-
Notifications
You must be signed in to change notification settings - Fork 10
/
covid-19.html
336 lines (270 loc) · 22.5 KB
/
covid-19.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
---
layout: default
permalink: /covid-19.html
---
<style>
.banner {
background-color: red;
color: white;
border-radius: 5px;
padding: 10px;
text-align: center;
margin: 20px 0px;
}
.banner__warning {
display: inline-block;
text-align: left;
width: 15%;
}
.banner__disclaimer {
display: inline-block;
text-align: start;
width: 80%;
}
.ribbon__category--cell, .ribbon__subject--cell, .ribbon__subject--cell--no-annotation, .ribbon__subject__label--link, tr, th, td {
/* font-size: 14px !important; */
line-height: 1.0 !important;
}
.ribbon__subject--cell {
box-shadow: 0 1px 1px rgba(0,0,0,.26);
}
.ribbon__category--cell:hover {
font-weight: 800 !important;
}
.wc-ribbon-cell, wc-ribbon-subject, wc-ribbon-strips {
line-height: 1.0 !important;
}
li {
margin-left: 30px;
}
</style>
<script src="js/covid.js"></script>
<script type="module" src="https://unpkg.com/@geneontology/wc-ribbon-strips/dist/wc-ribbon-strips/wc-ribbon-strips.esm.js"></script>
<script nomodule="" src="https://unpkg.com/@geneontology/wc-ribbon-strips/dist/wc-ribbon-strips/wc-ribbon-strips.js"></script>
<div class="container" style="width:95%">
<div class="row" style="margin:0rem 2rem">
<h1>SARS-CoV-2 - Coronavirus</h1>
<p>In an effort to <b>assist global research on the SARS-CoV-2 virus</b> (the cause of the COVID-19 disease), the Gene Ontology Consortium has made a central point of access to the relevant information available in our knowledgebase. Currently, we have compiled the following information:
<li><a href="#hp-sars-cov-2-ce">functions of human proteins used by the virus to enter a human cell</a></li>
<li><a href="#ohp-pt-sars-cov-2">functions of human proteins possibly targeted by the virus after cell entry</a></li></p>
<p>The Gene Ontology is a knowledgebase of descriptions of gene function that are both human-readable and computer-readable, based on evidence in the scientific literature. Because the GO knowledgebase is readable by computers, it enables computational analyses of biological systems and experimental results, accelerating biomedical research. <a href="/docs/introduction-to-go-resource/" target="blank">Read more</a>.</p>
<p>The “GO Ribbon” viewer below displays a horizontal list of broad categories of functions that a gene (or a protein encoded by a gene) can have. A colored box under that category indicates that the gene is known to have a function of that type, while a blank box indicates a function it is not known to have. Clicking on a colored box will bring up another page with more details, such as a more precise description of the function, and links to additional information such as the scientific evidence it is based on, and the specific GOC group that curated the information.</p>
<p>You can also <b>download</b> this information for use in computational analyses:
<li>GO annotations for the human genes that may be relevant for SARS-CoV-2 infection<sup><a href="#references">3</a></sup>: [<a href="/data/sars-cov-2_targets.gaf">GAF</a>] [<a href="/data/sars-cov-2_targets.gpad">GPAD</a>] [<a href="/data/sars-cov-2_targets.gpi">GPI</a>] </li>
<li>Human genes that may be relevant for SARS-CoV-2 infection<sup><a href="#references">3</a></sup>: [<a href="https://www.biorxiv.org/content/biorxiv/early/2020/03/27/2020.03.22.002386/DC6/embed/media-6.xlsx?download=true" target="_blank">Excel table</a>] [<a href="/data/sars-cov-2_targets.json">JSON</a>]</li>
<li>GO annotations for the SARS-CoV-2 virus genes: [<a href="data/uniprot_sars-cov-2.gpa">GPAD</a>] [<a href="/data/uniprot_reviewed_sars-cov-2.gpi">GPI</a>] </li>
<li>the full <a href="/docs/downloads/">GO knowledgebase</a></li></p>
<p>Learn more about: [<a href="/docs/go-annotation-file-gaf-format-2.1/">GAF</a>] [<a href="/docs/gene-product-association-data-gpad-format/">GPAD</a>] [<a href="/docs/gene-product-information-gpi-format/">GPI</a>].</p>
<h2 id="hp-sars-cov-2-ce">Human proteins used by SARS-CoV-2 to enter human cells</h2>
The virus has been shown to require two human proteins (<a href="https://amigo.geneontology.org/amigo/gene_product/UniProtKB:Q9BYF1" target="_blank">ACE2</a>, <a href="https://amigo.geneontology.org/amigo/gene_product/UniProtKB:O15393" target="_blank">TMPRSS2</a>) for cell entry<sup><a href="#references">1,2</a></sup>.
