ChromoHub: a data hub for navigators of chromatin-mediated signalling

Genes involved in chromatin-mediated signalling constitute emerging target classes for future therapies. Here, we map on phylogenetic trees information published by the scientific community on the therapeutic relevance, the biology, the structure of these genes, and related chemical inhibitors.

If you find this resource helpful in your research, thank you for citing the following article:
Liu L, Zhen XT, Denton E, Marsden BD, Schapira M., Bioinformatics (2012): ChromoHub: a data hub for navigators of chromatin-mediated signalling [pubmed]

Tree Type

Target Class
  Preview options for all classes (may be slow)

Chemical Modification of Proteins

KAT: Acetylate lysines PARP: ADP-ribosylate proteins
PMT: Methylate lysines
BAH: Read methyl-lysines BROMO: Read acetyl-lysines CW: methyl-lysine reader CHROMO: Read methyl-lysines MACRO: bind ADP-ribosylated proteins
MBT: Read methyl-lysines PHD: Read methyl-lysines, acetylated lysines, methyl-arginines, unmodified lysines PWWP: Read methyl-lysines, bind DNA SPINDLIN: methyl-lysine/arginine reader TUDOR: Read methyl-lysines, methyl-arginines YEATS: read acetyl-lysines and crotonyl-lysines
HDAC: Deacetylate lysines KDM: De-methylate lysines
PADI: Deiminate arginines

Chemical Modification of DNA

DNMT: Methylate CpG dinucleotides
CXXC: Bind to nonmethyl-CpG dinucleotides MBD: Bind to methyl-CpG dinucleotides
TET: DNA hydroxylases. Participate in DNA de-methylation

Chemical Modification of RNA

RNMT: Methylate RNA Pseudouridine synthases: catalyze the site-specific isomerization of uridines on RNA
YTH: bind to methylated RNA

Chromatin Remodelling

DEXDc: Involved in chromatin remodeling HELICc: Involved in chromatin remodeling SANT: Involved in chromatin remodeling




WDR: Versatile binding module
Click thumbnail above or search for a gene (or comma-separated gene list):

Disease Associations
     Chemical Probes

Browse inhibitors or visit ChEpiMod
Ligands in Structures

structure identity cut-off:
Search Gene
Domain Architecture

SGC Antibodies:
Antigen Produced
FAb Produced
IgG Produced

Cancer Genomics:
Expression in Cancer Lines

Only show cell lines which have mRNA expression data from:
Gene Fusions in Cancer
Known Chromosomal Aberrations in Cancer
RNASeq Gene Expression

     Show genes with a log2 fold change  in at least % of patients
     Exclude Cancer Types with < patients
     Show genes with at least one cancer type for which <= genes are more frequently overexpressed
Only show RNASeq expression results for:


Most symbols on the trees are clickable.
Trees are generated with this script.
| Full Length FASTA File | Full Length Alignment File | Domain-based fasta file | HKMT Alignment File | PRMT Alignment File
The phylogeny outlined in the tree is derived from a multiple sequence alignment of the PMT domain as specified in this table. If a domain is present multiple times in a protein, the protein is shown multiple times in the tree, followed by the sequential iteration of the domain in parenthesis: for example, PRMT7(2) corresponds to the second PMT domain of the protein PRMT7. If multiple variants with insertions or deletions were reported for a gene, the variant number according to Swiss-Prot nomenclature is indicated after a hyphen: for example, EZH2-2 corresponds to the second Swiss-Prot variant of the EZH2 gene. A seed alignment was derived from available protein structures by aligning residues that were superimposed in the three-dimensional space. Additional sequences were appended by aligning them to the closest seed sequence.