From 3de34936fcbdc5f252dcacdf4e0da63a7714436a Mon Sep 17 00:00:00 2001 From: Sam Ockman Date: Sat, 2 Jun 2012 03:21:01 -0400 Subject: Adding in show trait files --- .../wqflask/templates/trait_data_and_analysis.html | 6267 ++++++++++++++++---- 1 file changed, 5008 insertions(+), 1259 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/templates/trait_data_and_analysis.html b/wqflask/wqflask/templates/trait_data_and_analysis.html index 0e91b474..1325e4b0 100644 --- a/wqflask/wqflask/templates/trait_data_and_analysis.html +++ b/wqflask/wqflask/templates/trait_data_and_analysis.html @@ -1,1259 +1,5008 @@ -{% extends "base.html" %} -{% block title %}Trait Data and Analysis{% endblock %} -{% block content %} - - - - - - - - -

-

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Trait Data and Analysis  for Record ID 1441186_at

  Details and Links

Gene Symbol: Sall3
Aliases: B130022O04Rik, Msal, Msal-1, Sal, Salt, Spalt
Description: sal-like 3 (Drosophila)
Location: Chr 18 @ 81.163175 Mb on the minus strand
Target Score: BLAT specificity: 12.0   Score: 240  
Species and Group: Mouse, BXD
Database: Hippocampus Consortium M430v2 (Jun06) PDNN
Resource Links: Gene  UniGene  GenBank  HomoloGene  
UCSC  BioGPS  STRING  PANTHER  Gemma  SynDB  ABA  

Add To Collection Find similar expression data Check probe locations at UCSC Write or review comments about this gene View SNPs and Indels View probes, SNPs, and RNA-seq at UTHSC Check sequence of probes
AddFindVerifyGeneWikiSNPsRNA-seqProbes

  Basic Statistics

Include: -

-

-

StatisticValue
N of Samples99
Mean6.129
Median6.105
Standard Error (SE)0.018
Standard Deviation (SD)0.182
Minimum5.782
Maximum6.579
Range (log2)0.797
Range (fold)1.74
Interquartile Range1.18

nP_OE9u7BSx.gif


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

Box_gUFtEOVI.gif -

-More about Box Plots

Bar_y7L2rYlL.gif

Bar_1Z4GjYFq.gif

-

StatisticValue
N of Samples71
Mean6.109
Median6.084
Standard Error (SE)0.022
Standard Deviation (SD)0.187
Minimum5.782
Maximum6.579
Range (log2)0.797
Range (fold)1.74
Interquartile Range1.13

nP_eSYO7ZQg.gif


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

Box_PWNWQMfj.gif -

-More about Box Plots

Bar_VuPqYbR6.gif

Bar_9PbdvXZ9.gif

-

StatisticValue
N of Samples32
Mean6.176
Median6.170
Standard Error (SE)0.027
Standard Deviation (SD)0.150
Minimum5.906
Maximum6.485
Range (log2)0.579
Range (fold)1.49
Interquartile Range1.15

nP_swDAFlJy.gif


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

Box_6sQJ8xhK.gif -

-More about Box Plots

Bar_QMWE2VEp.gif

Bar_X07QmgsX.gif

  Calculate Correlations

-
-
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

-
Chromosome: -
Mapping Scale: -

-Permutation Test (n=2000)
-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 greater than: -
- 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: -

-Permutation Test (n=2000)
-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:     -    -    -
  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 .

