EcoliWiki - User contributions [en]

Bacteriome

2009-10-19T20:39:25Z

JohnP: /* External Links */

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

<protect>

{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

|-
!align=left {{table heading style}} |Link/URL:
||
[http://www.compsysbio.org/bacteriome/ Bacteriome]
|-
!align=left {{table heading style}} |What:
||
An integrated protein interaction database for E. coli. Bacteriome features a high quality functional interaction dataset of E. coli proteins togther with experimental datasets generated through tandem affinity purification screens.
|-
!align=left {{table heading style}} |Who:
||
[http://www.compsysbio.org/lab/ Parkinson Lab] together with Andrew Emili and Jack Greenblatt
|-
!align=left {{table heading style}} |Updates:
||

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

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

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.164885.S4a43c5f1f3874&page=164885&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

==About {{PAGENAME}}==
[[Image:Bacteriome_home.jpg|300px|right|thumb|Home Page]]
''Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase <ref name='PMID:17942431'/>.''

==Content==
Bacteriome offers access to two types of network:

1) A network of ~4,000 high quality functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework <ref name='PMID:19798435'/>. Interactions were generated from the integration of ten genome scale datasets and are predicted to be of equivalent quality to small scale experimental pull down experiments. See preceding reference and its supplementary data for further information on its validation and how it compares to equivalent datasets.

2) Two networks of experimentally derived protein-protein interactions - a 'core' network consisting of interactions deemed to be of 'high quality'; and an 'extended' network which extends the 'core' network by including interactions for which experimental evidence is less strong <ref name='PMID:19402753'/>. Note these experimental datasets do not correlate precisely with the experimental datasets described in the PLoS Biology reference. The datasets described in the PLoS Biology paper were subjected to a seperate and unrelated Bayesian integration exercise.

The Bacteriome website, offers the user the ability to select groups of proteins on the basis of simple text searches (e.g. 'kinase'), domian composition, functional and evolutionary relationships. Selected proteins and their interactions may then be visualised using a customized Java based applet. Unlike similar resources, Bacteriome allows the layering of meta-data within these interaction datasets - including the visualization of domain architectures and their phylogenetic profiles. Furthermore, clustering of protein interaction data using the robust algorithm - MCL, allows the proteins to be placed within discrete functional modules representing for example protein complexes or biochemical pathways. Again, a Java-based ap[plet is available for visualization and exploration of this modular representation of the E. coli proteome.

Alternatively the interaction datasets are also available for download without restriction.

==Using {{PAGENAME}} ==
===Searching===
The data in Bacteriome can be browsed through several distinct mechansisms:

1) Global protein view. The user can use a Java applet to display the modular organization of the data and select discrete functional modules for more in depth visualization of their components.
2) BLAST similarity searches. Bacteriome features a fully functional BLAST server, that allows users to identify significant sequence similarity matches to their protein of interest.
3) Gene names. Users can simply search for their favourite gene of interest.
4) Keyword search. Users can enter text refering to functional or domain based information (e.g. 'kinase' or 'ribosomal protein') to derive proteins of interest.
5) Phylogenetic profiles. Users can select proteins on the basis of their evolutionary history.

After the search, the user is provided with detailed descriptions of the proteins of interest, from which they may select groups of proteins for network visualization using the customized Java applet. The Java applet allows users to extend the interactions of interest and also to map on features of interest (e.g. protein domain architectures).

===Usage examples===
[[File:Bacteriome_networks.gif]]

Three examples of interaction views generated by the bacteriome website. From left to right: 1) Standard protein network view, colours of nodes represent COG functional categories, size represent selected proteins; 2) Complex network view, pie charts represent breakdown of COG functional categories of componjebnt proteins, size represent the number of proteins in the complex; 3) Phylogenetic profile view, nodes represent individual proteins, the coloured sectors represent the presence of a detectable homolog across ~200 different species.

==Other sites with related content {{HelpIcon|Help:Databases}}==
[http://string.embl.de STRING database of protein-protein interactions]

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

==External Links==
Bacteriome web site [http://www.bacteriome.org http://www.bacteriome.org]

Parkinson lab web site [http://www.compsysbio.org/lab http://www.compsysbio.org/lab]

[[Category:Databases]][[Category:E. coli Databases]]

Bacteriome

2009-10-19T20:29:02Z

JohnP: /* Usage examples */

Bacteriome

2009-10-19T20:28:03Z

JohnP: /* External Links */

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

<protect>

{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

|-
!align=left {{table heading style}} |Link/URL:
||
[http://www.compsysbio.org/bacteriome/ Bacteriome]
|-
!align=left {{table heading style}} |What:
||
An integrated protein interaction database for E. coli. Bacteriome features a high quality functional interaction dataset of E. coli proteins togther with experimental datasets generated through tandem affinity purification screens.
|-
!align=left {{table heading style}} |Who:
||
[http://www.compsysbio.org/lab/ Parkinson Lab] together with Andrew Emili and Jack Greenblatt
|-
!align=left {{table heading style}} |Updates:
||

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

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

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.164885.S4a43c5f1f3874&page=164885&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

==About {{PAGENAME}}==
[[Image:Bacteriome_home.jpg|300px|right|thumb|Home Page]]
''Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase <ref name='PMID:17942431'/>.''

