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-</script> <div style='mso-special-format:nobullet;text-align:left;font-family:"Gill Sans"; font-weight:normal;font-style:normal;text-decoration:none;text-shadow:none; text-effect:none;mso-fareast-hint:no;layout-flow:horizontal;color:#FBFDB8; font-size:213%;mso-text-raise:0%;mso-line-spacing:" 0 ";mso-margin-left-alt: 348;mso-text-indent-alt:56;mso-line-spacing:" 0 ";mso-margin-left-alt:348; mso-text-indent-alt:56'><span style='mso-special-format:nobullet;display:none; color:#FBFDB8;font-family:"Monotype Sorts";font-size:99%'>l</span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'>The </span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'><i>App</i></span><span style='font-size:106%;color:#E9EB5D;mso-color-index:3'> transcript neighborhood</span></div> </layer></div> </layer><script>
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-</script><span style='text-align:left'><span style='font-size:150%;color:#E9EB5D;mso-color-index: 3'><b>Question: </b></span><span style='font-size:133%;color:#E9EB5D; mso-color-index:3'><b>How </b></span></span></layer><script>
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-</script><span style='text-align:left'><span style='font-size:133%;color:#E9EB5D;mso-color-index: 3'><b>this imply.</b></span></span></layer></div> </layer></div> </LAYER>
- <layer> <div id=NotesObj style='display:none'> <table style='color:white' border=0 width="100%"> <tr> <td width=5 nowrap></td> <td width="100%"></td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>The answer is a strong Yes. A very large number of transcripts have correlations above 0.7 (absolute value) with App mRNA. The precise number today is 208. But this will change as we add more strains and arrays. In any case, this is a fairly large number and all of these correlations are significant at alpha .05 even when correcting for the enormous numbers<span style="mso-spacerun: yes">&nbsp; </span>of tests (12422 tests).</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>What does this imply?</font><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><br> </td> </tr> <tr> <td colspan=1></td> <td align=left colspan=1><font face=Helvetica size=3>That there can be massive codependence of expression variance among transcripts. App is NOT an isolated instance. This is improtant biologically and statistically. From a statistical perspective, we would like to know how many ÒindependentÓ test we effectively are performing when we use array data in this way. Are we testing 12000 independent transcripts or just 1200 transcriptional ÒmodulesÓ each with blurred boarders but each with about 10 effective members. There is no answer yet, but we probaby have a large enough data set to begin to answer this question.</font><br> </td> </tr> </table> </div> </layer> <script language=JavaScript><!--
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