Phenotype Annotations
From DictyWiki
Contents |
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Updating 'Downloads :Phenotype Annotations'
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Queries
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All mutants
SELECT SYSTEMATIC_NAME as Systematic_Strain_Name,
g.DESCRIPTION as Strain_Descriptor,
stragg( distinct gene_name ) as Associated_Genes,
stragg( distinct cv.name ) as Phenotype
FROM cgm_chado.feature_genotype fg
JOIN cgm_chado.v_gene_dictybaseid d on fg.feature_id = d.GENE_FEATURE_ID
JOIN cgm_chado.genotype g on fg.genotype_id= g.genotype_id
JOIN cgm_chado.phenstatement ph on fg.genotype_id = ph.genotype_id
JOIN cgm_chado.phenotype p on ph.phenotype_id= p.phenotype_id
JOIN cgm_chado.cvterm cv on p.observable_id=cv.cvterm_id
JOIN stock_center dsc on fg.genotype_id = dsc.genotype_id
WHERE d.gene_name is not null
GROUP BY SYSTEMATIC_NAME,
mutant_type,
description
- Save as all-curated-mutants.xls, .txt
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By mutant type
- MULTIPLE:
SELECT SYSTEMATIC_NAME as Systematic_Strain_Name,
g.DESCRIPTION as Strain_Descriptor,
stragg(distinct gene_name) as Associated_Genes,
stragg( distinct cv.name ) as Phenotype
FROM cgm_chado.feature_genotype fg
JOIN cgm_chado.v_gene_dictybaseid d on fg.feature_id = d.GENE_FEATURE_ID
JOIN cgm_chado.genotype g on fg.genotype_id= g.genotype_id
JOIN cgm_chado.phenstatement ph on fg.genotype_id = ph.genotype_id
JOIN cgm_chado.phenotype p on ph.phenotype_id= p.phenotype_id
JOIN cgm_chado.cvterm cv on p.observable_id=cv.cvterm_id
JOIN stock_center dsc on fg.genotype_id = dsc.genotype_id
WHERE d.gene_name is not null
AND id in ( SELECT id
FROM stock_center s
JOIN STRAIN_CHAR_CVTERM sc on s.id = sc.strain_id
JOIN cgm_chado.CVTERM cv on sc.CVTERM_ID = cv.CVTERM_ID
WHERE name ='multiple null mutant' or name = 'multiple mutant' )
GROUP BY SYSTEMATIC_NAME,
mutant_type, description
- Save as multiple-mutants.xls, .txt
NULL: ... WHERE name ='null mutant' ...
- Save as null-mutants.xls, .txt
OVEREXPRESSION: ... WHERE name ='overexpressor' ...
- Save as overexpression-mutants.xls, .txt
OTHER: ... WHERE name ='catalytic dead'
or name = 'cold sensitive mutant'
or name = 'constitutively active mutant'
or name = 'dominant negative mutant'
or name = 'regulatable expressor'
or name = 'temperature conditional mutant'
or name = 'underexpressor'
- Save as other-mutants.xls, .txt
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Developmental mutants
Part 1
SELECT SYSTEMATIC_NAME as Systematic_Strain_Name,
g.DESCRIPTION as Strain_Descriptor,
stragg(distinct gene_name) as Associated_Genes,
stragg( distinct cv.name ) as Phenotype
FROM cgm_chado.feature_genotype fg
JOIN cgm_chado.v_gene_dictybaseid d on fg.feature_id = d.GENE_FEATURE_ID
JOIN cgm_chado.genotype g on fg.genotype_id= g.genotype_id
JOIN cgm_chado.phenstatement ph on fg.genotype_id = ph.genotype_id
JOIN cgm_chado.phenotype p on ph.phenotype_id= p.phenotype_id
JOIN cgm_chado.cvterm cv on p.observable_id=cv.cvterm_id
JOIN stock_center dsc on fg.genotype_id = dsc.genotype_id
WHERE d.gene_name is not null
and
cv.dbxref_id in
(select dbxref_id from cgm_chado.dbxref where accession in
(
'DDPHENO:0000009', 'DDPHENO:0000013', 'DDPHENO:0000019', 'DDPHENO:0000026', 'DDPHENO:0000028',
