Answers.Body: <p><strong>Ensembl</strong> contains this information: When you <a href="http://www.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000164508;r=6:25726132-25726527;t=ENST00000297012#ALL_tablePanel" rel="noreferrer">go to the “phenotype” menu item of a given gene</a>, you will see a list of variants (potentially after clicking on “ALL associated variants”) with their associated genomic position.</p>
  
  <p>You can subtract the transcript’s start position from that position to find out the residue (of the translated sequence, and be careful to subtract the lengths of all preceding introns!). Unfortunately this seems to require some manual work.</p>
  
  <p>Alternatively you can <a href="http://www.ensembl.org/Homo_sapiens/Variation/Phenotype?db=core;g=ENSG00000164508;r=6:25726132-25726527;t=ENST00000297012;v=rs2275906;vdb=variation;vf=1677930" rel="noreferrer">query the individual SNPs</a>, which will tell you their position in all transcripts (in this case: Leu 298/68/244):
  <a href="https://i.sstatic.net/zr2Q4.png" rel="noreferrer"><img src="https://i.sstatic.net/zr2Q4.png" alt="enter image description here"></a></p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-07-14T16:12:50.580Z
Answers.LastActivityDate: 2017-07-14T16:12:50.580Z
Answers.UserDisplayName: Konrad Rudolph
Answers.Body: <p>I found <a href="http://www.disgenet.org/web/DisGeNET/menu" rel="nofollow noreferrer">DisGeNET</a> useful for my purpose, a database that associates genes with diseases and, if known, gene variants with diseases. It integrates several sources of information for computing a score of association of gene/variation with the disease ( <a href="https://academic.oup.com/nar/article/45/D1/D833/2290909" rel="nofollow noreferrer">Piñero et al., 2016</a>, <a href="http://www.ncbi.nlm.nih.gov/pubmed/25877637" rel="nofollow noreferrer">Piñero et al., 2015</a>):</p>
  
  <ul>
  <li><p><strong>Gene Disease Associations</strong> from UniProt, PsyGeNET, ClinVar, Orphanet, the GWAS Catalog, CTD (human data), and Human Phenotype Ontology, RGD, MGD, and CTD (mouse and rat data) GAD, LHGDN and BeFree</p></li>
  <li><p><strong>Variants Disease Associations</strong> from ClinVar, the GWAS Catalog, Uniprot, GAD, and from BEFREE</p></li>
  </ul>
  
  <p>If available, it provides the Pubmed ID of articles supporting the proposed association and the rs id from the dbSNP for variants associated to disease.</p>
  
  <p>In addition it provides an experimental R package, <a href="https://bitbucket.org/ibi_group/disgenet2r" rel="nofollow noreferrer">disgenet2r</a>, that allows to query the database in a programmatic manner and that provides some plot functions to generate representations of the associations founded.</p>
  
  <p>Using this approach, I have been able to found several human histone-disease associations (not my original purpose), together with some concrete histone residues that are mutated in specific diseases. </p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-06-21T10:27:10.710Z
Answers.LastActivityDate: 2017-06-21T12:40:37.340Z
Answers.LastEditDate: 2017-06-21T12:40:37.340Z
Answers.UserDisplayName: jxx_fa
Body: <p>I would like to look if there are mutations in residues of human histones associated with any disease. For instance, if a mutation in residue K6 (lysine 6) of histone <a href="http://www.uniprot.org/uniprot/Q96QV6#function" rel="nofollow noreferrer">H2A1A</a> is associated with any human disease, (with PUBMED evidence, preferably), but in a systematic way (for all types of histones and all residues). </p>
  
  <p>The purpose of this is to get some candidate residues to study. I have checked the <a href="https://www.omim.org/" rel="nofollow noreferrer">OMIM</a> database but I didn't find anything relevant. It seems that there is no systematic way to connect specific residues to diseases and search for them.</p>
  
  <p>Is there any web database or API available for this purpose?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-20T09:48:52.557Z
Comments.Text: Hi plat. What kind of database are you looking? One with residues in proteins and diseases? Have you looked at GWAS to find nucleotid sequence and then aa residue? BTW the question in the title is different from the one in the body. Which one want you answered?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-20T10:12:24.417Z
Comments.Text: I am looking for association of a protein (specifically histones) residue to a disease. So a database of residues in proteins and diseases that I can look at in a systematic way will be fine. However, what you comment about GWAS and check the extrapolated aa is a good idea also. Any recommendation?
Comments.UserDisplayName: jxx_fa
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-20T10:56:23.707Z
Comments.Text: Sorry, but I find your question too vague: What have you tried to do? What failed? What other databases has you searched? Why each one failed? What do you lack from those databases?. Please narrow down the question (by [editing]) or ask your advisor how you can approach this.
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-20T11:48:21.660Z
Comments.Text: Would HistoneHits be of use? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666297/
Comments.UserDisplayName: TW93
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-20T11:51:38.383Z
Comments.Text: The problem with HistoneHits is that it is for yeast not for humans, but thank you anyway!
Comments.UserDisplayName: jxx_fa
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-20T11:59:45.640Z
Comments.Text: I have tried OMIM and I didn't find any way of relate histone residues mutations (or nucleotides and its correspondent residues) with human diseases. I don't know if this is because there is no such association or because this is not the correct database to search. Because of that I am asking if there is any database to look at this problem (i.e associate mutations in human histone residues to diseases in human). I think the question is more or less specific enough.
Comments.UserDisplayName: jxx_fa
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-20T12:07:12.067Z
Comments.Text: Apologies, I can't read it would seem!
Comments.UserDisplayName: TW93
Tags: <database><variation><api>
Title: How can I find mutations associated with disease in human histone residues?
ThreadText: # How can I find mutations associated with disease in human histone residues?
  