==Content==
Bacteriome offers access to two types of network:

1) A network of ~4,000 high quality functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework <ref name='PMID:19798435'/>. Interactions were generated from the integration of ten genome scale datasets and are predicted to be of equivalent quality to small scale experimental pull down experiments. See preceding reference and its supplementary data for further information on its validation and how it compares to equivalent datasets.

2) Two networks of experimentally derived protein-protein interactions - a 'core' network consisting of interactions deemed to be of 'high quality'; and an 'extended' network which extends the 'core' network by including interactions for which experimental evidence is less strong <ref name='PMID:19402753'/>. Note these experimental datasets do not correlate precisely with the experimental datasets described in the PLoS Biology reference. The datasets described in the PLoS Biology paper were subjected to a seperate and unrelated Bayesian integration exercise.

The Bacteriome website, offers the user the ability to select groups of proteins on the basis of simple text searches (e.g. 'kinase'), domian composition, functional and evolutionary relationships. Selected proteins and their interactions may then be visualised using a customized Java based applet. Unlike similar resources, Bacteriome allows the layering of meta-data within these interaction datasets - including the visualization of domain architectures and their phylogenetic profiles. Furthermore, clustering of protein interaction data using the robust algorithm - MCL, allows the proteins to be placed within discrete functional modules representing for example protein complexes or biochemical pathways. Again, a Java-based ap[plet is available for visualization and exploration of this modular representation of the E. coli proteome.

Alternatively the interaction datasets are also available for download without restriction.

==Using {{PAGENAME}} ==
===Searching===
The data in Bacteriome can be browsed through several distinct mechansisms:

1) Global protein view. The user can use a Java applet to display the modular organization of the data and select discrete functional modules for more in depth visualization of their components.
2) BLAST similarity searches. Bacteriome features a fully functional BLAST server, that allows users to identify significant sequence similarity matches to their protein of interest.
3) Gene names. Users can simply search for their favourite gene of interest.
4) Keyword search. Users can enter text refering to functional or domain based information (e.g. 'kinase' or 'ribosomal protein') to derive proteins of interest.
5) Phylogenetic profiles. Users can select proteins on the basis of their evolutionary history.

After the search, the user is provided with detailed descriptions of the proteins of interest, from which they may select groups of proteins for network visualization using the customized Java applet. The Java applet allows users to extend the interactions of interest and also to map on features of interest (e.g. protein domain architectures).

===Usage examples===
[[File:Bacteriome_networks.gif]]

This view shows three examples of interaction views generated by the bacteriome website. From left to right: 1) Standard protein network view, colours of nodes represent COG functional categories, size represent selected proteins; 2) Complex network view, pie charts represent breakdown of COG functional categories of componjebnt proteins, size represent the number of proteins in the complex; 3) Phylogenetic profile view, nodes represent individual proteins, the coloured sectors represent the presence of a detectable homolog across ~200 different species.

==Other sites with related content {{HelpIcon|Help:Databases}}==
[http://string.embl.de STRING database of protein-protein interactions]

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

==External Links==
Bacteriome web site [http://www.bacteriome.org http://www.bacteriome.org]

Parkinson lab web site [http://www.compsysbio.org/lab http://www.compsysbio.org/lab]

[[Category:Databases]]

Bacteriome

2009-10-19T20:27:50Z

JohnP: /* External Links */

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

<protect>

{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

|-
!align=left {{table heading style}} |Link/URL:
||
[http://www.compsysbio.org/bacteriome/ Bacteriome]
|-
!align=left {{table heading style}} |What:
||
An integrated protein interaction database for E. coli. Bacteriome features a high quality functional interaction dataset of E. coli proteins togther with experimental datasets generated through tandem affinity purification screens.
|-
!align=left {{table heading style}} |Who:
||
[http://www.compsysbio.org/lab/ Parkinson Lab] together with Andrew Emili and Jack Greenblatt
|-
!align=left {{table heading style}} |Updates:
||

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

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

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.164885.S4a43c5f1f3874&page=164885&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

==About {{PAGENAME}}==
[[Image:Bacteriome_home.jpg|300px|right|thumb|Home Page]]
''Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase <ref name='PMID:17942431'/>.''

==Content==
Bacteriome offers access to two types of network:

1) A network of ~4,000 high quality functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework <ref name='PMID:19798435'/>. Interactions were generated from the integration of ten genome scale datasets and are predicted to be of equivalent quality to small scale experimental pull down experiments. See preceding reference and its supplementary data for further information on its validation and how it compares to equivalent datasets.

2) Two networks of experimentally derived protein-protein interactions - a 'core' network consisting of interactions deemed to be of 'high quality'; and an 'extended' network which extends the 'core' network by including interactions for which experimental evidence is less strong <ref name='PMID:19402753'/>. Note these experimental datasets do not correlate precisely with the experimental datasets described in the PLoS Biology reference. The datasets described in the PLoS Biology paper were subjected to a seperate and unrelated Bayesian integration exercise.

