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frontend/src/components/GeneDetails/AlternativeIdentifiers.vue
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<script setup lang="ts"> | ||
export interface Props { | ||
hgnc: any | ||
} | ||
const props = withDefaults(defineProps<Props>(), { | ||
hgnc: null | ||
}) | ||
</script> | ||
<template> | ||
<v-card> | ||
<v-card-title>Alternative Identifiers</v-card-title> | ||
<v-divider></v-divider> | ||
<v-card-text> | ||
<div> | ||
<strong> ENSEMBL: </strong> | ||
<a | ||
:href="`https://www.ensembl.org/Homo_sapiens/Gene/Summary?g=${props.hgnc?.ensembl_gene_id}`" | ||
target="_blank" | ||
> | ||
<v-icon>mdi-launch</v-icon> | ||
{{ props.hgnc?.ensembl_gene_id }} | ||
</a> | ||
</div> | ||
<div> | ||
<strong> HGNC: </strong> | ||
<a | ||
:href="`https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/${props.hgnc?.hgnc_id}`" | ||
target="_blank" | ||
> | ||
<v-icon>mdi-launch</v-icon> | ||
{{ props.hgnc?.hgnc_id }} | ||
</a> | ||
</div> | ||
<div v-if="props.hgnc?.mgd_id?.length"> | ||
<strong>MGI: </strong> | ||
<template v-for="(mgd_id, index) in props.hgnc.mgd_id" :key="mgd_id"> | ||
<template v-if="index > 0">, </template> | ||
<a :href="`https://www.informatics.jax.org/marker/${mgd_id}`" target="_blank"> | ||
<v-icon>mdi-launch</v-icon> | ||
{{ mgd_id }} | ||
</a> | ||
</template> | ||
</div> | ||
<span v-else> No MGI </span> | ||
<div v-if="props.hgnc?.pubmed_id?.length"> | ||
<strong>Primary PMID: </strong> | ||
<template v-for="(pmid, index) in props.hgnc.pubmed_id" :key="pmid"> | ||
<template v-if="index > 0">, </template> | ||
<a :href="`https://pubmed.ncbi.nlm.nih.gov/${pmid}/`" target="_blank"> | ||
<v-icon>mdi-launch</v-icon> | ||
{{ pmid }} | ||
</a> | ||
</template> | ||
</div> | ||
<div v-else>No primary PMID</div> | ||
<div v-if="props.hgnc?.refseq_accession?.length"> | ||
<strong> RefSeq: </strong> | ||
<template v-for="(accession, index) in props.hgnc.refseq_accession" :key="index"> | ||
<template v-if="index > 0">, </template> | ||
<a | ||
:href="`https://www.ncbi.nlm.nih.gov/nuccore/?term=${accession}+AND+srcdb_refseq[PROP]`" | ||
target="_blank" | ||
> | ||
<v-icon>mdi-launch</v-icon> | ||
{{ accession }} | ||
</a> | ||
</template> | ||
</div> | ||
<div v-else>No RefSeq</div> | ||
<div v-if="props.hgnc?.uniprot_ids?.length"> | ||
<strong> UniProt: </strong> | ||
<template v-for="(uniprotid, index) in props.hgnc.uniprot_ids" :key="index"> | ||
<template v-if="index > 0">, </template> | ||
<a :href="`https://www.uniprot.org/uniprotkb/${uniprotid}/entry`" target="_blank"> | ||
<v-icon>mdi-launch</v-icon> | ||
{{ uniprotid }} | ||
</a> | ||
</template> | ||
</div> | ||
<div v-else>No UniProt</div> | ||
</v-card-text> | ||
</v-card> | ||
</template> |
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<script setup lang="ts"> | ||
import { computed } from 'vue' | ||
export interface Props { | ||
geneClinvar: any | ||