  (Asked by: username_0 on 2017-06-20)
  
  I would like to look if there are mutations in residues of human histones associated with any disease. For instance, if a mutation in residue K6 (lysine 6) of histone [H2A1A](http://www.uniprot.org/uniprot/Q96QV6#function) is associated with any human disease, (with PUBMED evidence, preferably), but in a systematic way (for all types of histones and all residues).
  
  The purpose of this is to get some candidate residues to study. I have checked the [OMIM](https://www.omim.org/) database but I didn't find anything relevant. It seems that there is no systematic way to connect specific residues to diseases and search for them.
  
  Is there any web database or API available for this purpose?
  
  **Tags:** database, variation, api
  
  > **Comments:**
  > **username_1**: Hi plat. What kind of database are you looking? One with residues in proteins and diseases? Have you looked at GWAS to find nucleotid sequence and then aa residue? BTW the question in the title is different from the one in the body. Which one want you answered?  
  > **username_0**: I am looking for association of a protein (specifically histones) residue to a disease. So a database of residues in proteins and diseases that I can look at in a systematic way will be fine. However, what you comment about GWAS and check the extrapolated aa is a good idea also. Any recommendation?  
  > **username_1**: Sorry, but I find your question too vague: What have you tried to do? What failed? What other databases has you searched? Why each one failed? What do you lack from those databases?. Please narrow down the question (by [editing]) or ask your advisor how you can approach this.  
  > **username_2**: Would HistoneHits be of use? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666297/  
  > **username_0**: The problem with HistoneHits is that it is for yeast not for humans, but thank you anyway!  
  > **username_0**: I have tried OMIM and I didn't find any way of relate histone residues mutations (or nucleotides and its correspondent residues) with human diseases. I don't know if this is because there is no such association or because this is not the correct database to search. Because of that I am asking if there is any database to look at this problem (i.e associate mutations in human histone residues to diseases in human). I think the question is more or less specific enough.  
  > **username_2**: Apologies, I can't read it would seem!  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2017-07-14. Score: 5
  
  **Ensembl** contains this information: When you [go to the “phenotype” menu item of a given gene](http://www.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000164508;r=6:25726132-25726527;t=ENST00000297012#ALL_tablePanel), you will see a list of variants (potentially after clicking on “ALL associated variants”) with their associated genomic position.
  
  You can subtract the transcript’s start position from that position to find out the residue (of the translated sequence, and be careful to subtract the lengths of all preceding introns!). Unfortunately this seems to require some manual work.
  
  Alternatively you can [query the individual SNPs](http://www.ensembl.org/Homo_sapiens/Variation/Phenotype?db=core;g=ENSG00000164508;r=6:25726132-25726527;t=ENST00000297012;v=rs2275906;vdb=variation;vf=1677930), which will tell you their position in all transcripts (in this case: Leu 298/68/244):
  [![enter image description here](https://i.sstatic.net/zr2Q4.png)](https://i.sstatic.net/zr2Q4.png)
  
  
  ---
  
  ### Answer by username_0 on 2017-06-21. Score: 3
  
  I found [DisGeNET](http://www.disgenet.org/web/DisGeNET/menu) useful for my purpose, a database that associates genes with diseases and, if known, gene variants with diseases. It integrates several sources of information for computing a score of association of gene/variation with the disease ( [Piñero et al., 2016](https://academic.oup.com/nar/article/45/D1/D833/2290909), [Piñero et al., 2015](http://www.ncbi.nlm.nih.gov/pubmed/25877637)):
  
  * **Gene Disease Associations** from UniProt, PsyGeNET, ClinVar, Orphanet, the GWAS Catalog, CTD (human data), and Human Phenotype Ontology, RGD, MGD, and CTD (mouse and rat data) GAD, LHGDN and BeFree
  * **Variants Disease Associations** from ClinVar, the GWAS Catalog, Uniprot, GAD, and from BEFREE
  
  If available, it provides the Pubmed ID of articles supporting the proposed association and the rs id from the dbSNP for variants associated to disease.
  
  In addition it provides an experimental R package, [disgenet2r](https://bitbucket.org/ibi_group/disgenet2r), that allows to query the database in a programmatic manner and that provides some plot functions to generate representations of the associations founded.
  
  Using this approach, I have been able to found several human histone-disease associations (not my original purpose), together with some concrete histone residues that are mutated in specific diseases.
  
  
  ---
  
  