The Bacteriome website, offers the user the ability to select groups of proteins on the basis of simple text searches (e.g. 'kinase'), domian composition, functional and evolutionary relationships. Selected proteins and their interactions may then be visualised using a customized Java based applet. Unlike similar resources, Bacteriome allows the layering of meta-data within these interaction datasets - including the visualization of domain architectures and their phylogenetic profiles. Furthermore, clustering of protein interaction data using the robust algorithm - MCL, allows the proteins to be placed within discrete functional modules representing for example protein complexes or biochemical pathways. Again, a Java-based ap[plet is available for visualization and exploration of this modular representation of the E. coli proteome.

Alternatively the interaction datasets are also available for download without restriction.

==Using {{PAGENAME}} ==
===Searching===
The data in Bacteriome can be browsed through several distinct mechansisms:

1) Global protein view. The user can use a Java applet to display the modular organization of the data and select discrete functional modules for more in depth visualization of their components.
2) BLAST similarity searches. Bacteriome features a fully functional BLAST server, that allows users to identify significant sequence similarity matches to their protein of interest.
3) Gene names. Users can simply search for their favourite gene of interest.
4) Keyword search. Users can enter text refering to functional or domain based information (e.g. 'kinase' or 'ribosomal protein') to derive proteins of interest.
5) Phylogenetic profiles. Users can select proteins on the basis of their evolutionary history.

After the search, the user is provided with detailed descriptions of the proteins of interest, from which they may select groups of proteins for network visualization using the customized Java applet. The Java applet allows users to extend the interactions of interest and also to map on features of interest (e.g. protein domain architectures).

===Usage examples===
[[File:Bacteriome_networks.gif]]

This view shows three examples of interaction views generated by the bacteriome website. From left to right: 1) Standard protein network view, colours of nodes represent COG functional categories, size represent selected proteins; 2) Complex network view, pie charts represent breakdown of COG functional categories of componjebnt proteins, size represent the number of proteins in the complex; 3) Phylogenetic profile view, nodes represent individual proteins, the coloured sectors represent the presence of a detectable homolog across ~200 different species.

==Other sites with related content {{HelpIcon|Help:Databases}}==
[http://string.embl.de STRING database of protein-protein interactions]

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

==External Links==
Bacteriome web site [http://www.bacteriome.org http://www.bacteriome.org]
Parkinson lab web site [http://www.compsysbio.org/lab http://www.compsysbio.org/lab]

[[Category:Databases]]

Bacteriome

2009-10-19T20:25:50Z

JohnP: /* Discussion */

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

<protect>

{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

|-
!align=left {{table heading style}} |Link/URL:
||
[http://www.compsysbio.org/bacteriome/ Bacteriome]
|-
!align=left {{table heading style}} |What:
||
An integrated protein interaction database for E. coli. Bacteriome features a high quality functional interaction dataset of E. coli proteins togther with experimental datasets generated through tandem affinity purification screens.
|-
!align=left {{table heading style}} |Who:
||
[http://www.compsysbio.org/lab/ Parkinson Lab] together with Andrew Emili and Jack Greenblatt
|-
!align=left {{table heading style}} |Updates:
||

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

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

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.164885.S4a43c5f1f3874&page=164885&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

==About {{PAGENAME}}==
[[Image:Bacteriome_home.jpg|300px|right|thumb|Home Page]]
''Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase <ref name='PMID:17942431'/>.''

==Content==
Bacteriome offers access to two types of network:

1) A network of ~4,000 high quality functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework <ref name='PMID:19798435'/>. Interactions were generated from the integration of ten genome scale datasets and are predicted to be of equivalent quality to small scale experimental pull down experiments. See preceding reference and its supplementary data for further information on its validation and how it compares to equivalent datasets.

2) Two networks of experimentally derived protein-protein interactions - a 'core' network consisting of interactions deemed to be of 'high quality'; and an 'extended' network which extends the 'core' network by including interactions for which experimental evidence is less strong <ref name='PMID:19402753'/>. Note these experimental datasets do not correlate precisely with the experimental datasets described in the PLoS Biology reference. The datasets described in the PLoS Biology paper were subjected to a seperate and unrelated Bayesian integration exercise.

The Bacteriome website, offers the user the ability to select groups of proteins on the basis of simple text searches (e.g. 'kinase'), domian composition, functional and evolutionary relationships. Selected proteins and their interactions may then be visualised using a customized Java based applet. Unlike similar resources, Bacteriome allows the layering of meta-data within these interaction datasets - including the visualization of domain architectures and their phylogenetic profiles. Furthermore, clustering of protein interaction data using the robust algorithm - MCL, allows the proteins to be placed within discrete functional modules representing for example protein complexes or biochemical pathways. Again, a Java-based ap[plet is available for visualization and exploration of this modular representation of the E. coli proteome.

Alternatively the interaction datasets are also available for download without restriction.

