Hippocampus M430v2 BXD 06/06 PDNN : 1434280_at: Display Trait

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Trait Data and Analysis for Record ID 1434280_at

Details and Links

Gene Symbol: BG976607
Description: polymorphic long terminal repeat; LTR maps on Chr 6 (BXD hippocampus) or Chr 17 (BXD eye and Treg, not true trans eQTL)
Location: Chr 6 @ 124.800617 Mb
Target Score: BLAT specificity: 0.9   Score: 219
Species and Group: Mouse, BXD
Database 3: Hippocampus Consortium M430v2 (Jun06) PDNN
Resource Links: GenBank
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Basic Statistics

Include:

Basic Table
Probability Plot
Bar Graph (by name)
Bar Graph (by rank)
Box Plot

Statistic Value
N of Samples 99
Mean 7.939
Median 7.868
Standard Error (SE) 0.073
Standard Deviation (SD) 0.730
Minimum 6.404
Maximum 10.643
Range (log2) 4.239
Range (fold) 18.883
Interquartile Range 1.917

This plot evaluates whether data are normally distributed. Different symbols represent different groups.

More about Normal Probability Plots and more about interpreting these plots from the glossary

More about Box Plots

Basic Table
Probability Plot
Bar Graph (by name)
Bar Graph (by rank)
Box Plot

Statistic Value
N of Samples 71
Mean 7.916
Median 7.900
Standard Error (SE) 0.073
Standard Deviation (SD) 0.611
Minimum 6.404
Maximum 9.148
Range (log2) 2.744
Range (fold) 6.699
Interquartile Range 1.863

This plot evaluates whether data are normally distributed. Different symbols represent different groups.

More about Normal Probability Plots and more about interpreting these plots from the glossary

More about Box Plots

Basic Table
Probability Plot
Bar Graph (by name)
Bar Graph (by rank)
Box Plot

Statistic Value
N of Samples 32
Mean 7.985
Median 7.628
Standard Error (SE) 0.166
Standard Deviation (SD) 0.940
Minimum 6.722
Maximum 10.643
Range (log2) 3.921
Range (fold) 15.147
Interquartile Range 2.277

This plot evaluates whether data are normally distributed. Different symbols represent different groups.

More about Normal Probability Plots and more about interpreting these plots from the glossary

More about Box Plots

Calculate Correlations

Sample r
Literature r
Tissue r

Database:
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Samples:

Pearson Spearman Rank

The Sample Correlation is computed between trait data and any
other traits in the sample database selected above. Use Spearman Rank
when the sample size is small (<20) or when there are influential outliers.
Database:
Return:
Samples:

The Literature Correlation (Lit r) between this gene and all other genes is computed
using the Semantic Gene Organizer and human, rat, and mouse data from PubMed.
Values are ranked by Lit r, but Sample r and Tissue r are also displayed.

More on using Lit r
Database:
Return:
Samples:

Pearson Spearman Rank

The Tissue Correlation (Tissue r) estimates the similarity of expression of two genes
or transcripts across different cells, tissues, or organs (glossary). Tissue correlations
are generated by analyzing expression in multiple samples usually taken from single cases.
Pearson and Spearman Rank correlations have been computed for all pairs of genes
using data from mouse samples.

Mapping Tools

Interval
Marker Regression
Composite
Pair-Scan

Chromosome:
Mapping Scale:
Permutations:

Bootstrap Test (n=2000)
Use Parents
Use Weighted

Interval Mapping computes linkage maps for the entire genome or single
chromosomes. The Permutation Test estimates suggestive and significant
linkage scores. The Bootstrap Test estimates the precision of the QTL location.
Display LRS above:
Permutations:

Display all LRS
Use Parents
Use Weighted

Marker regression computes and displays LRS values for individual markers.
This function also lists additive effects (phenotype units per allele) and
dominance deviations for some datasets.

Chromosome:
Mapping Scale:
Control Locus:
Permutations:

Bootstrap Test (n=2000)
Use Parents

Composite Interval Mapping allows you to control for a single marker as
a cofactor. To find a control marker, run the Marker Regression function.
Sort by:
Return:

Permutation Test (n=500)

Pair-Scan searches for pairs of chromosomal regions that are
involved in two-locus epistatic interactions.

