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website overhaul with separate gene pages, literature and new logo
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@hdashnow
hdashnow committed May 3, 2024
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5 changes: 3 additions & 2 deletions about.html
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</a>
<a class="item" href="index.html">Home</a>
<a class="active item" href="about.html">About</a>
<a class="item" href="table.html">STR Database</a>
<a class="item" href="/database/index.html">STR Database</a>
<a class="item" href="plots.html">Plots</a>
<a class="item" href="resources.html">Resources</a>
<a class="item" href="contribute.html">Contribute</a>
<div class="right item">
<a class="ui inverted button" href="index.html">STRchive</a>
Expand Down Expand Up @@ -172,7 +173,7 @@ <h3 class="ui header">Why STRchive?</h3>
</p>
</div>
<div class="six wide right floated column">
<img src="images/STR-definition.png" class="ui large bordered rounded image">
<img src="images/STRchiveLogo.png" class="ui large rounded image">
</div>
</div>
<div class="row">
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3 changes: 2 additions & 1 deletion contribute.html
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</a>
<a class="item" href="index.html">Home</a>
<a class="item" href="about.html">About</a>
<a class="item" href="table.html">STR Database</a>
<a class="item" href="/database/index.html">STR Database</a>
<a class="item" href="plots.html">Plots</a>
<a class="item" href="resources.html">Resources</a>
<a class="active item" href="contribute.html">Contribute</a>
<div class="right item">
<a class="ui inverted button" href="index.html">STRchive</a>
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58 changes: 29 additions & 29 deletions data/STRchive-database.csv
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18 changes: 9 additions & 9 deletions data/STRchive-database.json
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"Mechanism_detail":"Polyglutamine\/toxic gain-of-function; Unknown ",
"Mechanism_source":"(OMIM) (doi.org\/10.1007\/s11604-022-01343-5)",
"source":"Hannan 2018, Mirkin 2007, GeneReviews NBK535148, s40478-021-01201-x",
"notes":"Two genes span the CTG\/CAG repeat and are expressed in opposite directions: ATXN8, which encodes a nearly pure polyglutamine expansion protein in the CAG direction, and ATXN8OS (603680), which, when transcribed, produces a noncoding CUG expansion RNA (Moseley et al., 2006). Roda et al. suggested that the ATXN8 or ATXN8OS gene should not be evaluated in isolation as a candidate gene for spinocerebellar degenerative disease. CCG•CGG interruptions in high‐penetrance SCA8 families increase RAN translation and protein toxicity (PMID: 34632710); 'Interruptions w/in CTG·CAG expansion by 1 or more CCG·CGG, CTA·TAG, CTC·GAG, CCA·TGG, or CTT·AAG trinucleotides have been observed in full-penetrance repeats [Moseley et al 2006; Authors, unpublished data].' (GeneReviews)",
"notes":"Two genes span the CTG\/CAG repeat and are expressed in opposite directions: ATXN8, which encodes a nearly pure polyglutamine expansion protein in the CAG direction, and ATXN8OS (603680), which, when transcribed, produces a noncoding CUG expansion RNA (Moseley et al., 2006). Roda et al. suggested that the ATXN8 or ATXN8OS gene should not be evaluated in isolation as a candidate gene for spinocerebellar degenerative disease. CCG\u2022CGG interruptions in high\u2010penetrance SCA8 families increase RAN translation and protein toxicity (PMID: 34632710); 'Interruptions w\/in CTG\u00b7CAG expansion by 1 or more CCG\u00b7CGG, CTA\u00b7TAG, CTC\u00b7GAG, CCA\u00b7TGG, or CTT\u00b7AAG trinucleotides have been observed in full-penetrance repeats [Moseley et al 2006; Authors, unpublished data].' (GeneReviews)",
"details":null,
"width":46.0,
"OMIM":"608768",
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"typ_age_onset_max":null,
"novel":"ref",
"Mechanism":"DNA hypermethylation and 11q deletion",
"Mechanism_detail":"DNA hypermethylation/11q deletion in sporadic cases",
"Mechanism_detail":"DNA hypermethylation\/11q deletion in sporadic cases",
"Mechanism_source":"PMID: 38467784",
"source":"https:\/\/doi.org\/10.1038\/s41580-021-00382-6, 7603564 (PubMed)",