==Using {{PAGENAME}} ==
===Searching===
The data in Bacteriome can be browsed through several distinct mechansisms:

1) Global protein view. The user can use a Java applet to display the modular organization of the data and select discrete functional modules for more in depth visualization of their components.
2) BLAST similarity searches. Bacteriome features a fully functional BLAST server, that allows users to identify significant sequence similarity matches to their protein of interest.
3) Gene names. Users can simply search for their favourite gene of interest.
4) Keyword search. Users can enter text refering to functional or domain based information (e.g. 'kinase' or 'ribosomal protein') to derive proteins of interest.
5) Phylogenetic profiles. Users can select proteins on the basis of their evolutionary history.

After the search, the user is provided with detailed descriptions of the proteins of interest, from which they may select groups of proteins for network visualization using the customized Java applet. The Java applet allows users to extend the interactions of interest and also to map on features of interest (e.g. protein domain architectures).

===Usage examples===
[[File:Bacteriome_networks.gif]]

This view shows three examples of interaction views generated by the bacteriome website. From left to right: 1) Standard protein network view, colours of nodes represent COG functional categories, size represent selected proteins; 2) Complex network view, pie charts represent breakdown of COG functional categories of componjebnt proteins, size represent the number of proteins in the complex; 3) Phylogenetic profile view, nodes represent individual proteins, the coloured sectors represent the presence of a detectable homolog across ~200 different species.

==Other sites with related content {{HelpIcon|Help:Databases}}==
[http://string.embl.de STRING database of protein-protein interactions]

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

==External Links==
[{{{1|link}}} {{PAGENAME}}] URL:{{{1|link}}}

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

[[Category:Databases]]

Bacteriome

2009-10-19T20:25:00Z

JohnP: /* Technology */

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

<protect>

{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

|-
!align=left {{table heading style}} |Link/URL:
||
[http://www.compsysbio.org/bacteriome/ Bacteriome]
|-
!align=left {{table heading style}} |What:
||
An integrated protein interaction database for E. coli. Bacteriome features a high quality functional interaction dataset of E. coli proteins togther with experimental datasets generated through tandem affinity purification screens.
|-
!align=left {{table heading style}} |Who:
||
[http://www.compsysbio.org/lab/ Parkinson Lab] together with Andrew Emili and Jack Greenblatt
|-
!align=left {{table heading style}} |Updates:
||

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

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

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.164885.S4a43c5f1f3874&page=164885&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

==About {{PAGENAME}}==
[[Image:Bacteriome_home.jpg|300px|right|thumb|Home Page]]
''Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase <ref name='PMID:17942431'/>.''

==Content==
Bacteriome offers access to two types of network:

1) A network of ~4,000 high quality functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework <ref name='PMID:19798435'/>. Interactions were generated from the integration of ten genome scale datasets and are predicted to be of equivalent quality to small scale experimental pull down experiments. See preceding reference and its supplementary data for further information on its validation and how it compares to equivalent datasets.

2) Two networks of experimentally derived protein-protein interactions - a 'core' network consisting of interactions deemed to be of 'high quality'; and an 'extended' network which extends the 'core' network by including interactions for which experimental evidence is less strong <ref name='PMID:19402753'/>. Note these experimental datasets do not correlate precisely with the experimental datasets described in the PLoS Biology reference. The datasets described in the PLoS Biology paper were subjected to a seperate and unrelated Bayesian integration exercise.

The Bacteriome website, offers the user the ability to select groups of proteins on the basis of simple text searches (e.g. 'kinase'), domian composition, functional and evolutionary relationships. Selected proteins and their interactions may then be visualised using a customized Java based applet. Unlike similar resources, Bacteriome allows the layering of meta-data within these interaction datasets - including the visualization of domain architectures and their phylogenetic profiles. Furthermore, clustering of protein interaction data using the robust algorithm - MCL, allows the proteins to be placed within discrete functional modules representing for example protein complexes or biochemical pathways. Again, a Java-based ap[plet is available for visualization and exploration of this modular representation of the E. coli proteome.

Alternatively the interaction datasets are also available for download without restriction.

==Using {{PAGENAME}} ==
===Searching===
The data in Bacteriome can be browsed through several distinct mechansisms:

1) Global protein view. The user can use a Java applet to display the modular organization of the data and select discrete functional modules for more in depth visualization of their components.
2) BLAST similarity searches. Bacteriome features a fully functional BLAST server, that allows users to identify significant sequence similarity matches to their protein of interest.
3) Gene names. Users can simply search for their favourite gene of interest.
4) Keyword search. Users can enter text refering to functional or domain based information (e.g. 'kinase' or 'ribosomal protein') to derive proteins of interest.
5) Phylogenetic profiles. Users can select proteins on the basis of their evolutionary history.

After the search, the user is provided with detailed descriptions of the proteins of interest, from which they may select groups of proteins for network visualization using the customized Java applet. The Java applet allows users to extend the interactions of interest and also to map on features of interest (e.g. protein domain architectures).

===Usage examples===
[[File:Bacteriome_networks.gif]]

This view shows three examples of interaction views generated by the bacteriome website. From left to right: 1) Standard protein network view, colours of nodes represent COG functional categories, size represent selected proteins; 2) Complex network view, pie charts represent breakdown of COG functional categories of componjebnt proteins, size represent the number of proteins in the complex; 3) Phylogenetic profile view, nodes represent individual proteins, the coloured sectors represent the presence of a detectable homolog across ~200 different species.

