EcoliWiki - User contributions [en]

COLOMBOS

2013-11-18T09:17:33Z

Kengelen: /* Content */

{{Pagetop}} 
{{See|Help:Databases|databases}}

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{| {{Prettytable}} width='30%' align="right" id="R4ee0f40687315" class=" tableEdit Database_table"

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!align=left {{table heading style}} |Link/URL:
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http://www.colombos.net
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!align=left {{table heading style}} |What:
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'''COL'''lection '''O'''f '''M'''icroarrays for '''B'''acterial '''O'''rganism'''S'''

Gene expression for E. coli and other model bacteria
|-
!align=left {{table heading style}} |Who:
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Kristof Engelen et al.
Department of Computational Biology, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
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!align=left {{table heading style}} |Updates:
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!align=left {{table heading style}} |Upcoming events:
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!align=left {{table heading style}} |Web Services:
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==About {{PAGENAME}}==
[{{{1|http://www.colombos.net/}}} {{PAGENAME}}]<ref name='PMID: 24214998'/> is a collection of expression data from published microarrays and RNAseq for E. coli, Salmonella enterica, Bacillus subtilis, Streptomyces coelicolor, Pseudomonas aeruginosa, Mycobacterium tuberculosis and Helicobacter pylori. COLOMBOS combines expression analysis across data from different papers, labs, and platforms. A key idea in COLOMBOS is to compare relative expression values to a reference state as sets of "condition contrasts". This should correct for platform-dependent differences between studies.

==Content==
As of the most recent update published in NAR, COLOMBOS coverage of the E. coli expression data included 3435 microarray or RNAseq samples from 131 experiments.

==Using {{PAGENAME}} ==
Key vocabulary:
* '''contrast''': the difference between a test and reference condition in a particular experiment
* '''module''': saved results of searches for genes, contrasts, or genes and contrasts.
COLOMBOS provides a kind of online workbench where you can create modules by giving lists of genes, experiments, or both. These modules can then be visualized and manipulated in various ways.

===Usage examples===
''Add links to additional pages describing success stories here.''

==Other sites with related content {{HelpIcon|Help:Databases}}==

==Technology==
===Web Services/API===

==Discussion==

==References==
{{RefHelp}}
<references />

==External Links==
[{{{1|http://bioi.biw.kuleuven.be/colombos/}}} {{PAGENAME}}]

===Discussion of {{PAGENAME}} on other websites===

[[Category:Databases]]
[[Category:Gene Expression Databases]]

COLOMBOS

2013-11-18T09:13:30Z

Kengelen: /* About {{PAGENAME}} */

{{Pagetop}} 
{{See|Help:Databases|databases}}

<protect>

{| {{Prettytable}} width='30%' align="right" id="R4ee0f40687315" class=" tableEdit Database_table"

|-
!align=left {{table heading style}} |Link/URL:
||
http://www.colombos.net
|-
!align=left {{table heading style}} |What:
||
'''COL'''lection '''O'''f '''M'''icroarrays for '''B'''acterial '''O'''rganism'''S'''

Gene expression for E. coli and other model bacteria
|-
!align=left {{table heading style}} |Who:
||
Kristof Engelen et al.
Department of Computational Biology, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
|-
!align=left {{table heading style}} |Updates:
||

|-
!align=left {{table heading style}} |Upcoming events:
||

|-
!align=left {{table heading style}} |Web Services:
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.180758.R4ee0f40687315&page=180758&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

==About {{PAGENAME}}==
[{{{1|http://www.colombos.net/}}} {{PAGENAME}}]<ref name='PMID: 24214998'/> is a collection of expression data from published microarrays and RNAseq for E. coli, Salmonella enterica, Bacillus subtilis, Streptomyces coelicolor, Pseudomonas aeruginosa, Mycobacterium tuberculosis and Helicobacter pylori. COLOMBOS combines expression analysis across data from different papers, labs, and platforms. A key idea in COLOMBOS is to compare relative expression values to a reference state as sets of "condition contrasts". This should correct for platform-dependent differences between studies.

==Content==
As of the publication of the PLoS ONE paper, COLOMBOS coverage of the E. coli microarray studies included 1483 microarrays from 83 experiments.
==Using {{PAGENAME}} ==
Key vocabulary:
* '''contrast''': the difference between a test and reference condition in a particular experiment
* '''module''': saved results of searches for genes, contrasts, or genes and contrasts.
COLOMBOS provides a kind of online workbench where you can create modules by giving lists of genes, experiments, or both. These modules can then be visualized and manipulated in various ways.

===Usage examples===
''Add links to additional pages describing success stories here.''