} | ||
const props = withDefaults(defineProps<Props>(), { | ||
geneClinvar: null | ||
}) | ||
const variantImpactLabels = [ | ||
"3' UTR", | ||
"5' UTR", | ||
'downstream', | ||
'frameshift', | ||
'inframe indel', | ||
'start lost', | ||
'intron', | ||
'missense', | ||
'non-coding', | ||
'stop gained', | ||
'no alteration', | ||
'splice acceptor', | ||
'splice donor', | ||
'stop lost', | ||
'synonymous', | ||
'upstream gene' | ||
] | ||
const clinsigLabels = [ | ||
'benign', // 0 | ||
'likely benign', // 1 | ||
'uncertain signifiance', // 2 | ||
'likely pathogenic', // 3 | ||
'pathogenic' // 4 | ||
] | ||
const clinsigColor = ['#5d9936', '#a3f56c', '#f5c964', '#f59f9f', '#b05454'] | ||
const perImpactCounts = computed(() => { | ||
const result = [] | ||
const sum = { | ||
impact: variantImpactLabels.length - 1, | ||
counts: [0, 0, 0, 0, 0] | ||
} | ||
if (props.geneClinvar?.per_impact_counts) { | ||
for (const perImpactCount of props.geneClinvar.per_impact_counts) { | ||
result.push(perImpactCount) | ||
for (let i = 0; i < sum.counts.length; ++i) { | ||
sum.counts[i] += perImpactCount.counts[i] | ||
} | ||
} | ||
result.push(sum) | ||
} | ||
return result | ||
}) | ||
</script> | ||
|
||
<template> | ||
<v-card id="clinvar-impact" class="gene-item"> | ||
<v-card-title>ClinVar By Impact</v-card-title> | ||
<v-divider /> | ||
<v-card-text v-if="props.geneClinvar?.per_impact_counts?.length"> | ||
<table> | ||
<tr> | ||
<thead> | ||
<th>impact</th> | ||
<th v-for="i in [0, 1, 2, 3, 4]" :key="i"> | ||
{{ clinsigLabels[i] }} | ||
</th> | ||
<th>total</th> | ||
</thead> | ||
<tbody> | ||
<tr v-for="row in perImpactCounts" :key="row"> | ||
<td | ||
:class="{ | ||
'font-weight-bolder': variantImpactLabels[row.impact] == 'overall' | ||
}" | ||
> | ||
{{ variantImpactLabels[row.impact] }} | ||
</td> | ||
<td | ||
class="text-right" | ||
:class="{ | ||
'font-weight-bolder': variantImpactLabels[row.impact] == 'overall' | ||
}" | ||
v-for="(count, idx) in row.counts" | ||
:style="`background-color: ${clinsigColor[idx]}`" | ||
:key="idx" | ||
> | ||
{{ count }} | ||
</td> | ||
<td | ||
class="text-right" | ||
:class="{ | ||
'font-weight-bolder': variantImpactLabels[row.impact] == 'overall' | ||
}" | ||
> | ||
{{ row.counts.reduce((a: any, b: any) => a + b, 0) }} | ||
</td> | ||
</tr> | ||
</tbody> | ||
</tr> | ||
</table> | ||
</v-card-text> | ||
<v-card-text v-else class="text-center font-italic">No ClinVar data for gene.</v-card-text> | ||
</v-card> | ||
</template> |
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<script setup lang="ts"> | ||
import { roundIt } from '@/lib/utils' | ||
export interface Props { | ||
gnomadConstraints: any | ||
} | ||
const props = withDefaults(defineProps<Props>(), { | ||
gnomadConstraints: null | ||
}) | ||
</script> | ||
<template> | ||
<v-card id="constraints-scores" class="gene-item"> | ||
<v-card-title>Constraints/Scores</v-card-title> | ||