Review and Edit Data

Edit or delete values in the Trait Data boxes, and use the Reset option as needed.
  Block samples by index:
  Block samples by group:


  Options:

  Outliers highlighted in yellow can be hidden using the Hide Outliers button,
  and samples with no value (x) can be hidden by clicking Hide No Value .

Index Sample Value SE N Status RRID Epoch SeqCvge
1 B6D2F1 ± Live JAX:100006 0
2 D2B6F1 ± Live 0
3 C57BL/6J ± Live JAX:000664 0 69
4 DBA/2J ± Live JAX:000671 0 108
5 BXD1 ± Live JAX:000036 1 36+39L
6 BXD2 ± Live JAX:000075 1 40
7 BXD5 ± UTHSC JAX:000037 1 40
8 BXD6 ± Cryo JAX:000007 1 32
9 BXD8 ± Cryo JAX:000084 1 37
10 BXD9 ± Cryo JAX:000105 1 38
11 BXD11 ± UTHSC2 JAX:000012 1 42
12 BXD12 ± Live JAX:000045 1 43
13 BXD13 ± Live JAX:000040 1 38
14 BXD14 ± Cryo JAX:000329 1 40
15 BXD15 ± Live JAX:000095 1 39
16 BXD16 ± Ext JAX:000013 1 37
17 BXD18 ± Cryo JAX:000015 1 35
18 BXD19 ± Cryo JAX:000010 1 36
19 BXD20 ± Live JAX:000330 1 43
20 BXD21 ± Live JAX:000077 1 41
21 BXD22 ± Cryo JAX:000043 1 37
22 BXD23 ± Ext JAX:000098 1
23 BXD24 ± Cryo JAX:000031 1 40
24 BXD24a ± UTHSC JAX:032926 1 36+30L
25 BXD25 ± Cryo JAX:000081 1
26 BXD27 ± Cryo JAX:000041 1 39
27 BXD28 ± Ext JAX:000047 1 35
28 BXD29 ± Live JAX:010981 1 40
29 BXD30 ± Ext JAX:000073 1
30 BXD31 ± UTHSC JAX:000083 1 40
31 BXD32 ± Live JAX:000078 1 38
32 BXD33 ± Live JAX:003222 2 39
33 BXD34 ± Live JAX:032926 2 40+54L
34 BXD35 ± Ext 2
35 BXD36 ± Live JAX:003225 2 42
36 BXD37 ±
37 BXD38 ± Live JAX:003227 2 41
38 BXD39 ± Live JAX:003228 2 30
39 BXD40 ± Live JAX:003229 2 40+35L
40 BXD41 ±
41 BXD42 ± Live JAX:003230 2 38
42 BXD43 ± Live JAX:007093 3a 40
43 BXD44 ± Live JAX:007094 3a 39
44 BXD45 ± Live JAX:007096 3a 34
45 BXD48 ± Live JAX:007097 3a 38
46 BXD48a (BXD96) ± Live JAX:007139 3a 41
47 BXD49 ± Cryo JAX:007098 3a 37
48 BXD50 ± Live JAX:007099 3a 40
49 BXD51 ± Cryo JAX:007100 3a 41
50 BXD52 ± Ext 3a
51 BXD53 ± Cryo JAX:017749 3a 34
52 BXD54 ±
53 BXD55 ± Cryo JAX:007103 3a 40
54 BXD56 ± Cryo JAX:007104 3a 40
55 BXD59 ± Ext 3b
56 BXD60 ± Live JAX:007105 3b 42
57 BXD61 ± Live JAX:007106 3b 40
58 BXD62 ± Live JAX:007107 3b 41
59 BXD63 ± Live JAX:007108 3b 38
60 BXD64 ± Live JAX:007109 3b 41
61 BXD65 ± Live JAX:007110 3b 39
62 BXD65a (BXD97) ± Live JAX:007140 3b 39
63 BXD65b (BXD92) ± Cryo JAX:009677 3b 37
64 BXD66 ± Live JAX:007111 3b 33
65 BXD67 ± Live JAX:007112 3b 39
66 BXD68 ± Live JAX:007113 3b 37
67 BXD69 ± Live JAX:007114 3b 39
68 BXD70 ± Live JAX:007115 3b 39
