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
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
|
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD><TITLE>U74Av2RMA August03 / WebQTL</TITLE>
<META http-equiv=Content-Type content="text/html; charset=iso-8859-1">
<LINK REL="stylesheet" TYPE="text/css" HREF='/css/general.css'>
<LINK REL="stylesheet" TYPE="text/css" HREF='/css/menu.css'>
<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT>
</HEAD>
<BODY bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff>
<TABLE cellSpacing=5 cellPadding=4 width="100%" border=0>
<TBODY>
<TR>
<script language="JavaScript" src="/javascript/header.js"></script>
</TR>
<TR>
<TD bgColor=#eeeeee class="solidBorder">
<Table width= "100%" cellSpacing=0 cellPadding=5><TR>
<!-- Body Start from Here -->
<TD valign="top" height="200" width="100%" bgcolor="#eeeeee">
<P class="title">U74Av2RMA Database (August/03 Freeze) <A HREF="/webqtl/main.py?FormID=editHtml"><img src="/images/modify.gif" alt="modify this page" border= 0 valign="middle"></A><BR><BR>Accession number: <A HREF="/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=19">GN19</A></P>
<P class="subtitle"> About the mice used to map microarray data:</P>
<Blockquote>The set of animals used for mapping (a mapping panel) consists of 30 groups of genetically uniform mice of the BXD type. The parental strains are C57BL/6J (B6 or B) and DBA/2J (D2 or D). The first generation hybrid is labeled F1. The F1 hybrids were made by crossing B6 females to D2 males.
All other lines are recombinant inbred strains derived from C57BL/6J and DBA/2J crosses. BXD2 through BXD32 were produced by Dr. Benjamin Taylor starting in the late 1970s. BXD33 through BXD42 were also produced by Dr. Taylor, but they were generated in the 1990s. Lines BXD67 and BXD68 are two partially inbred advanced recombinant strains (F8 and F9) that are part of a large set of BXD-Advanced strains being produced by Drs. Robert Williams, Lu Lu, Guomin Zhou, Lee Silver, and Jeremy Peirce. There will eventually be ~45 of these strains. For additional background on recombinant inbred strains, please see <a href="http://www.nervenet.org/papers/bxn.html" class="fs14">http://www.nervenet.org/papers/bxn.html</a>.
</Blockquote>
<Blockquote>The table below lists the arrays by strain, sex, and age. Each array was hybridized to a pool of mRNA from 3 mice.</Blockquote>
<TABLE border="0" cellpadding="0" cellspacing="0" bgcolor="#000000" width="85%" align="Center">
<TR>
<TD>
<TABLE border="0" cellpadding="5" cellspacing="1" width="100%">
<TR bgcolor="royalblue">
<td rowspan=2 align="Center"> <font color="#FFFFFF"> Strain
</font> </td>
<td colspan=3> <font color="#FFFFFF">
<center>
Age
</center>
</font> </td>
<td rowspan=2 align="Center"> <font color="#FFFFFF"> Strain
</font> </td>
<td colspan=3> <font color="#FFFFFF">
<center>
Age
</center>
</font> </td>
</tr>
<tr bgcolor="royalblue">
<td id="small"> <font color="#FFFFFF">
<center>
8 Wks
</center>
</font> </td>
<td id="small"> <font color="#FFFFFF">
<center>
20 Wks
</center>
</font> </td>
<td id="small"> <font color="#FFFFFF">
<center>
52 Wks
</center>
</font> </td>
<td id="small"> <font color="#FFFFFF">
<center>
8 Wks
</center>
</font> </td>
<td id="small"> <font color="#FFFFFF">
<center>
20 Wks
</center>
</font> </td>
<td id="small"> <font color="#FFFFFF">
<center>
52 Wks
</center>
</font> </td>
</tr>
<tr bgcolor="#eeeeee">
<td id="small">C57BL/6J (B6)</td>
<td id="small">♂♂♂</td>
<td id="small">♀</td>
<td id="small">♀</td>
<td id="small">DBA/2J (D2)</td>
<td id="small">♀</td>
<td id="small">♂♂♀</td>
<td id="small"> </td>
</tr>
<tr bgcolor="#eeeeee">
<td id="small">B6D2F1 (F1)</td>
<td id="small">♀ ♀</td>
<td id="small">♀</td>
<td id="small"> </td>
<td id="small">BXD1</td>
<td id="small">♀♀</td>
<td id="small"> </td>
<td id="small">♀</td>
</tr>
<tr bgcolor="#eeeeee">
<td id="small">BXD2</td>
<td id="small">♂</td>
<td id="small">♀</td>
