Trends Cell Biol. 2021; 31:671–685. - PMC - PubMed
    1. Su X., Ditlev J.A., Hui E., Xing W., Banjade S., Okrut J., King D.S., Taunton J., Rosen M.K., Vale R.D.. Phase separation of signaling molecules promotes T cell receptor signal transduction. Science. 2016; 352:595–599. - PMC - PubMed
    1. Fu A., Cohen-Kaplan V., Avni N., Livneh I., Ciechanover A.. p62-containing, proteolytically active nuclear condensates, increase the efficiency of the ubiquitin-proteasome system. Proc. Natl Acad. Sci. U.S.A. 2021; 118:e2107321118. - PMC - PubMed

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