Hippocampus Consortium M430v2 (Jun06) PDNN : 1425172_at: Display Trait

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Trait Data and Analysis for Record ID 1425172_at

Details and Links

Gene Symbol: Rho
Aliases: Opn2; Ops; RP4; RP5; CSNB; OPN2; CSNBAD1; MGC138309; MGC138311; RHO
Description: rhodopsin (rod photoreceptor pigment, retinitis pigmentosa-associated); last two coding exons and proximal 3' UTR
Location: Chr 6 @ 115.935584 Mb on the plus strand
Target Score: BLAT specificity: 10.3   Score: 207
Species and Group: Mouse, BXD
Database 3: Hippocampus Consortium M430v2 (Jun06) PDNN
Resource Links: Gene  OMIM  UniGene  GenBank  HomoloGene
UCSC  BioGPS  STRING  PANTHER  Gemma  ABA  EBI GWAS  Wiki-Pi

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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 7.499
Median 7.470
Standard Error (SE) 0.018
Standard Deviation (SD) 0.183
Minimum 7.199
Maximum 8.048
Range (log2) 0.849
Range (fold) 1.801
Interquartile Range 1.218

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 7.488
Median 7.470
Standard Error (SE) 0.020
Standard Deviation (SD) 0.167
Minimum 7.203
Maximum 7.978
Range (log2) 0.775
Range (fold) 1.711
Interquartile Range 1.176

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 7.517
Median 7.472
Standard Error (SE) 0.037
Standard Deviation (SD) 0.210
Minimum 7.199
Maximum 8.048
Range (log2) 0.849
Range (fold) 1.801
Interquartile Range 1.245