==Other sites with related content {{HelpIcon|Help:Databases}}==
[http://string.embl.de STRING database of protein-protein interactions]

==Discussion==

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

==External Links==
[{{{1|link}}} {{PAGENAME}}] URL:{{{1|link}}}

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

[[Category:Databases]]

Bacteriome

2009-10-19T20:23:41Z

JohnP: /* Other sites with related content {{HelpIcon|Help:Databases}} */

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

<protect>

{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

|-
!align=left {{table heading style}} |Link/URL:
||
[http://www.compsysbio.org/bacteriome/ Bacteriome]
|-
!align=left {{table heading style}} |What:
||
An integrated protein interaction database for E. coli. Bacteriome features a high quality functional interaction dataset of E. coli proteins togther with experimental datasets generated through tandem affinity purification screens.
|-
!align=left {{table heading style}} |Who:
||
[http://www.compsysbio.org/lab/ Parkinson Lab] together with Andrew Emili and Jack Greenblatt
|-
!align=left {{table heading style}} |Updates:
||

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

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

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.164885.S4a43c5f1f3874&page=164885&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

==About {{PAGENAME}}==
[[Image:Bacteriome_home.jpg|300px|right|thumb|Home Page]]
''Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase <ref name='PMID:17942431'/>.''

==Content==
Bacteriome offers access to two types of network:

1) A network of ~4,000 high quality functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework <ref name='PMID:19798435'/>. Interactions were generated from the integration of ten genome scale datasets and are predicted to be of equivalent quality to small scale experimental pull down experiments. See preceding reference and its supplementary data for further information on its validation and how it compares to equivalent datasets.

2) Two networks of experimentally derived protein-protein interactions - a 'core' network consisting of interactions deemed to be of 'high quality'; and an 'extended' network which extends the 'core' network by including interactions for which experimental evidence is less strong <ref name='PMID:19402753'/>. Note these experimental datasets do not correlate precisely with the experimental datasets described in the PLoS Biology reference. The datasets described in the PLoS Biology paper were subjected to a seperate and unrelated Bayesian integration exercise.

The Bacteriome website, offers the user the ability to select groups of proteins on the basis of simple text searches (e.g. 'kinase'), domian composition, functional and evolutionary relationships. Selected proteins and their interactions may then be visualised using a customized Java based applet. Unlike similar resources, Bacteriome allows the layering of meta-data within these interaction datasets - including the visualization of domain architectures and their phylogenetic profiles. Furthermore, clustering of protein interaction data using the robust algorithm - MCL, allows the proteins to be placed within discrete functional modules representing for example protein complexes or biochemical pathways. Again, a Java-based ap[plet is available for visualization and exploration of this modular representation of the E. coli proteome.

Alternatively the interaction datasets are also available for download without restriction.

==Using {{PAGENAME}} ==
===Searching===
The data in Bacteriome can be browsed through several distinct mechansisms:

1) Global protein view. The user can use a Java applet to display the modular organization of the data and select discrete functional modules for more in depth visualization of their components.
2) BLAST similarity searches. Bacteriome features a fully functional BLAST server, that allows users to identify significant sequence similarity matches to their protein of interest.
3) Gene names. Users can simply search for their favourite gene of interest.
4) Keyword search. Users can enter text refering to functional or domain based information (e.g. 'kinase' or 'ribosomal protein') to derive proteins of interest.
5) Phylogenetic profiles. Users can select proteins on the basis of their evolutionary history.

After the search, the user is provided with detailed descriptions of the proteins of interest, from which they may select groups of proteins for network visualization using the customized Java applet. The Java applet allows users to extend the interactions of interest and also to map on features of interest (e.g. protein domain architectures).

===Usage examples===
[[File:Bacteriome_networks.gif]]

This view shows three examples of interaction views generated by the bacteriome website. From left to right: 1) Standard protein network view, colours of nodes represent COG functional categories, size represent selected proteins; 2) Complex network view, pie charts represent breakdown of COG functional categories of componjebnt proteins, size represent the number of proteins in the complex; 3) Phylogenetic profile view, nodes represent individual proteins, the coloured sectors represent the presence of a detectable homolog across ~200 different species.

==Other sites with related content {{HelpIcon|Help:Databases}}==
[http://string.embl.de STRING database of protein-protein interactions]

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

==Discussion==

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

==External Links==
[{{{1|link}}} {{PAGENAME}}] URL:{{{1|link}}}

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

[[Category:Databases]]

Bacteriome

2009-10-19T20:13:54Z

JohnP: /* Usage examples */

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

<protect>

{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

|-
!align=left {{table heading style}} |Link/URL:
||
[http://www.compsysbio.org/bacteriome/ Bacteriome]
|-
!align=left {{table heading style}} |What:
||
An integrated protein interaction database for E. coli. Bacteriome features a high quality functional interaction dataset of E. coli proteins togther with experimental datasets generated through tandem affinity purification screens.
|-
!align=left {{table heading style}} |Who:
||
[http://www.compsysbio.org/lab/ Parkinson Lab] together with Andrew Emili and Jack Greenblatt
|-
!align=left {{table heading style}} |Updates:
||

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

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

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.164885.S4a43c5f1f3874&page=164885&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

==About {{PAGENAME}}==
[[Image:Bacteriome_home.jpg|300px|right|thumb|Home Page]]
''Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase <ref name='PMID:17942431'/>.''

