Interactive Figure 2

Protein domains co-occurence in SimChrom categories of chromatin regulators
Co-occurrence of protein domains that are often found in the chromatin regulators (Histone chaperones, Histone PTM erasers, Histone PTM writers, Histone PTM readers, Histone modification, Chromatin remodelers, Methylated DNA binding, DNA (de)methylation, RNA modification). From the list of PFAM domain pairs that were found in at least three chromatin regulator protein, domains involved in various histone post-translational modifications, chromatin remodeling, histone binding, DNA binding and protein dimerization/oligomerization were manually selected and classified based on the information currently available in the literature. The conditional probability of finding a corresponding domain A in a chromatin protein given that another domain B is already present was estimated and is presented (columns and rows correspond to domains A and B, respectively). The number of proteins with the corresponding domain pair is given for all SimChrom proteins.

Table 1. Constructed reference datasets of nuclear and non-nuclear proteins at different levels of confidence and uniqueness of localization in the nucleus or multi localization in the nucleus and other cellular compartments.

Download	Definition	Number of proteins
NULOC_CS	entries annotated as nuclear in both databases: UniProt (provided evidence code is available) AND HPA (with evidence tags: Enhanced, Supported, Approved), excludes proteins labeled only as non-nuclear in the OpenCell database (annotation grade 2 or 3)	3244
NULOC_CS_UL	entries annotated only as nuclear in both databases: UniProt (provided evidence code is available) AND HPA (with reliability score: Enhanced, Supported, Approved), excludes proteins labeled only as non-nuclear in the OpenCell database (annotation grade 2 or 3)	1263
NULOC_CS_UL_NECF	entries annotated only as nuclear in both databases: UniProt AND HPA, excludes proteins labeled only as non-nuclear in the OpenCell database	1310
NULOC_JT_UL	entries annotated only as nuclear in in at least one database: UniProt (provided evidence code is available) OR HPA (with reliability score: Enhanced, Supported, Approved) OR OpenCell database (annotation grade 2 or 3)	4256
NULOC_JT_UL_NECF	entries annotated only as nuclear in in at least one database: UniProt OR HPA, excludes proteins labeled only as non-nuclear in the OpenCell database	4280
NULOC_CS_NECF	entries annotated as nuclear in both databases: UniProt AND HPA, excludes proteins labeled only as non-nuclear in the OpenCell database	3962
NULOC_JT	entries annotated as nuclear in at least one database: UniProt (provided evidence code is available), HPA (with evidence tags: Enhanced, Supported, Approved), OpenCell (annotation grade 2 or 3)	8038
NULOC_JT_NECF	entries annotated as nuclear in at least one database: UniProt, HPA, OpenCell	8914
NON_NULOC_CS	proteins whose localization annotations exclude nuclear localization in both databases: UniProt (provided evidence code is available) and HPA (with evidence tags: Enhanced, Supported, Approved)	6056
CYTLOC_CS_UL	entries annotated only as cytoplasmic (see Methods) in both databases: UniProt (provided evidence code is available) AND HPA (with evidence tags: Enhanced, Supported, Approved)	2026

Table 2. Representative list of nuclear and chromatome datasets from MS-based experimental studies.

Year	Type of cells	Number of chromatin proteins (processed)	Methods, Notes	Reference	Download
2011	HeLa S3	1501	Three different chromatin purification methods: total chromatin extraction, salt extraction and total MNase digestion.	Torrente et al. 2011	torrente_2011
2014	HeLa S3	3509	Nascent chromatin capture (NCC) to profile chromatin proteome dynamics during replication in human cells. NCC relies on biotin–dUTP labelling of replicating DNA, affinity purification and quantitative proteomics.	Alabert et al., 2014	alabert_2014
2014	HepG2, HeLa, MCF-7	1941	ML-based classification based on Chromatin Enrichment for Proteomics (CheP) experiments (crosslinking + differential extraction under denaturing condition) in different conditions	Kustatscher et al. 2014	kustatscher_2014
2016	HeLa	1001	Crude nuclear extraction, identified "mostly nuclear" fraction by global intensity distribution	Itzhak et al., 2016	itzhak_2016
2018	T98G cell line (from glioblastoma multiforme)	3056	DEMAC method of chromatin extraction (with CsCl fractionation)	Ginno et al. 2018	ginno_2018
2021	K562 cell line	2848	BL-Hi-C method of chromatin extraction	Shi et al. 2021	shi_2021
2023	ESCs H9	1667	chromatin purification strategy: Chromatin Aggregation Capture (ChAC), with Data-Independent Acquisition (DIA) MS-based proteomics	Ugur et al., 2023	ugur_2023

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