==Other sites with related content {{HelpIcon|Help:Databases}}==

==Technology==
===Web Services/API===

==Discussion==

==References==
{{RefHelp}}
<references />

==External Links==
[{{{1|http://bioi.biw.kuleuven.be/colombos/}}} {{PAGENAME}}]

===Discussion of {{PAGENAME}} on other websites===

[[Category:Databases]]
[[Category:Gene Expression Databases]]

COLOMBOS

2013-11-18T09:10:15Z

Kengelen: /* About {{PAGENAME}} */

{{Pagetop}} 
{{See|Help:Databases|databases}}

<protect>

{| {{Prettytable}} width='30%' align="right" id="R4ee0f40687315" class=" tableEdit Database_table"

|-
!align=left {{table heading style}} |Link/URL:
||
http://www.colombos.net
|-
!align=left {{table heading style}} |What:
||
'''COL'''lection '''O'''f '''M'''icroarrays for '''B'''acterial '''O'''rganism'''S'''

Gene expression for E. coli and other model bacteria
|-
!align=left {{table heading style}} |Who:
||
Kristof Engelen et al.
Department of Computational Biology, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
|-
!align=left {{table heading style}} |Updates:
||

|-
!align=left {{table heading style}} |Upcoming events:
||

|-
!align=left {{table heading style}} |Web Services:
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.180758.R4ee0f40687315&page=180758&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

==About {{PAGENAME}}==
[{{{1|http://bioi.biw.kuleuven.be/colombos/}}} {{PAGENAME}}]<ref name='PMID: 24214998'/> is a collection of expression data from published microarrays for E. coli, Salmonella, and Bacillus subtilis. COLOMBOS combines expression analysis across data from different papers, labs, and platforms. A key idea in COLOMBOS is to compare relative expression values to a reference state as sets of "condition contrasts". This should correct for platform-dependent differences between studies.

==Content==
As of the publication of the PLoS ONE paper, COLOMBOS coverage of the E. coli microarray studies included 1483 microarrays from 83 experiments.
==Using {{PAGENAME}} ==
Key vocabulary:
* '''contrast''': the difference between a test and reference condition in a particular experiment
* '''module''': saved results of searches for genes, contrasts, or genes and contrasts.
COLOMBOS provides a kind of online workbench where you can create modules by giving lists of genes, experiments, or both. These modules can then be visualized and manipulated in various ways.

===Usage examples===
''Add links to additional pages describing success stories here.''

==Other sites with related content {{HelpIcon|Help:Databases}}==

==Technology==
===Web Services/API===

==Discussion==

==References==
{{RefHelp}}
<references />

==External Links==
[{{{1|http://bioi.biw.kuleuven.be/colombos/}}} {{PAGENAME}}]

===Discussion of {{PAGENAME}} on other websites===

[[Category:Databases]]
[[Category:Gene Expression Databases]]

COLOMBOS

2013-11-18T09:08:13Z

Kengelen: Table edited by Kengelen via TableEdit

{{Pagetop}} 
{{See|Help:Databases|databases}}

<protect>

{| {{Prettytable}} width='30%' align="right" id="R4ee0f40687315" class=" tableEdit Database_table"

|-
!align=left {{table heading style}} |Link/URL:
||
http://www.colombos.net
|-
!align=left {{table heading style}} |What:
||
'''COL'''lection '''O'''f '''M'''icroarrays for '''B'''acterial '''O'''rganism'''S'''

Gene expression for E. coli and other model bacteria
|-
!align=left {{table heading style}} |Who:
||
Kristof Engelen et al.
Department of Computational Biology, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
|-
!align=left {{table heading style}} |Updates:
||

|-
!align=left {{table heading style}} |Upcoming events:
||

|-
!align=left {{table heading style}} |Web Services:
||

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.180758.R4ee0f40687315&page=180758&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

==About {{PAGENAME}}==
[{{{1|http://bioi.biw.kuleuven.be/colombos/}}} {{PAGENAME}}]<ref name='PMID:21779320'/> is a collection of expression data from published microarrays for E. coli, Salmonella, and Bacillus subtilis. COLOMBOS combines expression analysis across data from different papers, labs, and platforms. A key idea in COLOMBOS is to compare relative expression values to a reference state as sets of "condition contrasts". This should correct for platform-dependent differences between studies.

==Content==
As of the publication of the PLoS ONE paper, COLOMBOS coverage of the E. coli microarray studies included 1483 microarrays from 83 experiments.
==Using {{PAGENAME}} ==
Key vocabulary:
* '''contrast''': the difference between a test and reference condition in a particular experiment
* '''module''': saved results of searches for genes, contrasts, or genes and contrasts.
COLOMBOS provides a kind of online workbench where you can create modules by giving lists of genes, experiments, or both. These modules can then be visualized and manipulated in various ways.

===Usage examples===
''Add links to additional pages describing success stories here.''

==Other sites with related content {{HelpIcon|Help:Databases}}==

==Technology==
===Web Services/API===

==Discussion==

==References==
{{RefHelp}}
<references />

==External Links==
[{{{1|http://bioi.biw.kuleuven.be/colombos/}}} {{PAGENAME}}]

===Discussion of {{PAGENAME}} on other websites===

[[Category:Databases]]
[[Category:Gene Expression Databases]]