69 BXD71 ± Cryo JAX:007116 3b 41
70 BXD72 ± Ext 3b
71 BXD73 ± Live JAX:007117 3b 33
72 BXD73a (BXD80) ± Live JAX:007124 3b 36
73 BXD73b (BXD103) ± Cryo JAX:007146 3b 37
74 BXD74 ± Live JAX:007118 3b 34
75 BXD75 ± Live JAX:007119 3b 39
76 BXD76 ± Ext 3b
77 BXD77 ± Cyro JAX:007121 3b 40
78 BXD78 ± Live JAX:024029 3b 41+61L
79 BXD79 ± Live JAX:007123 3b 37
80 BXD81 ± Live JAX:007125 3b 34
81 BXD83 ± Cryo JAX:007126 3b 38
82 BXD84 ± Live JAX:007127 3b 42
83 BXD85 ± Live JAX:007128 3b 41
84 BXD86 ± Live JAX:007129 3b 42
85 BXD87 ± Live JAX:007130 3b 40
86 BXD88 ± Cryo JAX:017750 3b 40
87 BXD89 ± Live JAX:007132 3b 42
88 BXD90 ± Live JAX:007133 3b 38
89 BXD91 ± Live JAX:017751 3b 34
90 BXD93 ± Ext 3b
91 BXD94 ± Ext 3b
92 BXD95 ± Live JAX:007138 3b 32
93 BXD98 ± Live JAX:007141 3b 38
94 BXD99 ± Cryo JAX:007142 3b 39
95 BXD100 ± Live JAX:007143 3b 40
96 BXD101 ± Live JAX:007144 3b 29
97 BXD102 ± Cryo JAX:007145 3b 43
98 BXD104 ± Ext 4
99 BXD105 ± Ext 4
100 BXD106 ± Ext 4
101 BXD107 ± Ext 4
102 BXD108 ± Ext 4
103 BXD109 ± Ext 4
104 BXD110 ± Ext 4
105 BXD111 ± Ext 4 40
106 BXD112 ± Ext 4
107 BXD113 ± Live JAX:024030 4 41
108 BXD114 ± Ext 4 37
109 BXD115 ± Ext 4
110 BXD116 ± Ext 4
111 BXD117 ± Ext 4
112 BXD119 ± Ext 4
113 BXD120 ± Ext 4
114 BXD121 ± Ext 4
115 BXD122 ± UTHSC JAX:030873 4 44
116 BXD123 ± Cyro JAX:025974 4 40
117 BXD124 ± Live JAX:025975 4 41
118 BXD125 ± Live JAX:024031 4 36
119 BXD126 ± Ext 4
120 BXD127 ± Ext 4 39
121 BXD128 ± Live JAX:030874 4 40
122 BXD128a ± Cryo JAX:030875 4 41
123 BXD130 ± Ext 4
124 BXD131 ± Live JAX:035596 4 42
125 BXD132 ± Ext 4
126 BXD133 ± Ext 4
127 BXD134 ± Ext 4
128 BXD135 ± Ext 4
129 BXD136 ± Ext 4
130 BXD137 ± Ext 4 37
131 BXD138 ± Ext 4
132 BXD139 ± Live JAX:035597 4
133 BXD141 ± Ext 4 37
134 BXD142 ± Ext 4
135 BXD144 ± Live JAX:025984 4 39
136 BXD145 ± Ext 4
137 BXD146 ± Ext 4
138 BXD147 ± Ext 4 41+43L
139 BXD148 ± Live JAX:035598 4 39
140 BXD149 ± Ext 4 41
141 BXD150 ± UTHSC JAX:029867 4 38
142 BXD151 ± Live JAX:029868 4
143 BXD152 ± Live JAX:029869 4 39
144 BXD153 ± Ext 4
145 BXD154 ± Live JAX:025976 4 41
146 BXD155 ± Live JAX:029870 4 38+55L
147 BXD156 ± Live JAX:029871 4 39
148 BXD157 ± Live JAX:029872 4 39
149 BXD160 ± UTHSC JAX:029873 5 36
150 BXD161 ± Live JAX:025985 5 40+31L
151 BXD162 ± UTHSC JAX:035599 5 41
152 BXD165 ± Ext 5
153 BXD168 ± Live JAX:029874 5 45
154 BXD169 ± Cryo JAX:029876 5 31
155 BXD170 ± Live JAX:029878 5 32
156 BXD171 ± Live JAX:029879 5 38
