User: ognjen011

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ognjen011150
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Posts by ognjen011

<prev • 41 results • page 1 of 5 • next >
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Connection of SNPs to Enzyme activity - database or tool
... Is there a resource - database or prediction tool - that maps SNPs to changes in enzyme activity? This could either be achieved through prediction of direct effects on structure, or the measurement of products. Either way works fine as long as it elucidates function effects. Tools like PolyPhen2 d ...
proteomics snp written 5 weeks ago by ognjen011150
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GTEX effect sizes and violin plots
... I am trying to understand the data at GTEX. Searching for data on the particular SNPs I get results in CSV form or browser table e.g. https://gtexportal.org/home/snp/rs1700184 1) Is there any way to get processed information from the violin plots (like medians) in CSV? They only seem available on c ...
expression eqtl gtex written 5 weeks ago by ognjen011150
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Comment: C: Finding SNPs RSID from older papers
... I see what was done. The accession link is actually: https://www.ncbi.nlm.nih.gov/nuccore/AF039228 And it was sequenced from -550-+61. As a result, -174 is not counted from the end of the sequence as I assumed. Unusual. ...
written 8 weeks ago by ognjen011150
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Comment: C: Finding SNPs RSID from older papers
... Hey, I've just found the explicit variant: https://www.snpedia.com/index.php/Rs1800795 The position of this base is 22727026. When counting -174 from the end of your aligned sequence, I get a position 22727024. Also, the "real" SNP is C > G. Could you comment on that? ...
written 8 weeks ago by ognjen011150
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Comment: C: Finding SNPs RSID from older papers
... Thanks for the reply. Using BLAST is a great idea. Is there a resource that could help me skip BLAST if the sequence has a known accession number? For example, if I know my variant is NM_001105580:c.1394T>C, how would one skip BLAST and directly get the absolute genomic position in the current bu ...
written 9 weeks ago by ognjen011150
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Comment: C: Finding SNPs RSID from older papers
... Thank you for clearly outlying your reasoning. ...
written 9 weeks ago by ognjen011150
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Finding SNPs RSID from older papers
... I encountered a paper which test an IL-6 polymorphism, but never clearly specifies it with an RSID, but simply calls it IL-6 -174: https://www.ncbi.nlm.nih.gov/pubmed/18930842 I tried using online resources to find the exact chromosomal position and thus find the RSID that corresponds to position ...
assembly rsid snp written 9 weeks ago by ognjen011150 • updated 9 weeks ago by Denise - Open Targets4.8k
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Meaning of TOP/BOTTOM strand and QC implications
... I've found a post explaining strand designations for some Illumina systems: https://www.illumina.com/documents/products/technotes/technote_topbot.pdf So the way they explain it is some local designation which is robust to reference genome build rearrangements. What confuses me is the supplementary ...
illumina snp written 12 weeks ago by ognjen011150
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Convention for protein-level changes
... I have come to understand that G37 or Gly37 are changes to aminoacid Gly at position 37. I ran into this paper: https://www.nature.com/articles/s41467-017-00257-5 What is PheSerTyr13? ...
protein nomenclature written 3 months ago by ognjen011150
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Comment: C: RSID for multiple alternative variants present in a single line
... Thanks for the reply! Can you answer the above question in the comment as well? ...
written 4 months ago by ognjen011150

Latest awards to ognjen011

Supporter 12 weeks ago, voted at least 25 times.
Appreciated 17 months ago, created a post with more than 5 votes. For BED files for SRA open projects
Good Question 17 months ago, asked a question that was upvoted at least 5 times. For BED files for SRA open projects
Student 17 months ago, asked a question with at least 3 up-votes. For BED files for SRA open projects

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