-
Notifications
You must be signed in to change notification settings - Fork 0
/
pas-expression.html
176 lines (176 loc) · 8.31 KB
/
pas-expression.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
<!DOCTYPE html>
<html>
<head>
<title>MAPP reports</title>
</head>
<body style="background-color: rgb(219, 219, 219)">
<br>
<center>
<img src=mapp_logo.png width="4%">
<h1>MAPP Report</h1>
<h3>Test run with reduced parameters on a sampled dataset</h3>
<br>
<a href="gene-expression.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Gene Expression</button>
</a>
<a href="transcript-expression.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Transcript Expression</button>
</a>
<a href="exon-inclusion.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Exon Inclusion Fractions</button>
</a>
<a href="pas-expression.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid #33a02c; background-color: #ffffff">Poly(A) Site Expressions</button>
</a>
<br>
<br>
<a href="activities-3ss.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">3'SS Activities & Counts</button>
</a>
<a href="activities-5ss.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">5'SS Activities & Counts</button>
</a>
<a href="activities-pas.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">PAS Activities & Counts</button>
</a>
</center>
<br>
<br>
<center>
<div style="width: 70%; text-align: left; border: 2px solid black; background-color: #ffffff; padding: 20px; line-height: 1.5;">
Tandem Poly(A) sites' expression has been quantified with the PAQR tool
(<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1415-3">Gruber A.J. et al.</a>).
<br>
<br>
Expression scores are stored as Transcripts-per-Milion (TPM) values in a tab-separated format (TSV) table.
<br>
<br>
Each row in the expression table represents a single, unique Poly(A) site (PAS).
The first 10 columns contain the following information:
<br>
<b>chrom</b> : PAS chromosome
<br>
<b>start</b> : PAS start coordinate (BED format)
<br>
<b>end</b> : PAS end coordinate (BED format)
<br>
<b>pas</b> : PAS ID (as in the PAS annotation used)
<br>
<b>score</b> : score of the PAS annotation used
<br>
<b>strand</b> : PAS strand
<br>
<b>polyAsite_exon_idx</b> : PAS index on a specific terminal exon
<br>
<b>nr_polyAsites_on_exon</b> : total number of Poly(A) sites on a specific terminal exon
<br>
<b>exon</b> : unique terminal exon ID
<br>
<b>gene</b> : transcript ID of this specific terminal exon
<br>
<br>
Each of the next columns stores TPM values of
a specific RNA-Seq sample, as in the scheme below:
<br>
<br>
<center>
<table border="2" style="border-collapse: collapse;">
<tr>
<th style="text-align: center; padding: 5px;"><b></b></th>
<th style="text-align: center; padding: 5px;"><b>chrom</b></th>
<th style="text-align: center; padding: 5px;"><b>start</b></th>
<th style="text-align: center; padding: 5px;"><b>end</b></th>
<th style="text-align: center; padding: 5px;"><b>pas</b></th>
<th style="text-align: center; padding: 5px;"><b>score</b></th>
<th style="text-align: center; padding: 5px;"><b>strand</b></th>
<th style="text-align: center; padding: 5px;"><b>polyAsite_exon_idx</b></th>
<th style="text-align: center; padding: 5px;"><b>nr_polyAsites_on_exon</b></th>
<th style="text-align: center; padding: 5px;"><b>exon</b></th>
<th style="text-align: center; padding: 5px;"><b>gene</b></th>
<th style="text-align: center; padding: 5px;"><b>Sample1</b></th>
<th style="text-align: center; padding: 5px;"><b>Sample2</b></th>
<th style="text-align: center; padding: 5px;"><b>...</b></th>
</tr>
<tr>
<td style="text-align: center; padding: 5px;"><b>PAS1</b></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
</tr>
<tr>
<td style="text-align: center; padding: 5px;"><b>PAS2</b></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
</tr>
<tr>
<td style="text-align: center; padding: 5px;"><b>PAS3</b></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
</tr>
<tr>
<td style="text-align: center; padding: 5px;"><b>...</b></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
</tr>
</table>
</center>
</div>
<br>
<a href="report.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Main Menu</button>
</a>
<a href="results/pas-expression-table.tsv" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Download Table</button>
</a>
</center>
</body>
</html>