<td id="small">♀</td>
<td id="small">BXD5</td>
<td id="small">♂♂♀</td>
<td id="small"> </td>
<td id="small"> </td>
</tr>
<tr bgcolor="#eeeeee">
<td id="small">BXD6</td>
<td id="small">♀</td>
<td id="small"> </td>
<td id="small"> </td>
<td id="small">BXD8</td>
<td id="small">♀</td>
<td id="small">♂♀</td>
<td id="small"> </td>
</tr>
<tr bgcolor="#eeeeee">
<td id="small">BXD9</td>
<td id="small">♂</td>
<td id="small">♀</td>
<td id="small">♀</td>
<td id="small">BXD11</td>
<td id="small">♀♀</td>
<td id="small"> </td>
<td id="small">♀</td>
</tr>
<tr bgcolor="#eeeeee">
<td id="small">BXD12</td>
<td id="small"> </td>
<td id="small">♂ </td>
<td id="small">♀</td>
<td id="small">BXD13</td>
<td id="small">♀ </td>
<td id="small"> </td>
<td id="small"> </td>
</tr>
<tr bgcolor="#eeeeee">
<td id="small">BXD14</td>
<td id="small"> </td>
<td id="small">♀♀</td>
<td id="small">♀</td>
<td id="small">BXD15</td>
<td id="small">♀</td>
<td id="small"> </td>
<td id="small">♀</td>
</tr>
<tr bgcolor="#eeeeee">
<td id="small">BXD16</td>
<td id="small">♀</td>
<td id="small">♀ </td>
<td id="small"> </td>
<td id="small">BXD18</td>
<td id="small">♀</td>
<td id="small">♂</td>
<td id="small">♀</td>
</tr>
<tr bgcolor="#eeeeee">
<td id="small">BXD19</td>
<td id="small">♀</td>
<td id="small">♀</td>
<td id="small">♀</td>
<td id="small">BXD21</td>
<td id="small">♀♀</td>
<td id="small">♂♂</td>
<td id="small"> </td>
</tr>
<tr bgcolor="#eeeeee">
<td id="small">BXD22</td>
<td id="small">♀</td>
<td id="small">♀♀</td>
<td id="small"> </td>
<td id="small">BXD23</td>
<td id="small">♀</td>
<td id="small"> </td>
<td id="small"> </td>
</tr>
<tr bgcolor="#eeeeee">
<td id="small">BXD24</td>
<td id="small">♀♀</td>
<td id="small"> </td>
<td id="small">♀</td>
<td id="small">BXD25</td>
<td id="small">♀♀ </td>
<td id="small">♀♀ </td>
<td id="small"> </td>
</tr>
<tr bgcolor="#eeeeee">
<td id="small">BXD27</td>
<td id="small"> </td>
<td id="small"> </td>
<td id="small">♀♀</td>
<td id="small">BXD28</td>
<td id="small">♀</td>
<td id="small">♀</td>
<td id="small">♀</td>
</tr>
<tr bgcolor="#eeeeee">
<td id="small">BXD29</td>
<td id="small">♂</td>
<td id="small"> </td>
<td id="small">♀</td>
<td id="small">BXD31</td>
<td id="small">♀♀</td>
<td id="small">♀♀</td>
<td id="small"> </td>
</tr>
<tr bgcolor="#eeeeee">
<td id="small">BXD32</td>
<td id="small">♀</td>
<td id="small">♂♀</td>
<td id="small">♀</td>
<td id="small">BXD33</td>
<td id="small">♂♀</td>
<td id="small">♀</td>
<td id="small"> </td>
</tr>
<tr bgcolor="#eeeeee">
<td id="small">BXD34</td>
<td id="small">♂♀</td>
<td id="small">♀</td>
<td id="small"> </td>
<td id="small">BXD38</td>
<td id="small">♂♀♀</td>
<td id="small"> </td>
<td id="small"> </td>
</tr>
<tr bgcolor="#eeeeee">
<td id="small">BXD39</td>
<td id="small">♂♀ </td>
<td id="small">♂</td>
<td id="small"> </td>
<td id="small">BXD40</td>
<td id="small">♂♂♀ </td>
<td id="small"> </td>
<td id="small"> </td>
</tr>
<tr bgcolor="#eeeeee">
<td id="small">BXD42</td>
<td id="small">♂♂ ♀</td>
<td id="small"> </td>
<td id="small"> </td>
<td id="small">BXD67</td>
<td id="small">♀ ♀</td>
<td id="small"> </td>
<td id="small"> </td>
</tr>
<tr bgcolor="#eeeeee">
<td height="30" id="small">BXD68</td>
<td id="small">♀ ♀</td>
<td id="small">♂</td>
<td id="small"> </td>
<td id="small"> </td>
<td id="small"> </td>
<td id="small"> </td>
<td id="small"> </td>
</tr>
</table></td>
</tr>
</table>
<P class="subtitle"> About the tissue used to generate these data:</P>
<Blockquote><P>Most expression data are averages based on three microarrays (U74Av2). Each individual array experiment involved a pool of brain tissue (forebrain plus the midbrain, but without the olfactory bulb) that was taken from three adult animals usually of the same age. A total of 83 arrays were used: 67 were female pools and 16 were male pools. Animals ranged in age from 56 to 441 days, usually with a balanced design (one pool at 8 weeks, one pool at ~20 weeks, one pool at approximately 1 year).