157 BXD172 ± Live JAX:029880 5 39+37L
158 BXD173 ± Ext 5 36
159 BXD174 ± Live JAX:035600 5 38
160 BXD175 ± Ext 5 33
161 BXD176 ± Ext JAX:035601 5 42
162 BXD177 ± Live JAX:029881 5 40
163 BXD178 ± Live JAX:029882 5 41
164 BXD180 ± Live JAX:029883 5 39
165 BXD181 ± Ext 5 34
166 BXD183 ± Live JAX:035602 5 42
167 BXD184 ± Ext 5 38
168 BXD186 ± Ext 5 37
169 BXD187 ± Live JAX:031974 6 34
170 BXD188 ± Ext 6
171 BXD189 ± Ext 6
172 BXD190 ± Live JAX:030876 6 40
173 BXD191 ± Live JAX:030877 6 38
174 BXD192 ± Ext 6
175 BXD193 ± Ext 6
176 BXD194 ± Live JAX:030878 6 36
177 BXD195 ± Ext 6 43
178 BXD196 ± Ext 6 42
179 BXD197 ± Live JAX:030880 6 29
180 BXD198 ± Ext 6 41
181 BXD199 ± Live JAX:030881 6 29
182 BXD200 ± Ext 6
183 BXD201 ± Ext 6 35
184 BXD202 ± Live JAX:031975 6 29
185 BXD203 ± Ext 6
186 BXD204 ± Ext 6 39
187 BXD205 ± Ext 6 40
188 BXD206 ± Ext 6
189 BXD207 ± Ext 6
190 BXD208 ± Ext 6
191 BXD209 ± Ext 6 46
192 BXD210 ± Ext 6 42
193 BXD211 ± Ext 6 41
194 BXD212 ± Ext 6
195 BXD213 ± Live JAX:035603 6 40
196 BXD214 ± Live JAX:030882 6 33
197 BXD215 ± UTHSC JAX:031977 6 27
198 BXD216 ± Live JAX:031978 6 39
199 BXD217 ± Ext 6 34
200 BXD218 ± UTHSC JAX:035604 6 36
201 BXD219 ± Ext 6 39
202 BXD220 ± Ext 6
203 C57BL/6JxBXD037F1 ±
204 BXD001xBXD065aF1 ±
205 BXD009xBXD170F1 ±
206 BXD009xBXD172F1 ±
207 BXD012xBXD002F1 ±
208 BXD012xBXD021F1 ±
209 BXD020xBXD012F1 ±
210 BXD021xBXD002F1 ±
211 BXD024xBXD034F1 ±
212 BXD032xBXD005F1 ±
213 BXD032xBXD028F1 ±
214 BXD032xBXD65bF1 ±
215 BXD034xBXD024F1 ±
216 BXD034xBXD073F1 ±
217 BXD055xBXD074F1 ±
218 BXD055xBXD65bF1 ±
219 BXD061xBXD071F1 ±
220 BXD062xBXD077F1 ±
221 BXD065xBXD077F1 ±
222 BXD069xBXD090F1 ±
223 BXD071xBXD061F1 ±
224 BXD073bxBXD065F1 ±
225 BXD073bxBXD077F1 ±
226 BXD073xBXD034F1 ±
227 BXD073xBXD065F1 ±
228 BXD073xBXD077F1 ±
229 BXD074xBXD055F1 ±
230 BXD077xBXD062F1 ±
231 BXD083xBXD045F1 ±
232 BXD087xBXD100F1 ±
233 BXD065bxBXD055F1 ±
234 BXD102xBXD077F1 ±
235 BXD102xBXD73bF1 ±
236 BXD170xBXD172F1 ±
237 BXD172xBXD197F1 ±
238 BXD197xBXD009F1 ±

Index Sample Value SE N Status RRID Epoch SeqCvge
1 B6D2F1 ± Live JAX:100006 0
2 D2B6F1 ± Live 0
3 C57BL/6J ± Live JAX:000664 0 69
4 DBA/2J ± Live JAX:000671 0 108
5 129S1/SvImJ ±
6 A/J ±
7 AKR/J ±
8 BALB/cByJ ±
9 BALB/cJ ±
10 C3H/HeJ ±
12 CAST/EiJ ±
13 CXB1 ±
15 CXB11 ±
16 CXB12 ±
17 CXB13 ±
18 CXB2 ±
22 CXB6 ±
24 CXB8 ±
25 CXB9 ±
26 KK/HlJ ±
27 LG/J ±
28 NOD/ShiLtJ ±
30 PWD/PhJ ±
32 WSB/EiJ ±

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