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


(The old version of the interface is still accessible but no longer maintained at http://apps.thesgc.org/resources/phylogenetic_trees_v1)

Genes involved in writing, reading and erasing the histone code 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.

We try hard to keep this resource up to date, but if you think some data is missing, please send us an e-mail or use the following form.

Missing Data to Add
Reference:

Target Class

Tree Type
Options
Summary
Summary: Swissprot summary of protein function
Inhibitors
Inhibitors: Small molecule modulators from the published and patent literature
Browser       3D Slides
Interactive mini-articles with 3D slides of published structures in complex with ligands. Powered with iSee technology.
[help] Ligands in Structures
compounds with MW < 1000 Da and at least 6 carbons complexed to target of interest

structure identity cut-off: Histone Substrates
Substrates: Published substrate specificity
Highlight with Search Gene
Search Gene: Targets that contain the keyword in either the name or synonyms will be highlighted.
Domains
Domains: PFAM domains identified by using HMMER-3.0 on the protein sequences (downloadable from a link at the top of the tree) against the PFAM database, with an Evalue threshold of 0.01
Disease Associations
Disease Associations: Articles are linked to genes based on NCBI's Gene <-> Pubmed associations (human and mouse orthologs). Genes are linked to diseases based on the presence of keywords in the Abstract or MeSH Terms of Pubmed entries. Click to see the list of Abstract and MeSH terms.


Most symbols on the trees are clickable.
Trees are generated with this script.
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.