"notes":null,
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"Mechanism_detail":"Aberrant splicing",
"Mechanism_source":"(doi.org\/10.1093\/hmg\/ddr568)",
"source":"Hannan 2018, Mirkin 2007, GeneReviews NBK1466, https:\/\/doi.org\/10.1038\/s41580-021-00382-6",
"notes":"(TG)n(TCTG)n(CCTG)n. CCTG expansion causes DM2 but the other repeat units are also variable. Interruptions include GCTG/TCTG/GGCT (PMID: 35245110)",
"notes":"(TG)n(TCTG)n(CCTG)n. CCTG expansion causes DM2 but the other repeat units are also variable. Interruptions include GCTG\/TCTG\/GGCT (PMID: 35245110)",
"details":"Penetrance is age-dependent and approaches 100%",
"width":82.0,
"OMIM":"602668",
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"Mechanism_detail":"RNA gain-of-function - RNA gelation leading to misregulation of alternative splicing",
"Mechanism_source":"(doi.org\/10.1007\/s11604-022-01343-5)",
"source":"Hannan 2018, Mirkin 2007, GeneReviews NBK1165, s40478-021-01201-x",
"notes":"'3%-8% of DM1 expansions contain variant repeats such as CCG and CGG. These are referred to as variant repeat interruptions and may be associated with later onset and milder phenotype [Miller et al 2020].'(GeneReviews) 'Interruptions of the CTG repeat with CCG, GGC, CTC or CAG motifs are estimated to occur in 3–11% of DM1 patients' (PMID: 35741732)",
"notes":"'3%-8% of DM1 expansions contain variant repeats such as CCG and CGG. These are referred to as variant repeat interruptions and may be associated with later onset and milder phenotype [Miller et al 2020].'(GeneReviews) 'Interruptions of the CTG repeat with CCG, GGC, CTC or CAG motifs are estimated to occur in 3\u201311% of DM1 patients' (PMID: 35741732)",
"details":null,
"width":62.0,
"OMIM":"160900",
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"pathogenic_motif_reference_orientation":"GAA",
"pathogenic_motif_gene_orientation":"CTT",
"benign_motif_reference_orientation":"GAAGGA, GAAGAAGAAGAAGCA",
"benign_motif_gene_orientation":"",
"benign_motif_gene_orientation":"CCTTCT,CTGCTTCTTCTTCTT",
"unknown_motif_reference_orientation":null,
"unknown_motif_gene_orientation":"",
"disease":"Spinocerebellar ataxia 27B",
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"Mechanism_detail":"RNA mediated toxicity hypothesized; unknown",
"Mechanism_source":"(OMIM), (doi.org\/10.1007\/s11604-022-01343-5)",
"source":"Pathogenic Short Tandem Repeats Gnomad v3.1.2, 32413282 (Pubmed)",
"notes":"Interruptions Seen: CGA (PMID: 35245110); Interruptions mentioned but not confirmed in primary literature: TCG/CCT/TTG (PMID: 38467784)",
"notes":"Interruptions Seen: CGA (PMID: 35245110); Interruptions mentioned but not confirmed in primary literature: TCG\/CCT\/TTG (PMID: 38467784)",
"details":null,
"width":33.0,
"OMIM":"618940",
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"typ_age_onset_min":30.0,
"typ_age_onset_max":52.0,
"novel":"ref",
"Mechanism":"LoF/GoF (RNA)",
"Mechanism":"LoF\/GoF (RNA)",
"Mechanism_detail":"\"unstable vertical transmission\"",
"Mechanism_source":"(doi.org\/10.1007\/s11604-022-01343-5), PMID: 38467784",
"source":"Hannan 2018, Mirkin 2007, GeneReviews NBK1529",
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"Mechanism_source":"(OMIM), (doi.org\/10.1007\/s11604-022-01343-5)",
"source":"OMIM 164310, Ishiura et al [2019], Ehdn, NBK535148, PMID 31332380",
"notes":"CGG\/CGT; Interruptions Seen: ACG, CCA (PMID: 35245110)",
"details":"Possible milder clinical phenotype of inherited peripheral neuropathy (IPN) associated with shorter expansions (https://doi.org/10.1212/WNL.000000000020478)",
"details":"Possible milder clinical phenotype of inherited peripheral neuropathy (IPN) associated with shorter expansions (https:\/\/doi.org\/10.1212\/WNL.000000000020478)",
"width":27.0,
"OMIM":"164310",
"Prevalence":null,
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"typ_age_onset_min":30.0,
"typ_age_onset_max":70.0,
"novel":"ref",
"Mechanism":"PolyG/RNA GoF",
"Mechanism":"PolyG\/RNA GoF",
"Mechanism_detail":"May relate to methylation or RNA pathogenicity",
"Mechanism_source":"(OMIM) (doi.org\/10.1007\/s11604-022-01343-5), PMID: 38467784",
"source":"doi: 10.1038\/s41588-019-0458-z, https:\/\/doi.org\/10.1016\/j.ajhg.2019.05.013, s40478-021-01201-x",
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