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	- Updated content on the RNA Evidence page, except
	the similar gene section
	- Updated content on the RNA Expression modal
	- Updated content of the Nomination Details tab
	- Updated the news component with the latest
	content
	- Added back the footer display for the news component
	- Added the News and NewsEntry interfaces
	- Related to #700
	- Closes #701
	- Closes #703
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Zaknarfen committed Jun 24, 2019
1 parent fd16c59 commit 4723b89
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Showing 25 changed files with 293 additions and 122 deletions.
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Expand Up @@ -9,5 +9,5 @@ <h4 class="center-text no-margin-bottom">{{getModel()}}</h4>
</div>
</div>
<div class="row x-axis-row">
<h4 class="no-margin-top x-axis-heading center-text">BRAIN TISSUE</h4>
<h4 class="no-margin-top x-axis-heading center-text">BRAIN REGION</h4>
</div>
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Expand Up @@ -4,3 +4,6 @@
</div>
</div>
</div>
<div class="row x-axis-row">
<h4 class="no-margin-top x-axis-heading center-text small-padding-top">BRAIN REGION</h4>
</div>
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@@ -0,0 +1,3 @@
.small-padding-top {
padding-top: 10px;
}
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Expand Up @@ -313,7 +313,7 @@ export class RowChartViewComponent implements OnInit, OnDestroy, AfterViewInit,
self.insertTextsInRows(chart, 'confidence-text-right');

// Add a label to the x axis
self.addXLabel(this.chart, 'LOG FOLD CHANGE', svg, width, height);
self.addXLabel(this.chart, 'LOG 2 FOLD CHANGE', svg, width, height);
}

// Finally redraw the lines in each row
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6 changes: 0 additions & 6 deletions src/app/core/about/about.component.scss
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@@ -1,12 +1,6 @@
@import "../../../assets/css/helpers/variables";
@import "../../../assets/css/helpers/mixins";

.overview-header {
.row {
align-items: center;
}
}

.about-desc {
margin-bottom: 2%;

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9 changes: 3 additions & 6 deletions src/app/core/contrib-teams/contrib-teams.component.scss
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@@ -1,19 +1,16 @@
@import "../../../assets/css/helpers/variables";
@import "../../../assets/css/helpers/mixins";

.contrib-teams{
.section-thin{
.contrib-teams {
.section-thin {
margin-top: 0;
}

.overview-header {
.fa-star::before {
color: $contrast-color;
}

.row {
align-items: center;
}

p-button {
@include respond-to('ex-small') {
width: 70%;
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2 changes: 1 addition & 1 deletion src/app/core/footer/footer.component.html
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@@ -1,7 +1,7 @@
<div class="row footer-row no-gutters">
<div class="col-md-6 col-sm-12 col-12 links-col">
<span class="footer-span" (click)="goToRoute('about')" tabindex="0">ABOUT</span>
<!--<span class="footer-span" (click)="goToRoute('news')" tabindex="0">NEWS</span>-->
<span class="footer-span" (click)="goToRoute('news')" tabindex="0">NEWS</span>
<span class="footer-span" (click)="goToRoute('help')" tabindex="0">HELP</span>
<span class="footer-span last-footer-span" (click)="goToRoute('terms')" tabindex="0">TERMS & PRIVACY</span>
</div>
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41 changes: 20 additions & 21 deletions src/app/core/news/news.component.html
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Expand Up @@ -12,34 +12,33 @@ <h2>
</h2>
<div class="row content-row" dir="ltr">
<div class="col-md-12 col-sm-12 col-12">
Agora hosts evidence for whether or not genes are associated with Alzheimer’s disease (AD). Agora also contains a list
of close to one hundred nascent drug targets for AD that were nominated by AD researchers. The initial list of
nominated targets was contributed by researchers from the National Institute on Aging’s Accelerating Medicines
Partnership in Alzheimer’s Disease (AMP-AD) consortium. Other evidence presented in Agora was either generated by
AMP-AD research teams or is aggregated from publicly available data sources. Future versions of Agora will incorporate
other types of -omics evidence as well as target nominations from additional AD research groups. Please include the
following acknowledgement statement in any publications stemming from data in Agora: <i>The results published here are in
whole or in part based on data obtained from Agora, a platform that shares evidence in support of AD target discovery
initially developed by the NIA-funded AMP-AD consortium.</i>
<div *ngFor="let newsObj of news" class="container no-margin news-container" tabindex="0">
<div class="row data-row">{{newsObj.data}}</div>
<div *ngFor="let newsEntry of newsObj.entry" class="row" tabindex="0">
<div class="col-md-12 col-sm-12 col-12 no-padding-bottom">
<h3 class="no-margin-bottom no-margin-top no-padding-bottom">{{newsEntry.header}}</h3>
</div>
<div class="col-md-12 col-sm-12 col-12 body-col">
{{newsEntry.body}}
</div>
</div>
</div>
</div>
</div>
</div>

