annotate shm_clonality.htm @ 46:cfc9a442e59d draft

Uploaded
author davidvanzessen
date Wed, 12 Apr 2017 04:28:16 -0400
parents b66e8946ba75
children ba33b94637ca
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
39
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
1 <html>
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
2
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
3 <head>
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
4 <meta http-equiv=Content-Type content="text/html; charset=windows-1252">
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
5 <meta name=Generator content="Microsoft Word 14 (filtered)">
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
6 <style>
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
7 <!--
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
8 /* Font Definitions */
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
9 @font-face
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
10 {font-family:Calibri;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
11 panose-1:2 15 5 2 2 2 4 3 2 4;}
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
12 @font-face
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
13 {font-family:Tahoma;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
14 panose-1:2 11 6 4 3 5 4 4 2 4;}
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
15 /* Style Definitions */
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
16 p.MsoNormal, li.MsoNormal, div.MsoNormal
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
17 {margin-top:0in;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
18 margin-right:0in;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
19 margin-bottom:10.0pt;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
20 margin-left:0in;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
21 line-height:115%;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
22 font-size:11.0pt;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
23 font-family:"Calibri","sans-serif";}
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
24 a:link, span.MsoHyperlink
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
25 {color:blue;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
26 text-decoration:underline;}
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
27 a:visited, span.MsoHyperlinkFollowed
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
28 {color:purple;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
29 text-decoration:underline;}
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
30 p
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
31 {margin-right:0in;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
32 margin-left:0in;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
33 font-size:12.0pt;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
34 font-family:"Times New Roman","serif";}
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
35 p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
36 {mso-style-link:"Balloon Text Char";
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
37 margin:0in;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
38 margin-bottom:.0001pt;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
39 font-size:8.0pt;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
40 font-family:"Tahoma","sans-serif";}
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
41 p.msochpdefault, li.msochpdefault, div.msochpdefault
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
42 {mso-style-name:msochpdefault;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
43 margin-right:0in;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
44 margin-left:0in;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
45 font-size:12.0pt;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
46 font-family:"Calibri","sans-serif";}
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
47 p.msopapdefault, li.msopapdefault, div.msopapdefault
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
48 {mso-style-name:msopapdefault;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
49 margin-right:0in;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
50 margin-bottom:10.0pt;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
51 margin-left:0in;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
52 line-height:115%;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
53 font-size:12.0pt;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
54 font-family:"Times New Roman","serif";}
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
55 span.apple-converted-space
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
56 {mso-style-name:apple-converted-space;}
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
57 span.BalloonTextChar
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
58 {mso-style-name:"Balloon Text Char";
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
59 mso-style-link:"Balloon Text";
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
60 font-family:"Tahoma","sans-serif";}
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
61 .MsoChpDefault
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
62 {font-size:10.0pt;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
63 font-family:"Calibri","sans-serif";}
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
64 .MsoPapDefault
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
65 {margin-bottom:10.0pt;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
66 line-height:115%;}
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
67 @page WordSection1
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
68 {size:8.5in 11.0in;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
69 margin:1.0in 1.0in 1.0in 1.0in;}
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
70 div.WordSection1
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
71 {page:WordSection1;}
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
72 -->
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
73 </style>
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
74
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
75 </head>
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
76
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
77 <body lang=EN-US link=blue vlink=purple>
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
78
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
79 <div class=WordSection1>
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
80
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
81 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
82 text-align:justify;background:white'><b><span lang=EN-GB style='color:black'>References</span></b></p>
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
83
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
84 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
85 text-align:justify;background:white'><span lang=EN-GB style='color:black'>Gupta,
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
86 Namita T. and Vander Heiden, Jason A. and Uduman, Mohamed and Gadala-Maria,
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
87 Daniel and Yaari, Gur and Kleinstein, Steven H. (2015). <a name="OLE_LINK106"></a><a
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
88 name="OLE_LINK107"></a>Change-O: a toolkit for analyzing large-scale B cell
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
89 immunoglobulin repertoire sequencing data: Table 1. In<span
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
90 class=apple-converted-space>&nbsp;</span><em>Bioinformatics, 31 (20), pp.