These are the same proteins used by <a href="https://www.ncbi.nlm.nih.gov/pubmed/21068237" target="blank">SARS-CoV<sup>4</sup></a>, the cause of the 2002-2004 SARS epidemic.
<div id="ribbon-covid-cell-entry" style="padding-top: 55px; padding-bottom: 30px; overflow-x: auto; width: 1400px;"></div>
<table style="width:100%">
<tr>
<td style="padding: 0px 15px;">
<div>
<b>Ribbon Tips</b>:
<small>
<li>click on the gene name of a ribbon line to show all GO terms (functions/processes/locations) associated</li>
<li>click on a high-level diagonal GO term (e.g. signaling) to show the term details and associated genes</li>
<li>click on a ribbon cell to show the detailed annotations for the selected high-level GO term</li>
</small>
</div>
</td>
</tr>
</table>
<h2 id="ohp-pt-sars-cov-2">Other human proteins that are possible targets of SARS-CoV-2</h2>
The SARS-CoV-2 viral genome encodes instructions for making <a href="https://www.ncbi.nlm.nih.gov/pubmed/31987001" target="blank">29 different proteins</a><sup><a href="#references">5</a></sup>. A recent study by Gordon et al.<sup><a href="#references">3</a></sup> expressed and purified 27 of those proteins, and tested them to see which human proteins they physically interact with. They found specific human protein interactions for 26 SARS-CoV-2 proteins. These human proteins may be targets of the SARS-CoV-2 virus, and enable the virus to infect human cells, replicate, and spread.
<br><br>
<b>Select one of the SARS-CoV-2 proteins to see the list of human proteins it interacts with<sup><a href="#references">3</a></sup>, and the normal functions of those human proteins.</b>
Scanning vertically down a column can help to see the functions these human proteins have in common, and may indicate how the virus may be using or disrupting normal human cell functions during infection.
<br><br>
<b>SARS-CoV-2 gene</b>: <select id="selected-covid-gene" onchange="changeCOVID()"></select>
<div id="ribbon-covid-gene" style="padding-top: 55px; padding-bottom: 30px; overflow-x: auto; width: 1400px;"></div>
<table style="width:100%"><tr>
<td style="padding: 0px 15px;">
<div>
<b>Ribbon Tips</b>:
<small>
<li>click on the gene name of a ribbon line to show all GO terms (functions/processes/locations) associated</li>
<li>click on a high-level diagonal GO term (e.g. signaling) to show the term details and associated genes</li>
<li>click on a ribbon cell to show the detailed annotations for the selected high-level GO term</li>
</small>
</div>
</td>
<td style="text-align: right; border: 1px solid rgba(0, 0, 0, 0.4); padding: 15px; width: 50%">
<span style="color: #1a1ac5; font-size: 1.5rem; font-weight: bold !important;">LIVE GO ENRICHMENT ANALYSIS <a href="/docs/go-enrichment-analysis/" target="_blank" style="font-weight: bold !important"><sup>(?)</sup></a></span>
<hr style="margin: 5px;"/>
<div style="display: block;
color: #1a1ac5; font-size: 1.5rem;
margin-bottom: 0.8rem;">
GO enrichment detects processes, functions or components that are unusually represented in a gene set.
For the above <b><span id="nb_partners" style="display: inline-block; font-weight: 800 !important;"></span> human proteins</b> that interact with <b><span id="virus-gene-name" style="display: inline-block; font-weight: 800 !important;"></span></b>, find (if any) the unusually represented :
<!-- Some of the human proteins targeted by the SARS-CoV-2 have unusual representations of these processes, functions and components. -->
<!-- Perform a GO enrichment analysis<a href="/docs/go-enrichment-analysis/" target="_blank" style="font-weight: bold !important"><sup>(?)</sup></a> on the <span id="nb_partners" style="display: inline-block"></span> human proteins that interact with <span id="virus-gene-name"></span> ON: -->
</div>
<form action="https://pantherdb.org/webservices/go/overrep.jsp" class="form-inline" role="form" method="POST" target="_blank" style="display: inline-block">
<input name="correction" value="fdr" type="hidden">
<input name="format" value="html" type="hidden">
<input name="resource" value="PANTHER" type="hidden">
<textarea id="enrich-covid-19-genes-bp" class="form-control" rows="6" name="input" placeholder="Your gene IDs here..." style="width:100%; resize: none; margin-bottom: 5px; font-size: 14px; display: none"></textarea>
<div class="form-group" style="margin-bottom: 5px; display: none">
<select id="rte_ontology" class="form-control" name="ontology">
<option value="biological_process">biological process</option>
</select>
</div>
<div class="input-group">
<div class="form-group" style="display:none">
<select id="rte_species" class="form-control" name="species" style="width: 100%;">
<option value="HUMAN">Homo sapiens</option>
</select>