<div class="section-thin about-desc" tabindex="0">
<h1 class="inner-section-divider"></h1>
<h2>
Coming Soon
</h2>
<div class="row content-row" dir="ltr">
<div class="col-md-12 col-sm-12 col-12">
Agora hosts evidence for whether or not genes are associated with Alzheimer’s disease (AD). Agora also contains a list
of close to one hundred nascent drug targets for AD that were nominated by AD researchers. The initial list of
nominated targets was contributed by researchers from the National Institute on Aging’s Accelerating Medicines
Partnership in Alzheimer’s Disease (AMP-AD) consortium. Other evidence presented in Agora was either generated by
AMP-AD research teams or is aggregated from publicly available data sources. Future versions of Agora will incorporate
other types of -omics evidence as well as target nominations from additional AD research groups. Please include the
following acknowledgement statement in any publications stemming from data in Agora: <i>The results published here are in
whole or in part based on data obtained from Agora, a platform that shares evidence in support of AD target discovery
initially developed by the NIA-funded AMP-AD consortium.</i>
<div class="container no-margin news-container" tabindex="0">
<div class="row data-row no-padding-bottom">FALL 2019</div>
<div class="row" tabindex="0">
<div class="col-md-12 col-sm-12 col-12 body-col">
RNAseq data from AD mouse models will be released.
</div>
</div>
</div>
</div>
</div>
</div>
46 changes: 34 additions & 12 deletions src/app/core/news/news.component.scss
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@@ -1,18 +1,46 @@
@import "../../../assets/css/helpers/variables";
@import "../../../assets/css/helpers/mixins";

.overview-header {
.row {
align-items: center;
}
}

.about-desc {
margin-bottom: 2%;

.about-paragraph {
margin-bottom: 40px;
}

.content-row{
@include lato-font('normal');
margin-bottom: 45px;
font-size: 18px;
color: color(text, secondary);
}

.data-row {
padding-left: 15px;
padding-right: 15px;
padding-bottom: 5px;
font-size: $font-size-xx-regular;
line-height: 24px;
}

.body-col {
padding-bottom: 20px;
}

.news-container {
padding-left: 0px;
padding-right: 0px;

:last-child {
.body-col {
padding-bottom: 0px;
}
}
}

.news-container:not(:last-child) {
padding-bottom: 60px;
}
}

.about-anchor {
Expand All @@ -26,9 +54,3 @@
line-height: normal;
font-size: $font-size-x-regular;
}
.content-row{
@include lato-font('normal');
margin-bottom: 45px;
font-size: 18px;
color: color(text, secondary);
}
67 changes: 66 additions & 1 deletion src/app/core/news/news.component.ts
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@@ -1,17 +1,82 @@
import { Component, OnInit, ViewEncapsulation } from '@angular/core';

import { News } from '../../models';

@Component({
selector: 'news',
templateUrl: './news.component.html',
styleUrls: [ './news.component.scss' ],
encapsulation: ViewEncapsulation.None
})
export class NewsComponent implements OnInit {
news: News[] = [];

ngOnInit() {
//
// Init the news array
this.initNews();
}

viewSynapseReg() {
window.open('https://www.synapse.org/#!RegisterAccount:0', '_blank');
}

initNews() {
this.news = [
{
data: 'JULY 2019',
entry: [
{
header: 'Druggability Information',
body: 'Druggability buckets have been updated with two additional ' +
'categories: antibody feasibility and safety.'
},
{
header: 'Proteomic Data',
body: 'Differential protein expression between AD cases and controls ' +
'is now available.'
},
{
header: 'Metabolomic Data',
body: 'Differential abundance of metabolites between AD cases and ' +
'controls is now available.'
}
]
},
{
data: 'JUNE 2019',
entry: [
{
header: 'Nominated Targets',
body: 'Researchers outside the AMP-AD consortium have submitted ' +
'nominated targets.'
},
{
header: 'Druggability Information',
body: 'Small Molecule Druggability is now available for all genes ' +
'across the genome.'
}
]
},
{
data: 'MAY 2019',
entry: [
{
header: 'Nominated Targets',
body: 'The total number of AMP-AD nominated targets has increased ' +
'to 500 targets.'
}
]
},
{
data: 'MARCH 2019',
entry: [
{
header: 'Transcriptomic Data',
body: 'Differential expression from RNAseq is now available for all ' +
'genes with measurable expression across the genome.'
}
]
}
];
}
}
6 changes: 0 additions & 6 deletions src/app/core/synapse-account/synapse-account.component.scss
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Expand Up @@ -7,12 +7,6 @@
}
}

.overview-header {
.row {
align-items: center;
}
}

.amp-ad-desc {
box-shadow: 0px 2px 6px color(black-box-shadow, a50);
margin-bottom: 2%;
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6 changes: 0 additions & 6 deletions src/app/core/terms/terms.component.scss
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@@ -1,12 +1,6 @@
@import "../../../assets/css/helpers/variables";
@import "../../../assets/css/helpers/mixins";

.overview-header {
.row {
align-items: center;
}
}

.download-terms-desc {
margin-bottom: 2%;