==Content==
Bacteriome offers access to two types of network:

1) A network of ~4,000 high quality functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework <ref name='PMID:19798435'/>. Interactions were generated from the integration of ten genome scale datasets and are predicted to be of equivalent quality to small scale experimental pull down experiments. See preceding reference and its supplementary data for further information on its validation and how it compares to equivalent datasets.

2) Two networks of experimentally derived protein-protein interactions - a 'core' network consisting of interactions deemed to be of 'high quality'; and an 'extended' network which extends the 'core' network by including interactions for which experimental evidence is less strong <ref name='PMID:19402753'/>. Note these experimental datasets do not correlate precisely with the experimental datasets described in the PLoS Biology reference. The datasets described in the PLoS Biology paper were subjected to a seperate and unrelated Bayesian integration exercise.

The Bacteriome website, offers the user the ability to select groups of proteins on the basis of simple text searches (e.g. 'kinase'), domian composition, functional and evolutionary relationships. Selected proteins and their interactions may then be visualised using a customized Java based applet. Unlike similar resources, Bacteriome allows the layering of meta-data within these interaction datasets - including the visualization of domain architectures and their phylogenetic profiles. Furthermore, clustering of protein interaction data using the robust algorithm - MCL, allows the proteins to be placed within discrete functional modules representing for example protein complexes or biochemical pathways. Again, a Java-based ap[plet is available for visualization and exploration of this modular representation of the E. coli proteome.

Alternatively the interaction datasets are also available for download without restriction.

==Using {{PAGENAME}} ==
===Searching===
The data in Bacteriome can be browsed through several distinct mechansisms:

1) Global protein view. The user can use a Java applet to display the modular organization of the data and select discrete functional modules for more in depth visualization of their components.
2) BLAST similarity searches. Bacteriome features a fully functional BLAST server, that allows users to identify significant sequence similarity matches to their protein of interest.
3) Gene names. Users can simply search for their favourite gene of interest.
4) Keyword search. Users can enter text refering to functional or domain based information (e.g. 'kinase' or 'ribosomal protein') to derive proteins of interest.
5) Phylogenetic profiles. Users can select proteins on the basis of their evolutionary history.

After the search, the user is provided with detailed descriptions of the proteins of interest, from which they may select groups of proteins for network visualization using the customized Java applet. The Java applet allows users to extend the interactions of interest and also to map on features of interest (e.g. protein domain architectures).

===Usage examples===
[[File:Bacteriome_networks.gif]]

This view shows three examples of interaction views generated by the bacteriome website. From left to right: 1) Standard protein network view, colours of nodes represent COG functional categories, size represent selected proteins; 2) Complex network view, pie charts represent breakdown of COG functional categories of componjebnt proteins, size represent the number of proteins in the complex; 3) Phylogenetic profile view, nodes represent individual proteins, the coloured sectors represent the presence of a detectable homolog across ~200 different species.

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

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

==Discussion==

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

==External Links==
[{{{1|link}}} {{PAGENAME}}] URL:{{{1|link}}}

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

[[Category:Databases]]

File:Bacteriome networks.gif

2009-10-19T20:09:35Z

JohnP:

Bacteriome

2009-10-19T20:05:42Z

JohnP: /* Searching */

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

<protect>

{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

|-
!align=left {{table heading style}} |Link/URL:
||
[http://www.compsysbio.org/bacteriome/ Bacteriome]
|-
!align=left {{table heading style}} |What:
||
An integrated protein interaction database for E. coli. Bacteriome features a high quality functional interaction dataset of E. coli proteins togther with experimental datasets generated through tandem affinity purification screens.
|-
!align=left {{table heading style}} |Who:
||
[http://www.compsysbio.org/lab/ Parkinson Lab] together with Andrew Emili and Jack Greenblatt
|-
!align=left {{table heading style}} |Updates:
||

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

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

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.164885.S4a43c5f1f3874&page=164885&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

==About {{PAGENAME}}==
[[Image:Bacteriome_home.jpg|300px|right|thumb|Home Page]]
''Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase <ref name='PMID:17942431'/>.''

==Content==
Bacteriome offers access to two types of network:

1) A network of ~4,000 high quality functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework <ref name='PMID:19798435'/>. Interactions were generated from the integration of ten genome scale datasets and are predicted to be of equivalent quality to small scale experimental pull down experiments. See preceding reference and its supplementary data for further information on its validation and how it compares to equivalent datasets.

2) Two networks of experimentally derived protein-protein interactions - a 'core' network consisting of interactions deemed to be of 'high quality'; and an 'extended' network which extends the 'core' network by including interactions for which experimental evidence is less strong <ref name='PMID:19402753'/>. Note these experimental datasets do not correlate precisely with the experimental datasets described in the PLoS Biology reference. The datasets described in the PLoS Biology paper were subjected to a seperate and unrelated Bayesian integration exercise.