IndexSampleValue SE
1 -B6D2F1 -± -
2 -D2B6F1 -± -
3 -C57BL/6J -± -
4 -DBA/2J -± -
5 -BXD1 -± -
6 -BXD2 -± -
7 -BXD5 -± -
8 -BXD6 -± -
9 -BXD8 -± -
10 -BXD9 -± -
11 -BXD11 -± -
12 -BXD12 -± -
13 -BXD13 -± -
14 -BXD14 -± -
15 -BXD15 -± -
16 -BXD16 -± -
17 -BXD18 -± -
18 -BXD19 -± -
19 -BXD20 -± -
20 -BXD21 -± -
21 -BXD22 -± -
22 -BXD23 -± -
23 -BXD24a -± -
24 -BXD24 -± -
25 -BXD25 -± -
26 -BXD27 -± -
27 -BXD28 -± -
28 -BXD29 -± -
29 -BXD30 -± -
30 -BXD31 -± -
31 -BXD32 -± -
32 -BXD33 -± -
33 -BXD34 -± -
34 -BXD35 -± -
35 -BXD36 -± -
36 -BXD37 -± -
37 -BXD38 -± -
38 -BXD39 -± -
39 -BXD40 -± -
40 -BXD41 -± -
41 -BXD42 -± -
42 -BXD43 -± -
43 -BXD44 -± -
44 -BXD45 -± -
45 -BXD48 -± -
46 -BXD49 -± -
47 -BXD50 -± -
48 -BXD51 -± -
49 -BXD52 -± -
50 -BXD53 -± -
51 -BXD54 -± -
52 -BXD55 -± -
53 -BXD56 -± -
54 -BXD59 -± -
55 -BXD60 -± -
56 -BXD61 -± -
57 -BXD62 -± -
58 -BXD63 -± -
59 -BXD64 -± -
60 -BXD65 -± -
61 -BXD66 -± -
62 -BXD67 -± -
63 -BXD68 -± -
64 -BXD69 -± -
65 -BXD70 -± -
66 -BXD71 -± -
67 -BXD72 -± -
68 -BXD73 -± -
69 -BXD74 -± -
70 -BXD75 -± -
71 -BXD76 -± -
72 -BXD77 -± -
73 -BXD78 -± -
74 -BXD79 -± -
75 -BXD80 -± -
76 -BXD81 -± -
77 -BXD83 -± -
78 -BXD84 -± -
79 -BXD85 -± -
80 -BXD86 -± -
81 -BXD87 -± -
82 -BXD88 -± -
83 -BXD89 -± -
84 -BXD90 -± -
85 -BXD91 -± -
86 -BXD92 -± -
87 -BXD93 -± -
88 -BXD94 -± -
89 -BXD95 -± -
90 -BXD96 -± -
91 -BXD97 -± -
92 -BXD98 -± -
93 -BXD99 -± -
94 -BXD100 -± -
95 -BXD101 -± -
96 -BXD102 -± -
97 -BXD103 -± -
 
IndexSampleValue SE
1 -B6D2F1 -± -
2 -D2B6F1 -± -
3 -C57BL/6J -± -
4 -DBA/2J -± -
5 -129S1/SvImJ -± -
6 -A/J -± -
7 -AKR/J -± -
8 -BALB/cByJ -± -
9 -BALB/cJ -± -
10 -C3H/HeJ -± -
11 -C57BL/6ByJ -± -
12 -CAST/EiJ -± -
13 -CXB1 -± -
14 -CXB10 -± -
15 -CXB11 -± -
16 -CXB12 -± -
17 -CXB13 -± -
18 -CXB2 -± -
19 -CXB3 -± -
20 -CXB4 -± -
21 -CXB5 -± -
22 -CXB6 -± -
23 -CXB7 -± -
24 -CXB8 -± -
25 -CXB9 -± -
26 -KK/HlJ -± -
27 -LG/J -± -
28 -NOD/ShiLtJ -± -
29 -NZO/HlLtJ -± -
30 -PWD/PhJ -± -
31 -PWK/PhJ -± -
32 -WSB/EiJ -± -

- -
-

- - - - - -{% endblock %} + + {% extends "base.html" %} + {% block title %}Trait Data and Analysis{% endblock %} + {% block content %} + + + + + + + +
+
+ + + + + + + + +
+
+ Trait Data and Analysis  for Record ID 1441186_at +
+
+ +

  Details and Links

+ +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Gene Symbol:Sall3
Aliases:B130022O04Rik, Msal, Msal-1, Sal, Salt, Spalt
Description:sal-like 3 (Drosophila)
Location:Chr 18 @ 81.163175 Mb on the minus strand
Target Score:BLAT specificity: 12.0   Score: 240  
Species and Group:Mouse, BXD
Database:Hippocampus Consortium M430v2 (Jun06) + PDNN
Resource Links:Gene  UniGene  GenBank  HomoloGene  
UCSC  BioGPS  STRING  PANTHER  Gemma  SynDB  ABA  

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
++ + Check probe locations at UCSC Write or review comments about this gene + View SNPs and Indels + View probes, SNPs, and RNA-seq at UTHSC + Check sequence of probes
AddFindVerifyGeneWikiSNPsRNA-seqProbes
+ +

  Basic Statistics

+ +

Include:
+
+
+
+ + + + + + +
+
+ + +
+ + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
StatisticValue
N of Samples99
Mean6.129
Median6.105
Standard Error (SE)0.018
Standard Deviation (SD)0.182
Minimum5.782
Maximum6.579
Range (log2)0.797
Range (fold)1.74
Interquartile Range1.18
+
+
+ +
+ + + + + + + + +
nP_OE9u7BSx.gif

+
+ 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
+
+ +
+ + + + +
+ Box_gUFtEOVI.gif + +

