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ui.R
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# This file defines the dashboard UI for the app
dash <- dashboardPage(
dashboardHeader(title = 'ARVID'),
# Sidebar content
dashboardSidebar(
sidebarMenu(
menuItem('About ARVID', tabName = 'arvid', icon = icon('dna')),
menuItem('ARVID Projects', tabName = 'projects', icon = icon('folder')),
menuItem('ARVID Evolution', tabName = 'evolution', icon = icon('forward')),
menuItem('Additional Info', tabName = 'about', icon = icon('circle-info'))
)),
# Body content
dashboardBody(
tabItems(
tabItem(
tabName = 'arvid',
tags$div(
style = 'width:800px',
tags$img(src = 'banner_dna.jpeg', width = '800px', height = '300px'),
tags$h3('Atlas of Regulatory Variants in Disease'),
tags$p('Advancements in our ability to sequence the human genome, with its vast 3.2 billion nucleotide base pairs have shaped the modern era of medicine.
A major insight from these efforts is that the variations in our DNA sequence that confer unique traits also mediate the risk of developing common diseases, including cancer, neuropsychiatric disease, heart disease, stroke, dementia, diabetes, and autoimmunity.'),
tags$p('Leveraging this insight to improve human health now represents the major challenge facing biomedicine.
That is because studies linking DNA sequence-disease relationships only identify large regions of the genome correlated with disease risk, but they are too low resolution to illuminate the underlying pathologic mechanisms needed to identify therapeutic targets.'),
tags$p('Additionally, multiple lines of data suggest that at least half of inherited disease risk occurs through DNA variants that alter the function of regulatory DNA.
The Atlas of Regulatory Variants in Disease (ARVID), NHGRI U24 HG010856, produced a resource of altered regulatory genomic variants in disease risk and putative target genes.
An atlas of functionally validated disease variants, the genes they control, and the proteins whose binding they alter helps the broader biomedical research community to understand, predict, and prevent common diseases.')
)
),
tabItem(
tabName = 'evolution',
h3('ARVID Evolution'),
tags$div(
style = 'width:800px',
tags$br(),
tags$p('The Atlas of Regulatory Variants in Disease (ARVID), NHGRI U24 HG010856, used massively parallel reporter assays (MPRA) to identify 1,627 disease risk-linked SNVs with differential transcription-directing activity (daSNVs) in 27 biologically-relevant normal human cell type contexts in 2D in vitro cultures. Binding quantitative trait loci (bQTLs) are a function of daSNVs that alter DNA motifs and display allele-specific binding (ASB) to transcription factors (TFs).'),
tags$br()
),
tags$div(
style = 'width:800px',
h4('ARVID Publications'),
tags$br(),
tags$a(href = 'https://www.nature.com/articles/s41588-024-02070-5',
tags$p(style = 'font-size:16px', '2025 - Functional analysis of cancer-associated germline risk variants. Nature Genetics.')),
tags$br(),
tags$br(),
tags$a(href = 'https://www.biorxiv.org/content/10.1101/2024.11.07.622542',
tags$p(style = 'font-size:16px', '2024 - Disease-Linked Regulatory DNA Variants and Homeostatic Transcription Factors in Epidermis. bioRxiv.')),
tags$br(),
tags$br(),
tags$a(href = 'https://www.nature.com/articles/s41588-023-01533-5',
tags$p(style = 'font-size:16px', '2023 - Integrative analyses highlight functional regulatory variants associated with neuropsychiatric diseases. Nature Genetics.')),
tags$br(),
tags$br(),
tags$a(href = 'https://www.cell.com/trends/genetics/abstract/S0168-9525(23)00054-9',
tags$p(style = 'font-size:16px', '2023 - Functional characterization of human genomic variation linked to polygenic diseases. Trends in Genetics.')),
tags$br(),
tags$br(),
tags$a(href = 'https://www.cell.com/cell-genomics/fulltext/S2666-979X(22)00140-9',
tags$p(style = 'font-size:16px', '2022 - A cis-regulatory lexicon of DNA motif combinations mediating cell-type-specific gene regulation. Cell Genomics.')),
tags$br(),
tags$br(),
tags$a(href = 'https://www.nature.com/articles/s41592-022-01552-w',
tags$p(style = 'font-size:16px', '2022 - PROBER identifies proteins associated with programmable sequence-specific DNA in living cells. Nature Methods.')),
tags$br(),
tags$br(),
tags$a(href = 'https://www.nature.com/articles/s41588-021-00947-3',
tags$p(style = 'font-size:16px', '2021 - The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation. Nature Genetics.')),
tags$br(),
tags$br(),
tags$p(style = 'font-size:16px', '2020 - Start of ARVID.'),
)
),
tabItem(
tabName = 'projects',
h3('ARVID Projects'),
tags$br(),
tags$div(
style = 'width:320px',
tags$img(src = 'proj_skin.png', width = '320px', height = '200px'),
tags$br(),
tags$a(href = 'https://arvid-data.shinyapps.io/skin/',
tags$p(style = 'text-align:center;font-size:16px', 'CRE variants in Prevalent Skin Diseases')),
tags$br(),
tags$br(),
tags$br(),
tags$img(src = 'proj_cancer.png', width = '320px', height = '200px'),
tags$br(),
tags$a(href = 'https://arvid-data.shinyapps.io/cancers/',
tags$p(style = 'text-align:center;font-size:16px', 'CRE variants in Common Human Cancers')),
tags$br(),
tags$br(),
tags$br(),
tags$img(src = 'proj_brain.png', width = '320px', height = '200px'),
tags$br(),
tags$a(href = 'https://arvid-data.shinyapps.io/neuropsychiatry/',
tags$p(style = 'text-align:center;font-size:16px', 'CRE variants in Neuropsychiatric Disorders')),
)
),
tabItem(
tabName = 'about',
tags$div(
tags$h3('Additional Information'),
tags$br(),
tags$p('Please use Suggested Citation found in the "Additional Information" page of respective projects.'),
tags$p(''),
tags$br(),
tags$h4('Contact Us'),
tags$p('For questions or feedback please email: suhas <dot> srinivasan <at> stanford <dot> edu'),
tags$a(href = 'https://khavarilab.stanford.edu/', 'Developed at the Khavari Lab', target = '_blank'),
tags$p(''),
tags$br(),
tags$h4('Funding Sources'),
tags$p('NHGRI: 5U24HG010856'),
tags$p('NIAMS: AR076965'),
tags$p('NIAMS: AR43799'),
tags$p('NCI: CA142635'),
tags$p('USVA: Office of Research and Development'),
tags$p('Donors: Kathy Fields and Garry Rayant')
),
tags$br(),
tags$div(
HTML('
<head>
<style>
* {
box-sizing: border-box;
}
.column {
float: left;
width: 25%;
padding: 5px;
}
.row::after {
content: "";
clear: both;
display: table;
}
</style>
</head>
<body>
<div class="row">
<div class="column">
<a href = "https://www.genome.gov/">
<img src="logo_nhgri.png" style="width:55%">
</a>
</div>
<div class="column">
<a href = "https://www.niams.nih.gov/">
<img src="logo_niams.png" style="width:60%">
</a>
</div>
<div class="column">
<a href = "https://www.cancer.gov/">
<img src="logo_nci.png" style="width:40%">
</a>
</div>
<div class="column">
<a href = "https://www.research.va.gov/">
<img src="logo_va.png" style="width:60%">
</a>
</div>
</div>
</body>
')
)
)
)
)
)