The Bacteriome website, offers the user the ability to select groups of proteins on the basis of simple text searches (e.g. 'kinase'), domian composition, functional and evolutionary relationships. Selected proteins and their interactions may then be visualised using a customized Java based applet. Unlike similar resources, Bacteriome allows the layering of meta-data within these interaction datasets - including the visualization of domain architectures and their phylogenetic profiles. Furthermore, clustering of protein interaction data using the robust algorithm - MCL, allows the proteins to be placed within discrete functional modules representing for example protein complexes or biochemical pathways. Again, a Java-based ap[plet is available for visualization and exploration of this modular representation of the E. coli proteome.

Alternatively the interaction datasets are also available for download without restriction.

==Using {{PAGENAME}} ==
===Searching===
The data in Bacteriome can be browsed through several distinct mechansisms:

1) Global protein view. The user can use a Java applet to display the modular organization of the data and select discrete functional modules for more in depth visualization of their components.
2) BLAST similarity searches. Bacteriome features a fully functional BLAST server, that allows users to identify significant sequence similarity matches to their protein of interest.
3) Gene names. Users can simply search for their favourite gene of interest.
4) Keyword search. Users can enter text refering to functional or domain based information (e.g. 'kinase' or 'ribosomal protein') to derive proteins of interest.
5) Phylogenetic profiles. Users can select proteins on the basis of their evolutionary history.

After the search, the user is provided with detailed descriptions of the proteins of interest, from which they may select groups of proteins for network visualization using the customized Java applet. The Java applet allows users to extend the interactions of interest and also to map on features of interest (e.g. protein domain architectures).

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

==External Links==
[{{{1|link}}} {{PAGENAME}}] URL:{{{1|link}}}

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

[[Category:Databases]]

Bacteriome

2009-10-19T19:59:16Z

JohnP: /* Using {{PAGENAME}} */

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

<protect>

{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

|-
!align=left {{table heading style}} |Link/URL:
||
[http://www.compsysbio.org/bacteriome/ Bacteriome]
|-
!align=left {{table heading style}} |What:
||
An integrated protein interaction database for E. coli. Bacteriome features a high quality functional interaction dataset of E. coli proteins togther with experimental datasets generated through tandem affinity purification screens.
|-
!align=left {{table heading style}} |Who:
||
[http://www.compsysbio.org/lab/ Parkinson Lab] together with Andrew Emili and Jack Greenblatt
|-
!align=left {{table heading style}} |Updates:
||

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

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

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.164885.S4a43c5f1f3874&page=164885&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

==About {{PAGENAME}}==
[[Image:Bacteriome_home.jpg|300px|right|thumb|Home Page]]
''Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase <ref name='PMID:17942431'/>.''

==Content==
Bacteriome offers access to two types of network:

1) A network of ~4,000 high quality functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework <ref name='PMID:19798435'/>. Interactions were generated from the integration of ten genome scale datasets and are predicted to be of equivalent quality to small scale experimental pull down experiments. See preceding reference and its supplementary data for further information on its validation and how it compares to equivalent datasets.

2) Two networks of experimentally derived protein-protein interactions - a 'core' network consisting of interactions deemed to be of 'high quality'; and an 'extended' network which extends the 'core' network by including interactions for which experimental evidence is less strong <ref name='PMID:19402753'/>. Note these experimental datasets do not correlate precisely with the experimental datasets described in the PLoS Biology reference. The datasets described in the PLoS Biology paper were subjected to a seperate and unrelated Bayesian integration exercise.

The Bacteriome website, offers the user the ability to select groups of proteins on the basis of simple text searches (e.g. 'kinase'), domian composition, functional and evolutionary relationships. Selected proteins and their interactions may then be visualised using a customized Java based applet. Unlike similar resources, Bacteriome allows the layering of meta-data within these interaction datasets - including the visualization of domain architectures and their phylogenetic profiles. Furthermore, clustering of protein interaction data using the robust algorithm - MCL, allows the proteins to be placed within discrete functional modules representing for example protein complexes or biochemical pathways. Again, a Java-based ap[plet is available for visualization and exploration of this modular representation of the E. coli proteome.

Alternatively the interaction datasets are also available for download without restriction.

==Using {{PAGENAME}} ==
===Searching===
===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==
{{BacktoTop}}
{{RefHelp}}
<references />

==External Links==
[{{{1|link}}} {{PAGENAME}}] URL:{{{1|link}}}

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

[[Category:Databases]]

Bacteriome

2009-10-19T19:58:20Z

JohnP: /* Content */

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

<protect>

{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align="right"

|-
!align=left {{table heading style}} |Link/URL:
||
[http://www.compsysbio.org/bacteriome/ Bacteriome]
|-
!align=left {{table heading style}} |What:
||
An integrated protein interaction database for E. coli. Bacteriome features a high quality functional interaction dataset of E. coli proteins togther with experimental datasets generated through tandem affinity purification screens.
|-
!align=left {{table heading style}} |Who:
||
[http://www.compsysbio.org/lab/ Parkinson Lab] together with Andrew Emili and Jack Greenblatt
|-
!align=left {{table heading style}} |Updates:
||

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

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

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.164885.S4a43c5f1f3874&page=164885&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] ||
|}
</protect>

==About {{PAGENAME}}==
[[Image:Bacteriome_home.jpg|300px|right|thumb|Home Page]]
''Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase <ref name='PMID:17942431'/>.''