<v-card-subtitle>gnomAD</v-card-subtitle> | ||
<v-divider></v-divider> | ||
<v-card-text> | ||
<v-table style="width: 100%"> | ||
<thead> | ||
<tr> | ||
<th>Category</th> | ||
<th>SNVs exp.</th> | ||
<th>SNVs obs.</th> | ||
<th>Constraint metrics</th> | ||
</tr> | ||
</thead> | ||
<tbody> | ||
<tr> | ||
<td>Synonymous</td> | ||
<td v-html="roundIt(props.gnomadConstraints?.exp_syn, 1)"></td> | ||
<td v-html="roundIt(props.gnomadConstraints?.obs_syn, 1)"></td> | ||
<td> | ||
Z = | ||
<span v-html="roundIt(props.gnomadConstraints?.syn_z)" /><br /> | ||
o/e = | ||
<span v-html="roundIt(props.gnomadConstraints?.oe_syn)" /> | ||
(<span v-html="roundIt(props.gnomadConstraints?.oe_syn_lower)" /> | ||
- | ||
<span v-html="roundIt(props.gnomadConstraints?.oe_syn_upper)" />) | ||
</td> | ||
</tr> | ||
<tr> | ||
<td>Missense</td> | ||
<td v-html="roundIt(props.gnomadConstraints?.exp_mis, 1)"></td> | ||
<td v-html="roundIt(props.gnomadConstraints?.obs_mis, 1)"></td> | ||
<td> | ||
Z = | ||
<span v-html="roundIt(props.gnomadConstraints?.mis_z)" /><br /> | ||
o/e = | ||
<span v-html="roundIt(props.gnomadConstraints?.oe_mis)" /> | ||
(<span v-html="roundIt(props.gnomadConstraints?.oe_mis_lower)" /> | ||
- | ||
<span v-html="roundIt(props.gnomadConstraints?.oe_mis_upper)" />) | ||
</td> | ||
</tr> | ||
<tr> | ||
<td>pLoF</td> | ||
<td v-html="roundIt(props.gnomadConstraints?.exp_lof, 1)"></td> | ||
<td v-html="roundIt(props.gnomadConstraints?.obs_lof, 1)"></td> | ||
<td> | ||
pLI = | ||
<span v-html="roundIt(props.gnomadConstraints?.pli)" /><br /> | ||
o/e = | ||
<span v-html="roundIt(props.gnomadConstraints?.oe_lof)" /> | ||
(<span v-html="roundIt(props.gnomadConstraints?.oe_lof_lower)" /> | ||
- | ||
<mark v-html="roundIt(props.gnomadConstraints?.oe_lof_upper, 2, 'LOEUF')" />) | ||
</td> | ||
</tr> | ||
</tbody> | ||
</v-table> | ||
</v-card-text> | ||
</v-card> | ||
</template> |
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<script setup lang="ts"> | ||
export interface Props { | ||
dbnsfp: any | ||
} | ||
const props = withDefaults(defineProps<Props>(), { | ||
dbnsfp: null | ||
}) | ||
</script> | ||
|
||
<template> | ||
<v-card> | ||
<v-card-title>Disease Annotation</v-card-title> | ||
<v-divider></v-divider> | ||
<v-card-text> | ||
<v-table> | ||
<thead> | ||
<tr> | ||
<th>Orphanet Disorders</th> | ||
<th>OMIM Diseases</th> | ||
</tr> | ||
</thead> | ||
<tbody> | ||
<tr> | ||
<th> | ||
<div v-if="props.dbnsfp?.orphanet_disorder?.length"> | ||
{{ props.dbnsfp.orphanet_disorder.join(', ') }} | ||
</div> | ||
<div v-else>No Orphanet disorders annotated in dbNSFP.</div> | ||
</th> | ||
<th> | ||
<div v-if="props.dbnsfp?.mim_disease?.length"> | ||
{{ props.dbnsfp.mim_disease.join(', ') }} | ||
</div> | ||
<div v-else>No OMIM diseases annotated in dbNSFP.</div> | ||
</th> | ||
</tr> | ||
</tbody> | ||
</v-table></v-card-text | ||
> | ||
</v-card> | ||
</template> |
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