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:
Return:
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 Status Strain RRID Epoch SeqCvge
1 B6D2F1 Live B6D2F1 JAX:100006 0
2 D2B6F1 Live D2B6F1 0
3 BXD1 Live BXD1 JAX:000036 1 36+39L
4 BXD2 Live BXD2 JAX:000075 1 40
5 BXD5 UTHSC BXD5 JAX:000037 1 40
6 BXD6 Cryo BXD6 JAX:000007 1 32
7 BXD8 Cryo BXD8 JAX:000084 1 37
8 BXD9 Cryo BXD9 JAX:000105 1 38
9 BXD11 UTHSC BXD11 JAX:000012 1 42
10 BXD12 Live BXD12 JAX:000045 1 43
11 BXD13 Live BXD13 JAX:000040 1 38
12 BXD14 Cryo BXD14 JAX:000329 1 40
13 BXD15 Live BXD15 JAX:000095 1 39
14 BXD16 Ext BXD16 JAX:000013 1 37
15 BXD18 Cryo BXD18 JAX:000015 1 35
16 BXD19 Cryo BXD19 JAX:000010 1 36
17 BXD20 Live BXD20 JAX:000330 1 43
18 BXD21 Live BXD21 JAX:000077 1 41
19 BXD22 Cryo BXD22 JAX:000043 1 37
20 BXD23 Ext BXD23 JAX:000098 1
21 BXD24 Cryo BXD24 JAX:000031 1 40
22 BXD24a UTHSC BXD24a JAX:032926 1 36+30L
23 BXD25 Cryo BXD25 JAX:000081 1
24 BXD27 Cryo BXD27 JAX:000041 1 39
25 BXD28 Ext BXD28 JAX:000047 1 35
26 BXD29 Live BXD29 JAX:010981 1 40
27 BXD30 Ext BXD30 JAX:000073 1
28 BXD31 UTHSC BXD31 JAX:000083 1 40
29 BXD32 Live BXD32 JAX:000078 1 38
30 BXD33 Live BXD33 JAX:003222 2 39
31 BXD34 Live BXD34 JAX:032926 2 40+54L
32 BXD35 Ext BXD35 2
33 BXD36 Live BXD36 JAX:003225 2 42
34 BXD37
35 BXD38 Live BXD38 JAX:003227 2 41
36 BXD39 Live BXD39 JAX:003228 2 30
37 BXD40 Live BXD40 JAX:003229 2 40+35L
38 BXD41
39 BXD42 Live BXD42 JAX:003230 2 38
40 BXD43 Live BXD43 JAX:007093 3a 40
41 BXD44 Live BXD44 JAX:007094 3a 39
42 BXD45 Live BXD45 JAX:007096 3a 34
43 BXD48 Live BXD48 JAX:007097 3a 38
44 BXD48a (BXD96) Live BXD48a JAX:007139 3a 41
45 BXD49 Cryo BXD49 JAX:007098 3a 37
46 BXD50 Live BXD50 JAX:007099 3a 40
47 BXD51 Cryo BXD51 JAX:007100 3a 41
48 BXD52 Ext BXD52 3a
49 BXD53 Cryo BXD53 JAX:017749 3a 34
50 BXD54
51 BXD55 Cryo BXD55 JAX:007103 3a 40
52 BXD56 Cryo BXD56 JAX:007104 3a 40
53 BXD59 Ext BXD59 3b
54 BXD60 Live BXD60 JAX:007105 3b 42
55 BXD61 Live BXD61 JAX:007106 3b 40
56 BXD62 Live BXD62 JAX:007107 3b 41
57 BXD63 Live BXD63 JAX:007108 3b 38
58 BXD64 Live BXD64 JAX:007109 3b 41
59 BXD65 Live BXD65 JAX:007110 3b 39
60 BXD65a (BXD97) Live BXD65a JAX:007140 3b 39
61 BXD65b (BXD92) Cryo BXD65b JAX:009677 3b 37
62 BXD66 Live BXD66 JAX:007111 3b 33
63 BXD67 Live BXD67 JAX:007112 3b 39
64 BXD68 Live BXD68 JAX:007113 3b 37
65 BXD69 Live BXD69 JAX:007114 3b 39
66 BXD70 Live BXD70 JAX:007115 3b 39
67 BXD71 Cryo BXD71 JAX:007116 3b 41
68 BXD72 Ext BXD72 3b
69 BXD73 Live BXD73 JAX:007117 3b 33
70 BXD73a (BXD80) Live BXD73a JAX:007124 3b 36
71 BXD73b (BXD103) Cryo BXD73b JAX:007146 3b 37
72 BXD74 Live BXD74 JAX:007118 3b 34
73 BXD75 Live BXD75 JAX:007119 3b 39
74 BXD76 Ext BXD76 3b
75 BXD77 Cyro BXD77 JAX:007121 3b 40
76 BXD78 Live BXD78 JAX:024029 3b 41+61L
77 BXD79 Live BXD79 JAX:007123 3b 37
78 BXD81 Live BXD81 JAX:007125 3b 34
79 BXD83 Cryo BXD83 JAX:007126 3b 38
80 BXD84 Live BXD84 JAX:007127 3b 42
81 BXD85 Live BXD85 JAX:007128 3b 41
82 BXD86 Live BXD86 JAX:007129 3b 42
83 BXD87 Live BXD87 JAX:007130 3b 40
84 BXD88 Cryo BXD88 JAX:017750 3b 40
85 BXD89 Live BXD89 JAX:007132 3b 42
86 BXD90 Live BXD90 JAX:007133 3b 38
87 BXD91 Live BXD91 JAX:017751 3b 34
88 BXD93 Ext BXD93 3b
89 BXD94 Ext BXD94 3b
90 BXD95 Live BXD95 JAX:007138 3b 32
91 BXD98 Live BXD98 JAX:007141 3b 38
92 BXD99 Cryo BXD99 JAX:007142 3b 39
93 BXD100 Live BXD100 JAX:007143 3b 40
94 BXD101 Live BXD101 JAX:007144 3b 29
95 BXD102 Cryo BXD102 JAX:007145 3b 43
96 BXD104 Ext BXD104 4
97 BXD105 Ext BXD105 4
98 BXD106 Ext BXD106 4
99 BXD107 Ext BXD107 4
100 BXD108 Ext BXD108 4
101 BXD109 Ext BXD109 4
102 BXD110 Ext BXD110 4
103 BXD111 Ext BXD111 4 40
104 BXD112 Ext BXD112 4
105 BXD113 Live BXD113 JAX:024030 4 41
106 BXD114 Ext BXD114 4 37
107 BXD115 Ext BXD115 4