</div>
<span class="input-group-btn">
<button type="submit" class="btn btn-primary u-no-transform u-anim-move-right" style="border-color: #22612C; margin-left: 4px; background: linear-gradient(150deg,#00158c,rgba(16,122,222,.5) 100%); padding: 5px 10px; border-radius: 15px" title="Find biological processes over/under represented for that gene set">
GO Processes <i class="fa-solid fa-chevron-right u-line-height-single"></i>
</button>
</span>
</div>
</form>
<form action="https://pantherdb.org/webservices/go/overrep.jsp" class="form-inline" role="form" method="POST" target="_blank" style="display: inline-block">
<input name="correction" value="fdr" type="hidden">
<input name="format" value="html" type="hidden">
<input name="resource" value="PANTHER" type="hidden">
<textarea id="enrich-covid-19-genes-mf" class="form-control" rows="6" name="input" placeholder="Your gene IDs here..." style="width:100%; resize: none; margin-bottom: 5px; font-size: 14px; display: none"></textarea>
<div class="form-group" style="margin-bottom: 5px; display: none">
<select id="rte_ontology" class="form-control" name="ontology">
<option value="molecular_function">molecular function</option>
</select>
</div>
<div class="input-group">
<div class="form-group" style="display:none">
<select id="rte_species" class="form-control" name="species" style="width: 100%;">
<option value="HUMAN">Homo sapiens</option>
</select>
</div>
<span class="input-group-btn">
<button type="submit" class="btn btn-primary u-no-transform u-anim-move-right" style="border-color: #22612C; margin-left: 4px; background: linear-gradient(150deg,#ca113b,rgba(189,50,80,.5) 100%); padding: 5px 10px; border-radius: 15px" title="Find molecular functions over/under represented for that gene set">
GO Functions <i class="fa-solid fa-chevron-right u-line-height-single"></i>
</button>
</span>
</div>
</form>
<form action="https://pantherdb.org/webservices/go/overrep.jsp" class="form-inline" role="form" method="POST" target="_blank" style="display: inline-block">
<input name="correction" value="fdr" type="hidden">
<input name="format" value="html" type="hidden">
<input name="resource" value="PANTHER" type="hidden">
<textarea id="enrich-covid-19-genes-cc" class="form-control" rows="6" name="input" placeholder="Your gene IDs here..." style="width:100%; resize: none; margin-bottom: 5px; font-size: 14px; display: none"></textarea>
<div class="form-group" style="margin-bottom: 5px; display: none">
<select id="rte_ontology" class="form-control" name="ontology">
<option value="cellular_component">cellular component</option>
</select>
</div>
<div class="input-group">
<div class="form-group" style="display:none">
<select id="rte_species" class="form-control" name="species" style="width: 100%;">
<option value="HUMAN">Homo sapiens</option>
</select>
</div>
<span class="input-group-btn">
<button type="submit" class="btn btn-primary u-no-transform u-anim-move-right" style="border-color: #22612C; margin-left: 4px; background: linear-gradient(150deg,#dab61a,rgba(253,253,131,.5) 100%); padding: 5px 10px; border-radius: 15px; color: black" title="Find cellular components over/under represented for that gene set">
GO Components <i class="fa-solid fa-chevron-right u-line-height-single"></i>
</button>
</span>
</div>
</form>
</td>
</tr></table>
<h2>GO enrichment analysis of human proteins targeted by SARS-CoV-2</h2>
<p><b>Click one of the following button to perform a live GO enrichment analysis of human proteins that physically interact with SARS-CoV-2 proteins.</b>
This analysis shows the human biological functions that may be preferentially targeted by the SARS-CoV-2 virus.</p>
<div>
<form action="https://pantherdb.org/webservices/go/overrep.jsp" class="form-inline" role="form" method="POST" target="_blank" style="display: inline-block">
<input name="correction" value="fdr" type="hidden">
<input name="format" value="html" type="hidden">
<input name="resource" value="PANTHER" type="hidden">
<textarea id="enrich-all-covid-19-genes-bp" class="form-control" rows="6" name="input" placeholder="Your gene IDs here..." style="width:100%; resize: none; margin-bottom: 5px; font-size: 14px; display: none"></textarea>
<div class="form-group" style="margin-bottom: 5px; display: none">
<select id="rte_ontology" class="form-control" name="ontology">
<option value="biological_process">biological process</option>
</select>
</div>
<div class="input-group">
<div class="form-group" style="display:none">
<select id="rte_species" class="form-control" name="species" style="width: 100%;">
<option value="HUMAN">Homo sapiens</option>
</select>
</div>
<span class="input-group-btn">
