Mercurial > repos > davidvanzessen > shm_csr
annotate shm_csr.htm @ 98:d714f5ea83d7 draft default tip
planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
| author | rhpvorderman |
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| date | Wed, 10 Jan 2024 12:32:47 +0000 |
| parents | 6809c63d9161 |
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| rev | line source |
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| 67 | 1 <html> |
| 2 | |
| 3 <head> | |
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4 <meta http-equiv=Content-Type content="text/html; charset=UTF-8"> |
| 67 | 5 <meta name=Generator content="Microsoft Word 14 (filtered)"> |
| 6 <style> | |
| 7 <!-- | |
| 8 /* Font Definitions */ | |
| 9 @font-face | |
| 10 {font-family:Calibri; | |
| 11 panose-1:2 15 5 2 2 2 4 3 2 4;} | |
| 12 /* Style Definitions */ | |
| 13 p.MsoNormal, li.MsoNormal, div.MsoNormal | |
| 14 {margin-top:0in; | |
| 15 margin-right:0in; | |
| 16 margin-bottom:10.0pt; | |
| 17 margin-left:0in; | |
| 18 line-height:115%; | |
| 19 font-size:11.0pt; | |
| 20 font-family:"Calibri","sans-serif";} | |
| 21 a:link, span.MsoHyperlink | |
| 22 {color:blue; | |
| 23 text-decoration:underline;} | |
| 24 a:visited, span.MsoHyperlinkFollowed | |
| 25 {color:purple; | |
| 26 text-decoration:underline;} | |
| 27 span.apple-converted-space | |
| 28 {mso-style-name:apple-converted-space;} | |
| 29 .MsoChpDefault | |
| 30 {font-family:"Calibri","sans-serif";} | |
| 31 .MsoPapDefault | |
| 32 {margin-bottom:10.0pt; | |
| 33 line-height:115%;} | |
| 34 @page WordSection1 | |
| 35 {size:8.5in 11.0in; | |
| 36 margin:1.0in 1.0in 1.0in 1.0in;} | |
| 37 div.WordSection1 | |
| 38 {page:WordSection1;} | |
| 39 --> | |
| 40 </style> | |
| 41 | |
| 42 </head> | |
| 43 | |
| 44 <body lang=EN-US link=blue vlink=purple> | |
| 45 | |
| 46 <div class=WordSection1> | |
| 47 | |
| 48 <p class=MsoNormalCxSpFirst style='text-align:justify'><span lang=EN-GB | |
| 49 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The | |
| 50 graphs in this tab give insight into the subclass distribution of IGG and IGA | |
| 51 transcripts. </span><span lang=EN-GB style='font-size:12.0pt;line-height:115%; | |
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rhpvorderman
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52 font-family:"Times New Roman","serif"'>Human Cµ, Cα, Cγ and Cε |
| 67 | 53 constant genes are assigned using a </span><span lang=EN-GB style='font-size: |
| 54 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>custom script | |
| 55 specifically designed for human (sub)class assignment in repertoire data as | |
| 56 described in van Schouwenburg and IJspeert et al, submitted for publication. In | |
| 57 this script the reference sequences for the subclasses are divided in 8 | |
| 58 nucleotide chunks which overlap by 4 nucleotides. These overlapping chunks are | |
| 59 then individually aligned in the right order to each input sequence. The | |
| 60 percentage of the chunks identified in each rearrangement is calculated in the | |
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rhpvorderman
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changeset
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61 ‘chunk hit percentage’. </span><span lang=EN-GB style='font-size:12.0pt; |
| 67 | 62 line-height:115%;font-family:"Times New Roman","serif"'>Cα and Cγ |
| 63 subclasses are very homologous and only differ in a few nucleotides. To assign | |
| 64 subclasses the </span><span lang=EN-GB style='font-size:12.0pt;line-height: | |
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65 115%;font-family:"Times New Roman","serif"'>‘nt hit percentage’ is calculated. |
| 67 | 66 This percentage indicates how well the chunks covering the subclass specific |
| 67 nucleotide match with the different subclasses. </span><span lang=EN-GB | |
| 68 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Information | |
| 69 on normal distribution of subclasses in healthy individuals of different ages | |
| 70 can be found in IJspeert and van Schouwenburg et al, PMID: 27799928.</span></p> | |
| 71 | |
| 72 <p class=MsoNormalCxSpMiddle style='text-align:justify'><a name="OLE_LINK100"></a><a | |
| 73 name="OLE_LINK99"></a><a name="OLE_LINK25"><u><span lang=EN-GB | |
| 74 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>IGA | |
| 75 subclass distribution</span></u></a></p> | |
| 76 | |
| 77 <p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB | |
| 78 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Pie | |
| 79 chart showing the relative distribution of IGA1 and IGA2 transcripts in the | |
| 80 sample.</span></p> | |
| 81 | |
| 82 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB | |
| 83 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>IGG | |
| 84 subclass distribution</span></u></p> | |
| 85 | |
| 86 <p class=MsoNormalCxSpLast style='text-align:justify'><span lang=EN-GB | |
| 87 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Pie | |
| 88 chart showing the relative distribution of IGG1, IGG2, IGG3 and IGG4 | |
| 89 transcripts in the sample.</span></p> | |
| 90 | |
| 91 </div> | |
| 92 | |
| 93 </body> | |
| 94 | |
| 95 </html> |