</P></Blockquote>
<P class="subtitle"> About data processing:</P>
<Blockquote><B>Probe set data from the .TXT file: </B>These .TXT files
were generated using the PDNN.
<UL>
<LI>Step 1: We added an offset of 1.0 to the .TXT expression values
for each cell to ensure that all values could be logged without
generating negative values.
<LI>Step 2: We took the log base 2 of each cell.
<LI>Step 3: We computed the Z-score for each cell.
<LI>Step 4: We multiplied all Z scores by 2.
<LI>Step 5: We added 8 to the value of all Z-scores. The consequence
of this simple set of transformations is to produce a set of Z-scores
that have a mean of 8, a variance of 4, and a standard deviation
of 2. The advantage of this modified Z-score is that a two-fold
difference in expression level corresponds approximately to a 1
unit difference.
<LI>Step 6: We computed the arithmetic mean of the values for the
set of microarrays for each of the individual strains.
</UL>
<p>Every microarray data set therefore has a mean expression of 8 with
a standard deviation of 2. A 1-unit difference therefor represents
roughly a two-fold difference in expression level. Expression levels
below 5 are usually close to background noise levels.</p>
</Blockquote>
<P class="subtitle"> About the chromosome and megabase position values:</P>
<Blockquote>The chromosomal locations of probe sets and gene markers were determined by BLAT analysis using the Mouse Genome Sequencing Consortium Oct 2003 Assembly (see <a href="http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse" class="fs14">http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse</a>). We thank Dr. Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis.</Blockquote>
<P class="subtitle"> About the array probe set names:</P>
<Blockquote> In addition to the<b> _at </b> (anti-sense target) and <b> _st </b> (sense target) probe set name designations, there are other designations that reflect special characteristics of a particular probe set based on probe design and selection crieteria. These designaions are listed below.
<p><b> Probe set name designations </b></p>
<li> <p><b>_f_at (sequence family)</b>: Includes probes that target identical and/or slightly polymorphic regions of different transcripts.</p></li>
<li> <p><b>_s_at (similarity constraint)</b>: Probes all target common sequences found in multiple transcripts. </p></li>
<li> <p><b>_g_at (common groups)</b>: Some of the probes target identical sequences and some target unique sequences regions .</p></li>
<li> <p><b>_r_at (rules dropped)</b>: "Designates sequences for which it was not possible to pick a full set of unique probes using Affymetrix' probe selection rules. Probes were picked after dropping some of the selection rules."</p></li>
<li> <p><b>_i_at (incomplete)</b>: "Designates sequences for which there are fewer than the required numbers of unique probes specified in the design."</p></li>
Most of the descriptions for the probe set ID extensions above were taken from the Affymetrix<a href="./dbdoc/data_analysis_fundamentals_manual.pdf" class="fs14"> GeneChip Expression Analysis Fundamentals.</a>
</Blockquote>
<P class="subtitle"> Data source acknowledgment:</P>
<Blockquote><P>Data were generated with funds to RWW from the Dunavant Chair of
Excellence, University of Tennessee Health Science Center, Department
of Pediatrics. The majority of arrays were processed at <a href="http://www.genomeexplorations.com" target="_blank" class="fs14">Genome Explorations</A> by Dr. Divyen Patel.
</P></Blockquote>
<P></P>
</TD>
</TR></TABLE>
</TD>
</TR>
<TR>
<TD align=center bgColor=#ddddff class="solidBorder">
<!--Start of footer-->
<TABLE width="90%">
<script language='JavaScript' src='/javascript/footer.js'></script>
</TABLE>
<!--End of footer-->
</TD>
</TR>
</TABLE>
<!-- /Footer -->
<!-- menu script itself. you should not modify this file -->
<script language="JavaScript" src="/javascript/menu_new.js"></script>
<!-- items structure. menu hierarchy and links are stored there -->
<script language="JavaScript" src="/javascript/menu_items.js"></script>
<!-- files with geometry and styles structures -->
<script language="JavaScript" src="/javascript/menu_tpl.js"></script>
<script language="JavaScript">
<!--//
// Note where menu initialization block is located in HTML document.
// Don't try to position menu locating menu initialization block in
// some table cell or other HTML element. Always put it before </body>
// each menu gets two parameters (see demo files)
// 1. items structure
// 2. geometry structure
new menu (MENU_ITEMS, MENU_POS);
// make sure files containing definitions for these variables are linked to the document
// if you got some javascript error like "MENU_POS is not defined", then you've made syntax
// error in menu_tpl.js file or that file isn't linked properly.
// also take a look at stylesheets loaded in header in order to set styles
//-->
</script>
</BODY>
</HTML>
|