'DDPHENO:0000032', 'DDPHENO:0000036', 'DDPHENO:0000077', 'DDPHENO:0000094', 'DDPHENO:0000098',
'DDPHENO:0000102', 'DDPHENO:0000111', 'DDPHENO:0000123', 'DDPHENO:0000124', 'DDPHENO:0000126',
'DDPHENO:0000130', 'DDPHENO:0000140', 'DDPHENO:0000143', 'DDPHENO:0000145', 'DDPHENO:0000154',
'DDPHENO:0000155', 'DDPHENO:0000156', 'DDPHENO:0000157', 'DDPHENO:0000158', 'DDPHENO:0000159',
'DDPHENO:0000160', 'DDPHENO:0000161', 'DDPHENO:0000162', 'DDPHENO:0000163', 'DDPHENO:0000165',
'DDPHENO:0000166', 'DDPHENO:0000167', 'DDPHENO:0000168', 'DDPHENO:0000169', 'DDPHENO:0000170',
'DDPHENO:0000173', 'DDPHENO:0000175', 'DDPHENO:0000176', 'DDPHENO:0000178', 'DDPHENO:0000181',
'DDPHENO:0000191', 'DDPHENO:0000192', 'DDPHENO:0000193', 'DDPHENO:0000195', 'DDPHENO:0000197',
'DDPHENO:0000198', 'DDPHENO:0000199', 'DDPHENO:0000200', 'DDPHENO:0000206', 'DDPHENO:0000207',
'DDPHENO:0000208', 'DDPHENO:0000210', 'DDPHENO:0000214', 'DDPHENO:0000216', 'DDPHENO:0000222',
'DDPHENO:0000223', 'DDPHENO:0000225', 'DDPHENO:0000226', 'DDPHENO:0000232', 'DDPHENO:0000260',
'DDPHENO:0000261', 'DDPHENO:0000262', 'DDPHENO:0000269', 'DDPHENO:0000305', 'DDPHENO:0000374',
'DDPHENO:0000383', 'DDPHENO:0000384', 'DDPHENO:0000387', 'DDPHENO:0000389', 'DDPHENO:0000390',
'DDPHENO:0000421', 'DDPHENO:0000422', 'DDPHENO:0000424', 'DDPHENO:0000445', 'DDPHENO:0000446',
'DDPHENO:0000450', 'DDPHENO:0000480', 'DDPHENO:0000482', 'DDPHENO:0000483', 'DDPHENO:0000484',
'DDPHENO:0000487', 'DDPHENO:0000488', 'DDPHENO:0000492', 'DDPHENO:0000493', 'DDPHENO:0000494',
'DDPHENO:0000503', 'DDPHENO:0000504', 'DDPHENO:0000510', 'DDPHENO:0000512', 'DDPHENO:0000513',
'DDPHENO:0000514', 'DDPHENO:0000516', 'DDPHENO:0000517', 'DDPHENO:0000518', 'DDPHENO:0000519',
'DDPHENO:0000520', 'DDPHENO:0000521', 'DDPHENO:0000524', 'DDPHENO:0000526', 'DDPHENO:0000529',
'DDPHENO:0000546', 'DDPHENO:0000547', 'DDPHENO:0000549','DDPHENO:0001001', 'DDPHENO:0001012',
'DDPHENO:0001013', 'DDPHENO:0001014', 'DDPHENO:0001015',
'DDPHENO:0001016', 'DDPHENO:0001017', 'DDPHENO:0001020', 'DDPHENO:0001021', 'DDPHENO:0001022',
'DDPHENO:0001023', 'DDPHENO:0001024', 'DDPHENO:0001025', 'DDPHENO:0001037', 'DDPHENO:0001038',
'DDPHENO:0001046', 'DDPHENO:0001051', 'DDPHENO:0001054', 'DDPHENO:0001055', 'DDPHENO:0001059',
'DDPHENO:0001075', 'DDPHENO:0001076', 'DDPHENO:0001077', 'DDPHENO:0001080', 'DDPHENO:0001089',
'DDPHENO:0001090', 'DDPHENO:0001091', 'DDPHENO:0001092', 'DDPHENO:0001093', 'DDPHENO:0001094',
'DDPHENO:0001095', 'DDPHENO:0001097', 'DDPHENO:0001098', 'DDPHENO:0001099', 'DDPHENO:0001103',
'DDPHENO:0001104', 'DDPHENO:0001113', 'DDPHENO:0001114', 'DDPHENO:0001115', 'DDPHENO:0001116',
'DDPHENO:0001117', 'DDPHENO:0001121', 'DDPHENO:0001122', 'DDPHENO:0001123', 'DDPHENO:0001124',
'DDPHENO:0001125', 'DDPHENO:0001126', 'DDPHENO:0001127', 'DDPHENO:0001128', 'DDPHENO:0001129'
))
GROUP BY gene_name,
mutant_type, SYSTEMATIC_NAME,
description
Add to
Part2
SELECT SYSTEMATIC_NAME as Systematic_Strain_Name,
g.DESCRIPTION as Strain_Descriptor,
stragg(distinct gene_name) as Associated_Genes,
stragg( distinct cv.name ) as PHENOTYPES
FROM cgm_chado.feature_genotype fg
JOIN cgm_chado.v_gene_dictybaseid d on fg.feature_id = d.GENE_FEATURE_ID
JOIN cgm_chado.genotype g on fg.genotype_id= g.genotype_id
