Mercurial > repos > davidvanzessen > shm_csr
diff shm_csr.htm @ 39:a24f8c93583a draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 22 Dec 2016 09:39:27 -0500 |
| parents | |
| children | ba33b94637ca |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/shm_csr.htm Thu Dec 22 09:39:27 2016 -0500 @@ -0,0 +1,95 @@ +<html> + +<head> +<meta http-equiv=Content-Type content="text/html; charset=windows-1252"> +<meta name=Generator content="Microsoft Word 14 (filtered)"> +<style> +<!-- + /* Font Definitions */ + @font-face + {font-family:Calibri; + panose-1:2 15 5 2 2 2 4 3 2 4;} + /* Style Definitions */ + p.MsoNormal, li.MsoNormal, div.MsoNormal + {margin-top:0in; + margin-right:0in; + margin-bottom:10.0pt; + margin-left:0in; + line-height:115%; + font-size:11.0pt; + font-family:"Calibri","sans-serif";} +a:link, span.MsoHyperlink + {color:blue; + text-decoration:underline;} +a:visited, span.MsoHyperlinkFollowed + {color:purple; + text-decoration:underline;} +span.apple-converted-space + {mso-style-name:apple-converted-space;} +.MsoChpDefault + {font-family:"Calibri","sans-serif";} +.MsoPapDefault + {margin-bottom:10.0pt; + line-height:115%;} +@page WordSection1 + {size:8.5in 11.0in; + margin:1.0in 1.0in 1.0in 1.0in;} +div.WordSection1 + {page:WordSection1;} +--> +</style> + +</head> + +<body lang=EN-US link=blue vlink=purple> + +<div class=WordSection1> + +<p class=MsoNormalCxSpFirst style='text-align:justify'><span lang=EN-GB +style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The +graphs in this tab give insight into the subclass distribution of IGG and IGA +transcripts. </span><span lang=EN-GB style='font-size:12.0pt;line-height:115%; +font-family:"Times New Roman","serif"'>Human Cµ, Cα, Cγ and Cε +constant genes are assigned using a </span><span lang=EN-GB style='font-size: +12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>custom script +specifically designed for human (sub)class assignment in repertoire data as +described in van Schouwenburg and IJspeert et al, submitted for publication. In +this script the reference sequences for the subclasses are divided in 8 +nucleotide chunks which overlap by 4 nucleotides. These overlapping chunks are +then individually aligned in the right order to each input sequence. The +percentage of the chunks identified in each rearrangement is calculated in the +‘chunk hit percentage’. </span><span lang=EN-GB style='font-size:12.0pt; +line-height:115%;font-family:"Times New Roman","serif"'>Cα and Cγ +subclasses are very homologous and only differ in a few nucleotides. To assign +subclasses the </span><span lang=EN-GB style='font-size:12.0pt;line-height: +115%;font-family:"Times New Roman","serif"'>‘nt hit percentage’ is calculated. +This percentage indicates how well the chunks covering the subclass specific +nucleotide match with the different subclasses. </span><span lang=EN-GB +style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Information +on normal distribution of subclasses in healthy individuals of different ages +can be found in IJspeert and van Schouwenburg et al, PMID: 27799928.</span></p> + +<p class=MsoNormalCxSpMiddle style='text-align:justify'><a name="OLE_LINK100"></a><a +name="OLE_LINK99"></a><a name="OLE_LINK25"><u><span lang=EN-GB +style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>IGA +subclass distribution</span></u></a></p> + +<p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB +style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Pie +chart showing the relative distribution of IGA1 and IGA2 transcripts in the +sample.</span></p> + +<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB +style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>IGG +subclass distribution</span></u></p> + +<p class=MsoNormalCxSpLast style='text-align:justify'><span lang=EN-GB +style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Pie +chart showing the relative distribution of IGG1, IGG2, IGG3 and IGG4 +transcripts in the sample.</span></p> + +</div> + +</body> + +</html>