108 BXD116 Ext BXD116 4
109 BXD117 Ext BXD117 4
110 BXD119 Ext BXD119 4
111 BXD120 Ext BXD120 4
112 BXD121 Ext BXD121 4
113 BXD122 UTHSC BXD122 JAX:030873 4 44
114 BXD123 Cyro BXD123 JAX:025974 4 40
115 BXD124 Live BXD124 JAX:025975 4 41
116 BXD125 Live BXD125 JAX:024031 4 36
117 BXD126 Ext BXD126 4
118 BXD127 Ext BXD127 4 39
119 BXD128 Live BXD128 JAX:030874 4 40
120 BXD128a Cryo BXD128a JAX:030875 4 41
121 BXD130 Ext BXD130 4
122 BXD131 Live BXD131 JAX:035596 4 42
123 BXD132 Ext BXD132 4
124 BXD133 Ext BXD133 4
125 BXD134 Ext BXD134 4
126 BXD135 Ext BXD135 4
127 BXD136 Ext BXD136 4
128 BXD137 Ext BXD137 4 37
129 BXD138 Ext BXD138 4
130 BXD139 Live BXD139 JAX:035597 4
131 BXD141 Ext BXD141 4 37
132 BXD142 Ext BXD142 4
133 BXD144 Live BXD144 JAX:025984 4 39
134 BXD145 Ext BXD145 4
135 BXD146 Ext BXD146 4
136 BXD147 Ext BXD147 4 41+43L
137 BXD148 Live BXD148 JAX:035598 4 39
138 BXD149 Ext BXD149 4 41
139 BXD150 UTHSC BXD150 JAX:029867 4 38
140 BXD151 Live BXD151 JAX:029868 4
141 BXD152 Live BXD152 JAX:029869 4 39
142 BXD153 Ext BXD153 4
143 BXD154 Live BXD154 JAX:025976 4 41
144 BXD155 Live BXD155 JAX:029870 4 38+55L
145 BXD156 Live BXD156 JAX:029871 4 39
146 BXD157 Live BXD157 JAX:029872 4 39
147 BXD160 UTHSC BXD160 JAX:029873 5 36
148 BXD161 Live BXD161 JAX:025985 5 40+31L
149 BXD162 UTHSC BXD162 JAX:035599 5 41
150 BXD165 Ext BXD165 5
151 BXD168 Live BXD168 JAX:029874 5 45
152 BXD169 Cryo BXD169 JAX:029876 5 31
153 BXD170 Live BXD170 JAX:029878 5 32
154 BXD171 Live BXD171 JAX:029879 5 38
155 BXD172 Live BXD172 JAX:029880 5 39+37L
156 BXD173 Ext BXD173 5 36
157 BXD174 Live BXD174 JAX:035600 5 38
158 BXD175 Ext BXD175 5 33
159 BXD176 Ext BXD176 JAX:035601 5 42
160 BXD177 Live BXD177 JAX:029881 5 40
161 BXD178 Live BXD178 JAX:029882 5 41
162 BXD180 Live BXD180 JAX:029883 5 39
163 BXD181 Ext BXD181 5 34
164 BXD183 Live BXD183 JAX:035602 5 42
165 BXD184 Ext BXD184 5 38
166 BXD186 Ext BXD186 5 37
167 BXD187 Live BXD187 JAX:031974 6 34
168 BXD188 Ext BXD188 6
169 BXD189 Ext BXD189 6
170 BXD190 Live BXD190 JAX:030876 6 40
171 BXD191 Live BXD191 JAX:030877 6 38
172 BXD192 Ext BXD192 6
173 BXD193 Ext BXD193 6
174 BXD194 Live BXD194 JAX:030878 6 36
175 BXD195 Ext BXD195 6 43
176 BXD196 Ext BXD196 6 42
177 BXD197 Live BXD197 JAX:030880 6 29
178 BXD198 Ext BXD198 6 41
179 BXD199 Live BXD199 JAX:030881 6 29
180 BXD200 Ext BXD200 6
181 BXD201 Ext BXD201 6 35
182 BXD202 Live BXD202 JAX:031975 6 29
183 BXD203 Ext BXD203 6
184 BXD204 Ext BXD204 6 39
185 BXD205 Ext BXD205 6 40
186 BXD206 Ext BXD206 6
187 BXD207 Ext BXD207 6
188 BXD208 Ext BXD208 6
189 BXD209 Ext BXD209 6 46
190 BXD210 Ext BXD210 6 42
191 BXD211 Ext BXD211 6 41
192 BXD212 Ext BXD212 6
193 BXD213 Live BXD213 JAX:035603 6 40
194 BXD214 Live BXD214 JAX:030882 6 33
195 BXD215 UTHSC BXD215 JAX:031977 6 27
196 BXD216 Live BXD216 JAX:031978 6 39
197 BXD217 Ext BXD217 6 34
198 BXD218 UTHSC BXD218 JAX:035604 6 36
199 BXD219 Ext BXD219 6 39
200 BXD220 Ext BXD220 6
201 BXD223
202 C57BL/6JxBXD037F1
203 BXD001xBXD065aF1
204 BXD009xBXD170F1
205 BXD009xBXD172F1
206 BXD012xBXD002F1
207 BXD012xBXD021F1
208 BXD020xBXD012F1
209 BXD021xBXD002F1
210 BXD024xBXD034F1
211 BXD032xBXD005F1
212 BXD032xBXD028F1
213 BXD032xBXD65bF1
214 BXD034xBXD024F1
215 BXD034xBXD073F1
216 BXD055xBXD074F1
217 BXD055xBXD65bF1
218 BXD061xBXD071F1
219 BXD062xBXD077F1
220 BXD065xBXD077F1
221 BXD069xBXD090F1
222 BXD071xBXD061F1
223 BXD073bxBXD065F1
224 BXD073bxBXD077F1
225 BXD073xBXD034F1
226 BXD073xBXD065F1
227 BXD073xBXD077F1
228 BXD074xBXD055F1
229 BXD077xBXD062F1
230 BXD083xBXD045F1
231 BXD087xBXD100F1
232 BXD065bxBXD055F1
233 BXD102xBXD077F1
234 BXD102xBXD73bF1
235 BXD170xBXD172F1
236 BXD172xBXD197F1
237 BXD197xBXD009F1

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

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