More about Box Plots

+
+
+ +
+ + + + +
Bar_y7L2rYlL.gif
+
+ +
+ + + + +
Bar_1Z4GjYFq.gif
+
+
+ +
+ + +
+ + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
StatisticValue
N of Samples71
Mean6.109
Median6.084
Standard Error (SE)0.022
Standard Deviation (SD)0.187
Minimum5.782
Maximum6.579
Range (log2)0.797
Range (fold)1.74
Interquartile Range1.13
+
+
+ +
+ + + + + + + + +
nP_eSYO7ZQg.gif

+
+ 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
+
+ +
+ + + + +
+ Box_PWNWQMfj.gif + +

More about Box Plots

+
+
+ +
+ + + + +
Bar_VuPqYbR6.gif
+
+ +
+ + + + +
Bar_9PbdvXZ9.gif
+
+
+ +
+ + +
+ + + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
StatisticValue
N of Samples32
Mean6.176
Median6.170
Standard Error (SE)0.027
Standard Deviation (SD)0.150
Minimum5.906
Maximum6.485
Range (log2)0.579
Range (fold)1.49
Interquartile Range1.15
+
+
+ +
+ + + + + + + + +
nP_swDAFlJy.gif

+
+ 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
+
+ +
+ + + + +
+ Box_6sQJ8xhK.gif + +

More about Box Plots

+
+
+ +
+ + + + +
Bar_QMWE2VEp.gif
+
+ +
+ + + + +
Bar_X07QmgsX.gif
+
+
+
+ +

  Calculate Correlations

+ +

+ + + + + +
+
+ + +
+ + + + +
+ + + + + + + + + + + + + + + + + + + + +
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

+ +

+ + + + + +
+
+ + +
+ + + + + + + + +
+ + + + + + + + + + + + +
Chromosome:
Mapping Scale:

+ Permutation Test (n=2000)
+ 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 greater than:
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:

+ Permutation Test (n=2000)
+ 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:     +        
+   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 .
+

+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
IndexSampleValue SE
1 B6D2F1±
2 D2B6F1±
3 C57BL/6J±
4 DBA/2J±
5 BXD1±
6 BXD2±
7 BXD5±
8 BXD6±
9 BXD8±
10 BXD9±
11 BXD11±
12 BXD12±
13 BXD13±
14 BXD14±
15 BXD15±
16 BXD16±
17 BXD18±
18 BXD19±
19 BXD20±
20 BXD21±
21 BXD22±
22 BXD23±
23 BXD24a±
24 BXD24±
25 BXD25±
26 BXD27±
27 BXD28±
28 BXD29±
29 BXD30±
30 BXD31±
31 BXD32±
32 BXD33±
33 BXD34±
34 BXD35±
35 BXD36±
36 BXD37±
37 BXD38±
38 BXD39±
39 BXD40±
40 BXD41±
41 BXD42±
42 BXD43±
43 BXD44±
44 BXD45±
45 BXD48±
46 BXD49±
47 BXD50±
48 BXD51±
49 BXD52±
50 BXD53±
51 BXD54±
52 BXD55±
53 BXD56±
54 BXD59±
55 BXD60±
56 BXD61±
57 BXD62±
58 BXD63±
59 BXD64±
60 BXD65±
61 BXD66±
62 BXD67±
63 BXD68±
64 BXD69±
65 BXD70±
66 BXD71±
67 BXD72±
68 BXD73±
69 BXD74±
70 BXD75±
71 BXD76±
72 BXD77±
73 BXD78±
74 BXD79±
75 BXD80±
76 BXD81±
77 BXD83±
78 BXD84±
79 BXD85±
80 BXD86±
81 BXD87±
82 BXD88±
83 BXD89±
84 BXD90±
85 BXD91±
86 BXD92±
87 BXD93±
88 BXD94±
89 BXD95±
90 BXD96±
91 BXD97±
92 BXD98±
93 BXD99±
94 BXD100±
95 BXD101±
96 BXD102±
97 BXD103±
+
+ +
+   +
+ +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
IndexSampleValue SE
1 B6D2F1±
2 D2B6F1±
3 C57BL/6J±
4 DBA/2J±
5 129S1/SvImJ±
6 A/J±
7 AKR/J±
8 BALB/cByJ±
9 BALB/cJ±
10 C3H/HeJ±
11 C57BL/6ByJ±
12 CAST/EiJ±
13 CXB1±
14 CXB10±
15 CXB11±
16 CXB12±
17 CXB13±
18 CXB2±
19 CXB3±
20 CXB4±
21 CXB5±
22 CXB6±
23 CXB7±
24 CXB8±
25 CXB9±
26 KK/HlJ±
27 LG/J±
28 NOD/ShiLtJ±
29 NZO/HlLtJ±
30 PWD/PhJ±
31 PWK/PhJ±
32 WSB/EiJ±
+
+
+
+
+
+ + + {% endblock %} + -- cgit v1.2.3