Frequently Asked Questions

  1. What are the updated data or entries in Histome2?
  2. Histome2 has updated entries for human and addition of information for mouse and rat organisms. It also has information regarding epidrugs. Each of the organisms has detailed information about following categories.

    • Histone isoforms, Histone variants, Histone PTMs, Epigenetic modifiers (writer and eraser) – updated information, their role in the write up, respective genes and proteins for all the entries.
    • Expression analysis and miR identification – All the histones and epigenetic modifiers of humans have been linked to TCGA FireBrowse to see the normalized RNA expression in normal and cancer tissue types. All entries of humans were linked to Targetscan to identify the putative mIRs.
    • Epidrugs – As epitherapy is in clinical trials (www.clinicaltrials.gov) for targeting of epigenetic modifiers, new component ‘epi-drugs’ is added in histome2 to highlight their importance in the treatment of different diseases. There are 200 entries in epi-drugs section and they have been categorized like HATi, HDACi, DNMTi etc.

  3. What are the tools added in Histome2?
  4. Histome2 is added with tools for data analysis

    • Multiple sequence alignment: The protein sequences of histone variants and isoforms of human, mouse, and rat can be selected using checkboxes and can be compared by multiple sequence alignment using ‘Clustal Omega’.
    • Energy minimization of histone dimers: The 3D structure of histone dimer is generated and energy minimized to calculate the potential energy. Heatmap along with value of potential energy has been provided in the tool.
    • Advanced search: The advanced search is modified by the addition of rat and mouse database along with human database with sub-categorization of histones into isoforms and variants.

  5. What message is displayed when no data or information is available?
  6. If the data for text, OMIM id or sequence is not available then the message “No Information available (NA)” is displayed.

  7. What if the links to the external database are not working?
  8. We have updated the link to the current URL for the external database. If in-case the link to the external database is not working, it seems the server is temporarily out of service.

  9. What if the promoter sequence is not available?
  10. If data for promoter sequence is not available only the sequence identifier will be displayed and not the sequence.

  11. Why sometimes hyperlink to PubMed for additional information may fetch non-relevant information?
  12. The idea behind giving the hyperlink embedded with the keywords to PubMed is to fetch real time updated references. For some entries, the results in the PubMed may show non-relevant references for other organisms. This may be due to the fact that in the paper the gene or protein has been studied in multiple organisms.

  13. How to search for original and more information for particular entry?
  14. The pubmed search will give you the relevant research on particular enzyme and histones. However the original information related to a particular enzyme or histone will be available on RefSeq NP (protein) and NM (gene) id.

  15. Can multiple sequence alignment be done for all the histone variants and isoforms across three species?
  16. Yes, a user can select sequences of histone isoforms and variants of all three organisms from different tabs of histones and perform multiple sequence alignment. From the output page of MSA, user can download the aligned file in text format by clicking ‘Download Alignment file’. By clicking on ‘Download Raw Sequence’, user can get FASTA format of sequences which can be used as input to any tools for further analysis.

  17. Why sometimes the number of PTM sites numbers are not matching?
  18. In most of the literature the PTM sites are numbered by not considering first methionine in the protein sequence. But is some literature for rat and mouse, the first methionine is considered for numbering the PTM sites. Therefore, for these cases, the PTMs site numbering will be reported by minus one and will not match with the literature PTM sites.

  19. How the downloaded 2D structure (.sdf) file from EpiDrug can be viewed?
  20. The downloaded 2D structure file in .sdf extension can be viewed in freeware softwares like PyMol viewer and Discovery studio Visualizer.

  21. Which energy values are reported for minimized H2A & H2B dimers?
  22. The heatmap plotted shows the potential energy values between dimers of histone H2A and H2B isoforms for all organisms. The potential energy are calculated using Gromacs software. For better visualisation of potential energy values on heatmap, user can right click on heatmap and click on save image to open image in any visualizer.

  23. How to contact for any queries in Histome2?
  24. For any further queries on the Histome2, user may write an email to Gupta Lab