==Content==
Bacteriome offers access to two types of network:

1) A network of ~4,000 high quality functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework <ref name='PMID:19798435'/>. Interactions were generated from the integration of ten genome scale datasets and are predicted to be of equivalent quality to small scale experimental pull down experiments. See preceding reference and its supplementary data for further information on its validation and how it compares to equivalent datasets.

2) Two networks of experimentally derived protein-protein interactions - a 'core' network consisting of interactions deemed to be of 'high quality'; and an 'extended' network which extends the 'core' network by including interactions for which experimental evidence is less strong <ref name='PMID:19402753'/>. Note these experimental datasets do not correlate precisely with the experimental datasets described in the PLoS Biology reference. The datasets described in the PLoS Biology paper were subjected to a seperate and unrelated Bayesian integration exercise.

The Bacteriome website, offers the user the ability to select groups of proteins on the basis of simple text searches (e.g. 'kinase'), domian composition, functional and evolutionary relationships. Selected proteins and their interactions may then be visualised using a customized Java based applet. Unlike similar resources, Bacteriome allows the layering of meta-data within these interaction datasets - including the visualization of domain architectures and their phylogenetic profiles. Furthermore, clustering of protein interaction data using the robust algorithm - MCL, allows the proteins to be placed within discrete functional modules representing for example protein complexes or biochemical pathways. Again, a Java-based ap[plet is available for visualization and exploration of this modular representation of the E. coli proteome.

Alternatively the interaction datasets are also available for download without restriction.

==Using {{PAGENAME}} ==
===Browsing===
===Searching===
===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==
{{BacktoTop}}
{{RefHelp}}
<references />

==External Links==
[{{{1|link}}} {{PAGENAME}}] URL:{{{1|link}}}

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

[[Category:Databases]]

Bacteriome

2009-10-19T19:48:59Z

JohnP: Table edited by JohnP via TableEdit

PMID:19798435

2009-10-19T19:37:51Z

JohnP: Fill PMID: Page!

{{RightTOC}}
<protect>
 '''Peregrín-Alvarez, JM, Xiong, X, Su, C and Parkinson, J''' (2009) The Modular Organization of Protein Interactions in Escherichia coli.''PLoS Comput. Biol.'' '''5''':e1000523

{|{{Prettytable}} align = 'center' width= '70%'
|-
|{{TableHeadingColor}} |'''Abstract''' || <protect>Escherichia coli serves as an excellent model for the study of fundamental cellular processes such as metabolism, signalling and gene expression. Understanding the function and organization of proteins within these processes is an important step towards a 'systems' view of E. coli. Integrating experimental and computational interaction data, we present a reliable network of 3,989 functional interactions between 1,941 E. coli proteins ( approximately 45% of its proteome). These were combined with a recently generated set of 3,888 high-quality physical interactions between 918 proteins and clustered to reveal 316 discrete modules. In addition to known protein complexes (e.g., RNA and DNA polymerases), we identified modules that represent biochemical pathways (e.g., nitrate regulation and cell wall biosynthesis) as well as batteries of functionally and evolutionarily related processes. To aid the interpretation of modular relationships, several case examples are presented, including both well characterized and novel biochemical systems. Together these data provide a global view of the modular organization of the E. coli proteome and yield unique insights into structural and evolutionary relationships in bacterial networks.</protect>
|-
|{{TableHeadingColor}} nowrap |'''Links''' || [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=19798435 PubMed] Online version:[http://dx.doi.org/10.1371/journal.pcbi.1000523 10.1371/journal.pcbi.1000523]
|}
</protect>
==Significance {{HelpIcon|Help:Literature}} ==
{{LitSignificance}}

== Useful Materials and Methods {{HelpIcon|Help:Literature}}==
{{LitMaterials}}

==Annotations {{HelpIcon|Help:Literature}}==
<protect>

{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
|- {{table heading style}}
!|Gene product!!Qualifier!!GO ID!!GO term name!!Evidence Code!!with/from!!Aspect!!Notes!!Status

|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.166485.T4adcc00f6336d&page=166485&pagename={{FULLPAGENAMEE}}&type=0&template=GO_table_reference edit table] || || || || || || || ||
|}
</protect>

==EcoliWiki Links {{HelpIcon|Help:Literature}} ==
{{LitLinks}}

==See also==

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

PMID:19798435

2009-10-19T19:37:51Z

JohnP: New PMID: Page!

Bacteriome

2009-10-19T19:37:14Z

JohnP: /* Content */

Bacteriome

2009-10-19T19:23:06Z

JohnP: /* About {{PAGENAME}} */

Bacteriome

2009-10-19T19:21:17Z

JohnP: /* About {{PAGENAME}} */

Bacteriome

2009-10-19T19:19:35Z

JohnP: Table edited by JohnP via TableEdit