JOIN cgm_chado.phenstatement ph on fg.genotype_id = ph.genotype_id
JOIN cgm_chado.phenotype p on ph.phenotype_id= p.phenotype_id
JOIN cgm_chado.cvterm cv on p.observable_id=cv.cvterm_id
JOIN stock_center dsc on fg.genotype_id = dsc.genotype_id
WHERE d.gene_name is not null
and
cv.dbxref_id in
(select dbxref_id from cgm_chado.dbxref where accession in
(
'DDPHENO:0001130', 'DDPHENO:0001131', 'DDPHENO:0001163', 'DDPHENO:0001164', 'DDPHENO:0001165',
'DDPHENO:0001166', 'DDPHENO:0001167', 'DDPHENO:0001168' , 'DDPHENO:0001182', 'DDPHENO:0001183'))
GROUP BY gene_name,
mutant_type, SYSTEMATIC_NAME,
description
- save as developmental-mutants.xls, .txt
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Convert to html
- replace ',' by ', '
- replace ':' by ": '
- In Excel, create a new column to the right of the systematic strain name; add this formula:
=CONCATENATE("<a target =#new# href=#/db/cgi-bin/search/search.pl?query=", A2, "#>", A2, "</a>")
- Copy and paste special -> values
- delete first column (without the links)
- save as text
- open in word
- replace " by [nothing]
- replace # by "
- replace ^p by </td></tr>^p<tr class=row2><td>
- replace ^t by </td><td>
-check first and last column
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Insert header
<!--#set var="title" value="Dictyostelium Mutants"-->
<!--#include virtual="/inc/header_noSide.html"-->
<style type="text/css">
table.download {
table-layout: fixed;
width: 100%;
spacing: 2px;
border: none;
}
table.download td {padding: 4px}
tr.row1 {
background-color: #ACBDCC;
font-weight: bold;
font-size: 18px;
}
tr.row2 {
background-color: #dddddd;
}
</style>
<a name="top"></a>
<h1>Phenotypes for Dictyostelium mutants </h1>
<h3>View other mutant types:
<a href="all-mutants.html">All mutant strains</a> -
<a href="null-mutants.html">Null</a> -
<a href="overexpression-mutants.html">Overexpression</a> -
<a href="multiple-mutants.html">Multiple</a> -
<a href="other-mutants.html">Other</a> -
<a href="developmental-mutants.html">Developmental</a>
</h3>
<p align="right"><a href="index.html">BACK TO DOWNLOADS INDEX</a></p>
<hr>
<p>To view more details, including parent strains and references, click on the corresponding dictyBase ID. <br>
</p>
<table class="download">
<col width="12%"/><col width="14%"/><col width="12%"/><col width="60%"/>
<tr class="row1">
<td>Strain ID</td>
<td>Strain Descriptor</td>
<td>Associated gene(s)</td>
<td>Phenotypes</td>
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Phenotypes for Dictyostelium mutants
View other mutant types: <a href="all-mutants.html">All mutant strains</a> <a href="null-mutants.html">Null</a> - <a href="overexpression-mutants.html">Overexpression</a> - <a href="multiple-mutants.html">Multiple</a> - <a href="other-mutants.html">Other</a> - <a href="developmental-mutants.html">Developmental</a>
<a href="index.html">BACK TO DOWNLOADS INDEX</a>
To view more details, including parent strains and references, click on the corresponding dictyBase ID.
| Strain ID | Strain Descriptor | Associated gene(s) | Phenotypes |
| Strain ID | Strain Descriptor | Associated gene(s) | Phenotypes |
| Strain ID | Strain Descriptor | Associated gene(s) | Strain Name(s) | Phenotypes |
| Strain ID | Strain Descriptor | Associated gene(s) | Strain Name(s) | Phenotypes |