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65 changes: 49 additions & 16 deletions src/app/dialogs/rna-dialog/rna-dialog.component.html
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@@ -1,22 +1,55 @@
<div class="ui-rtl" dir="rtl">
<p-dialog header="RNA Expression Analysis" [(visible)]="display" [modal]="true" [blockScroll]="false" [responsive]="true" [minY]="256"
<p-dialog header="About the RNAseq Analysis" [(visible)]="display" [modal]="true" [blockScroll]="false" [responsive]="true" [minY]="256"
[baseZIndex]="10000" [styleClass]="'rna-dialog'" [ngStyle]="{'minWidth': 330}">
<div class="row content-row first-bp-dia-row" dir="ltr">
<div class="col-md-12 col-sm-12 col-12">
RNA-seq data used for these analyses was generated from over 2100 samples from post-mortem brains of more than 1100
individuals. In total there are seven distinct brain regions (Dorsolateral Prefrontal Cortex (DLPFC), Temporal Cortex
(TCX), Cerebellum (CBE), Parahippocampal Gyrus (PHG), Inferior Frontal Gyrus (IFG), Superior Temporal Gyrus (STG),
Frontal Pole (FP)) from three human cohort studies (<a class="link" href="https://www.synapse.org/#!Synapse:syn3219045" target="_blank">Religious Orders Study and Memory and Aging Project</a>,
<a class="link" href="https://www.synapse.org/#!Synapse:syn5550404" target="_blank">Mayo RNAseq</a>,
and <a class="link" href="https://www.synapse.org/#!Synapse:syn3159438" target="_blank">Mount Sinai Brain Bank</a>).

RNA-seq data from these studies was processed through a harmonized <a class="link" href="https://www.synapse.org/#!Synapse:syn9702085" target="_blank">computational pipeline</a> to reveal overall expression
levels, measure differential expression between AD cases and controls and describe the gene coexpression network. The
data is publicly available through these links: RNA-seq <a class="link" href="https://www.synapse.org/#!Synapse:syn14237651" target="_blank">differential expression summary statistics</a>, RNA-seq network
coexpression analysis.

You will need a <a class="link" href="https://www.synapse.org/" target="_blank">Synapse</a> account to access the RNA-seq data and analytical results. To establish a Synapse account,
please follow the instructions on <span class="link" (click)="goToRoute('/synapse-account')">this page</span>.
<div class="col-md-12 col-sm-12 col-12 container-col">
<div class="row first-content-row">
RNA-seq data used for these analyses was generated from over 2100 samples from post-mortem brains of more
than 1100 individuals. In total there are seven distinct brain regions from three human cohort studies:
</div>
<div class="row header-row">
<div class="col-md-6 col-sm-6 col-6 auto-col">
Cohort Study
</div>
<div class="col-md-6 col-sm-6 col-6 auto-col">
Brain Region(s)
</div>
</div>
<div class="row body-row colored-row">
<div class="col-md-6 col-sm-6 col-6 auto-col">
<a class="link no-bold" href="https://www.synapse.org/#!Synapse:syn3219045" target="_blank">Religious Orders Study and Memory and Aging Project (ROSMAP)</a>
</div>
<div class="col-md-6 col-sm-6 col-6 auto-col">
Dorsolateral Prefrontal Cortex (DLPFC)
</div>
</div>
<div class="row body-row">
<div class="col-md-6 col-sm-6 col-6 auto-col">
<a class="link no-bold" href="https://www.synapse.org/#!Synapse:syn5550404" target="_blank">Mayo RNAseq (MAYO)</a>
</div>
<div class="col-md-6 col-sm-6 col-6 auto-col">
Cerebellum (CBE), Temporal Cortex (TCX)
</div>
</div>
<div class="row body-row colored-row">
<div class="col-md-6 col-sm-6 col-6 auto-col">
<a class="link no-bold" href="https://www.synapse.org/#!Synapse:syn3159438" target="_blank">Mount Sinai Brain Bank (MSBB)</a>
</div>
<div class="col-md-6 col-sm-6 col-6 auto-col">
Frontal Pole (FP), Inferior Frontal Gyrus (IFG), Parahippocampal Gyrus (PHG), Superior Temporal Gyrus (STG)
</div>
</div>
<div class="row last-content-row">
Note that not all genes are detected in all brain regions; for these genes, the plots show fewer than seven brain regions.
</div>
<div class="row last-content-row">
RNA-seq data from these studies was processed through a&nbsp;<a class="link auto-width no-bold" href="https://www.synapse.org/#!Synapse:syn9702085" target="_blank">harmonized computational pipeline</a>&nbsp;to reveal overall expression levels, measure differential expression between AD cases and controls, and describe the gene coexpression network.
</div>
<div class="row last-content-row">
The data is publicly available in&nbsp;<a class="link auto-width no-bold" href="https://www.synapse.org/" target="_blank">Synapse</a>&nbsp;through
these links:&nbsp;<a class="link auto-width no-bold" href="https://www.synapse.org/#!Synapse:syn14237651" target="_blank">RNA-seq differential expression summary statistics;</a>&nbsp;
<a class="link auto-width no-bold" href="https://doi.org/10.1101/510420" target="_blank">RNA-seq network coexpression analysis </a>.
</div>
</div>
</div>
</p-dialog>
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