<button type="submit" class="btn btn-primary u-no-transform u-anim-move-right" style="border-color: #22612C; margin-left: 4px; background: linear-gradient(150deg,#00158c,rgba(16,122,222,.5) 100%); padding: 5px 10px; border-radius: 15px" title="Find biological processes over/under represented for that gene set">
GO Processes <i class="fa-solid fa-chevron-right u-line-height-single"></i>
</button>
</span>
</div>
</form>
<form action="https://pantherdb.org/webservices/go/overrep.jsp" class="form-inline" role="form" method="POST" target="_blank" style="display: inline-block">
<input name="correction" value="fdr" type="hidden">
<input name="format" value="html" type="hidden">
<input name="resource" value="PANTHER" type="hidden">
<textarea id="enrich-all-covid-19-genes-mf" class="form-control" rows="6" name="input" placeholder="Your gene IDs here..." style="width:100%; resize: none; margin-bottom: 5px; font-size: 14px; display: none"></textarea>
<div class="form-group" style="margin-bottom: 5px; display: none">
<select id="rte_ontology" class="form-control" name="ontology">
<option value="molecular_function">molecular function</option>
</select>
</div>
<div class="input-group">
<div class="form-group" style="display:none">
<select id="rte_species" class="form-control" name="species" style="width: 100%;">
<option value="HUMAN">Homo sapiens</option>
</select>
</div>
<span class="input-group-btn">
<button type="submit" class="btn btn-primary u-no-transform u-anim-move-right" style="border-color: #22612C; margin-left: 4px; background: linear-gradient(150deg,#ca113b,rgba(189,50,80,.5) 100%); padding: 5px 10px; border-radius: 15px" title="Find molecular functions over/under represented for that gene set">
GO Functions <i class="fa-solid fa-chevron-right u-line-height-single"></i>
</button>
</span>
</div>
</form>
<form action="https://pantherdb.org/webservices/go/overrep.jsp" class="form-inline" role="form" method="POST" target="_blank" style="display: inline-block">
<input name="correction" value="fdr" type="hidden">
<input name="format" value="html" type="hidden">
<input name="resource" value="PANTHER" type="hidden">
<textarea id="enrich-all-covid-19-genes-cc" class="form-control" rows="6" name="input" placeholder="Your gene IDs here..." style="width:100%; resize: none; margin-bottom: 5px; font-size: 14px; display: none"></textarea>
<div class="form-group" style="margin-bottom: 5px; display: none">
<select id="rte_ontology" class="form-control" name="ontology">
<option value="cellular_component">cellular component</option>
</select>
</div>
<div class="input-group">
<div class="form-group" style="display:none">
<select id="rte_species" class="form-control" name="species" style="width: 100%;">
<option value="HUMAN">Homo sapiens</option>
</select>
</div>
<span class="input-group-btn">
<button type="submit" class="btn btn-primary u-no-transform u-anim-move-right" style="border-color: #22612C; margin-left: 4px; background: linear-gradient(150deg,#dab61a,rgba(253,253,131,.5) 100%); padding: 5px 10px; border-radius: 15px; color: black" title="Find cellular components over/under represented for that gene set">
GO Components <i class="fa-solid fa-chevron-right u-line-height-single"></i>
</button>
</span>
</div>
</form>
</div>
<h2>Ongoing work of the GO Consortium</h2>
<ul>
<li>Integrating the SARS-CoV-2 genes to allow for the <a href="/docs/go-annotations/">curation</a> and reuse of recent articles on SARS-CoV-2.</li>
<li>Producing <a href="/docs/gocam-overview/">GO-CAMs</a> to further detail the infectious mechanisms of SARS-CoV-2.</li>
<li>Providing interactive <a href="https://github.com/biolink/ontobio/tree/master/notebooks" target="_blank">jupyter notebooks</a> to learn how to rapidly use and integrate GO data in larger analysis.</li>
</ul>
<h2 id="references">References</h2>
<ul>
<li><sup>1</sup> : <a href="https://www.ncbi.nlm.nih.gov/pubmed/32142651" target="_blank">SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor</a></li>
<li><sup>2</sup> : <a href="https://www.ncbi.nlm.nih.gov/pubmed/32132184" target="_blank">Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2</a></li>
<li><sup>3</sup> : <a href="https://www.biorxiv.org/content/10.1101/2020.03.22.002386v2" target="_blank">A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing</a></li>
<li><sup>4</sup> : <a href="https://www.ncbi.nlm.nih.gov/pubmed/21068237" target="_blank">A transmembrane serine protease is linked to the severe acute respiratory syndrome coronavirus receptor and activates virus entry</a></li>
<li><sup>5</sup> : <a href="https://www.ncbi.nlm.nih.gov/pubmed/31987001" target="_blank" style="display: inline;">Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan</a></li>
</ul>
<br><br>
</div>
</div>
<script>
initUI(covid_data);
</script>