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
91 3356–3358.</em><span class=apple-converted-space><i>&nbsp;</i></span>[</span><a
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
92 href="http://dx.doi.org/10.1093/bioinformatics/btv359" target="_blank"><span
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
93 lang=EN-GB style='color:#303030'>doi:10.1093/bioinformatics/btv359</span></a><span
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
94 lang=EN-GB style='color:black'>][</span><a
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
95 href="http://dx.doi.org/10.1093/bioinformatics/btv359" target="_blank"><span
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
96 lang=EN-GB style='color:#303030'>Link</span></a><span lang=EN-GB
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
97 style='color:black'>]</span></p>
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
98
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
99 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
100 text-align:justify;background:white'><span lang=EN-GB style='color:black'>&nbsp;</span></p>
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
101
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
102 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
103 text-align:justify;background:white'><a name="OLE_LINK110"><u><span lang=EN-GB
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
104 style='color:black'>All, IGA, IGG, IGM and IGE tabs</span></u></a></p>
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
105
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
106 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
107 text-align:justify;background:white'><span lang=EN-GB style='color:black'>In
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
108 these tabs information on the clonal relation of transcripts can be found. To
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
109 calculate clonal relation Change-O is used (Gupta et al, PMID: 26069265).
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
110 Transcripts are considered clonally related if they have maximal three nucleotides
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
111 difference in their CDR3 sequence and the same first V segment (as assigned by
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
112 IMGT). Results are represented in a table format showing the clone size and the
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
113 number of clones or sequences with this clone size. Change-O settings used are
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
114 the </span><span lang=EN-GB>nucleotide hamming distance substitution model with
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
115 a complete distance of maximal three. For clonal assignment the first gene
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
116 segments were used, and the distances were not normalized. In case of
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
117 asymmetric distances, the minimal distance was used.<span style='color:black'> </span></span></p>
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
118
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
119 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
120 text-align:justify;background:white'><span lang=EN-GB style='color:black'>&nbsp;</span></p>
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
121
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
122 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
123 text-align:justify;background:white'><u><span lang=EN-GB style='color:black'>Overlap
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
124 tab</span></u><span lang=EN-GB style='color:black'> </span></p>
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
125
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
126 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
127 text-align:justify;background:white'><span lang=EN-GB style='color:black'>This
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
128 tab gives information on with which (sub)classe(s) each unique analyzed region
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
129 (based on the exact nucleotide sequence of the analyzes region and the CDR3
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
130 nucleotide sequence) is found with. This gives information if the combination
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
131 of the exact same nucleotide sequence of the analyzed region and the CDR3
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
132 sequence can be found in multiple (sub)classes.</span></p>
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
133
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
134 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
135 text-align:justify;background:white'><span style='color:black'><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAA8AAAAPCAYAAAA71pVKAAAAzElEQVQoka2TwQ2CQBBFpwTshw4ImW8ogJMlUIMmhNCDxgasAi50oSXA8XlAjCG7aqKTzGX/vsnM31mzR0gk7tTudO5MEizpzvQ4ryUSe408J3Xn+grE0p1rnpOamVmWsZG4rS+dzzAMsN8Hi9yyjI1JNGtxu4VxBJgLRLpoTKIPiW0LlwtUVRTubW2OBGUJu92cZRmdfbKQMAw8o+vi5v0fLorZ7Y9waGYJjsf38DJz0O1PsEQffOcv4Sa6YYfDDJ5Obzbsp93+5VfdATueO1fdLdI0AAAAAElFTkSuQmCC"> Please note that this tab is based on all
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
136 sequences before filter unique sequences and the remove duplicates based on
45
b66e8946ba75 Uploaded
davidvanzessen
parents: 39
diff changeset
137 filters are applied. In this table only sequences occuring more than once are
39
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
138 included. </span></p>
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
139
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
140 </div>
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
141
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
142 </body>
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
143
a24f8c93583a Uploaded
davidvanzessen
parents:
diff changeset
144 </html>