/
go.html
98 lines (86 loc) · 6.64 KB
/
go.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
<!DOCTYPE html>
<html lang='en'>
<head>
<meta charset='utf-8'>
<meta name='viewport' content='width=device-width, initial-scale=1'>
<link rel='stylesheet' href='https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css'>
<link rel='stylesheet' href='stylesheet/eorna.css'>
<link rel='icon' href='images/eorna-mini-logo.png'>
<title>EoRNA - GO Enrichment</title>
<script src='https://ajax.googleapis.com/ajax/libs/jquery/3.5.1/jquery.min.js'></script>
<script src='https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js'></script>
<script src='https://cdn.plot.ly/plotly-latest.min.js'></script>
</head>
<body class='body-pos' data-spy='scroll' data-target='#list-data' data-offset='35' id='content'>
<div class="container-fluid">
<div class="row">
<nav class="col-md-2 d-none d-md-block grey sidebar">
<div class="sidebar-sticky">
<ul class="nav flex-column">
<li class="nav-item nav-link" id="nav-title"><img class='img-fluid' src='images/eorna-logo.png' width=150'><span class='app-title'>EoRNA</span></li>
<li class="nav-item nav-link" id="nav-header"><b>Utilities Menu</b></li>
<div class="list-group">
<li class="nav-item"><a class="nav-link" href="index.html">Home</a></li>
<li class="nav-item"><a class="nav-link" href="blast.html">Homology Search</a></li>
<li class="nav-item"><a class="nav-link" href="keyword.html">Annotation Search</a></li>
<li class="nav-item"><a class="nav-link" href="download.html">Bulk Data Download</a></li>
<li class="nav-item"><a class="nav-link" href="bart_lookup.html">Translate HORVU to BART IDs</a></li>
<li class="nav-item"><a class="nav-link active" href="go.html">GO Enrichment</a></li>
</div>
<li class="nav-item nav-link" id="nav-title"></li>
<li class="nav-item nav-link" id="nav-header"><b>Links</b></li>
<li class="nav-item nav-link" id="nav-title"></li>
<li class='nav-item'><a class='nav-link ext-links' href='contact.html'>Citation / About Authors</a></li>
<li class="nav-item"><a class="nav-link ext-links" href='http://ics.hutton.ac.uk/barleyrtd'>BarleyRTD Website</a></li>
<li class="nav-item"><a class="nav-link ext-links" href='http://ics.hutton.ac.uk'>Information and Computing Sciences @Hutton</a></li>
<li class="nav-item"><a class="nav-link ext-links" href='http://www.hutton.ac.uk'>The James Hutton Institute</a></li>
<li class="nav-item"><a class="nav-link ext-links" href='https://www.barleyhub.org/'>International Barley Hub</a></li>
<li class="nav-item nav-link" id="nav-title"></li>
<li class="nav-item nav-link" id="nav-header"><b>Funders</b></li>
<li class="nav-item nav-link" id="nav-title"></li>
<li class="nav-item nav-link" id="nav-title"><img class='img-fluid' src='images/resas.svg' width=150'></li>
<li class="nav-item nav-link" id="nav-title"><img class='img-fluid' src='images/bbsrc.svg' width=150'></li>
</ul>
</div>
</nav>
<main role="main" class="col-md-9 ml-sm-auto col-lg-10 pt-3 px-4">
<div class='data-header'>GO Analysis and Annotation</div>
<br>
<div class='data-body'>
GO annotations for the BaRT dataset is available in a spreadsheet <a download href="downloads/BaRTv1_0_GO_annotation_withLookup.xlsx">BaRTv1_0_GO_annotation_withLookup.xlsx </a>. In addition, this file contains a sheet where you can paste your own lists of BaRT gene IDs and it will look up their annotation in the sheet with the GO data:
<ul>
<li>1. Copy and paste a column with gene IDS from the padded BaRT version into column 1 of the sheet named "lookup"</li>
<li>2. Row 2 contains the formulas that do the lookup and results should appear in this row immediately (columns B-F)</li>
<li>3. To generate the results for the remaining rows, select fields B2 to F2, then double-click the little green square at the bottom right of the selection outline. This should auto-fill all the fields below and generate the lookup results</li>
</ul>
</div>
<div class='data-header'>External GO enrichment analysis with BaRT</div>
<br>
<div class='data-body'>
<ul>
<li>1. Go the gProfiler page at <a href='https://biit.cs.ut.ee/gprofiler/gost'>https://biit.cs.ut.ee/gprofiler/gost</a></li>
<li>2. Copy and paste a list of BaRT gene identifiers (one per line) into the query input box</li>
</ul>
<img class='img-fluid' src='images/go_1.png'>
<br>
<ul>
<li>3. Expand the Custom GMT field at the bottom right and select the BaRT GMT file (<a download href='downloads/BaRT_v_1_0.gmt'>download the BaRT_v_1_0.gmt file</a>) from your local file system. The file will then get uploaded to the web server. </li>
<li>4. Click "Run query".</li>
<li>5. Your results will appear below after a few seconds. The interactive graph itself is quite informative: </li>
</ul>
<img class='img-fluid' src='images/go_2.png'>
<br>
<ul>
<li>6. Click the "Detailed Results" tab:</li>
</ul>
<img class='img-fluid' src='images/go_3.png'>
<br>
<ul>
<li>7. Click the "CSV" button to download your results file and save it to your local disk. </li>
</ul>
</div>
</main>
</div>
</div>
</body>
</html>