PHOSIDA - Revision history

127.0.0.1: /Volumes/r3/t3/ul/working/touchTables/touch_all_tables.php

2010-05-23T00:10:46Z

/Volumes/r3/t3/ul/working/touchTables/touch_all_tables.php

← Older revision		Revision as of 00:10, 23 May 2010
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	*		*
	****************************************************************************************** -->		****************************************************************************************** -->
	{\|{{Prettytable}} width='30%' align="right" id="Q4a26971c93b4a" class=" tableEdit Database_table"		{\| {{Prettytable}} width='30%' align="right" id="Q4a26971c93b4a" class=" tableEdit Database_table"

	\|-		\|-
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	*		*
	****************************************************************************************** -->		****************************************************************************************** -->
	{\| id="Y47deabc9524d9" class=" tableEdit Organism"		{\| {{Prettytable}} id="Y47deabc9524d9" class=" tableEdit Organism"
	\|-		\|-
	!\|[[Template:Organism]] not found		!\|[[Template:Organism]] not found

JimHu: Table edited by JimHu via TableEdit

2010-04-15T07:05:27Z

Table edited by JimHu via TableEdit

← Older revision		Revision as of 07:05, 15 April 2010
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	*		*
	****************************************************************************************** -->		****************************************************************************************** -->
	{\| id="Q4a26971c93b4a" class=" tableEdit Database_table"		{\|{{Prettytable}} width='30%' align="right" id="Q4a26971c93b4a" class=" tableEdit Database_table"

	\|-		\|-
	!align=left \|Link/URL:		!align=left {{table heading style}} \|Link/URL:
	\|\|		\|\|
	[http://www.phosida.de/ www.phosida.de/]		[http://www.phosida.de/ www.phosida.de/]
	\|-		\|-
	!align=left \|What:		!align=left {{table heading style}} \|What:
	\|\|		\|\|
	Phosida - Phosphorylation Site Database		Phosida - Phosphorylation Site Database
	\|-		\|-
	!align=left \|Who:		!align=left {{table heading style}} \|Who:
	\|\|		\|\|
	*Florian Gnad		*Florian Gnad
	*Matthias Mann		*Matthias Mann
	\|-		\|-
	!align=left \|Updates:		!align=left {{table heading style}} \|Updates:
	\|\|		\|\|
	Genome Annotation Section		Genome Annotation Section
	\|-		\|-
	!align=left \|Upcoming events:		!align=left {{table heading style}} \|Upcoming events:
	\|\|		\|\|
	Inclusion of additional phosphoproteomes of various organisms		Inclusion of additional phosphoproteomes of various organisms
	\|-		\|-
	!align=left \|Web Services:		!align=left {{table heading style}} \|Web Services:
	\|\|		\|\|

Bmcintosh: /* Usage examples */

2010-02-18T21:48:49Z

Usage examples

← Older revision		Revision as of 21:48, 18 February 2010
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	===Usage examples===		===Usage examples===
	''Add links to additional pages describing success stories here.''		''Add links to additional pages describing success stories here.''

			===p-values===

			p-values are the probability that a particular site is phosphorylated. If the p-value was greater than 75% (or 0.75/1), this was considered a high p-value score.

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

127.0.0.1: Update TableEdit tables.

2010-01-09T03:35:07Z

Update TableEdit tables.

← Older revision		Revision as of 03:35, 9 January 2010
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	****************************************************************************************** -->		****************************************************************************************** -->
	{\|~~border~~="2" ~~cellpadding~~="4" ~~cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align=right~~		{\| id="Q4a26971c93b4a" class=" tableEdit Database_table"

	\|-		\|-
	!align=left ~~{{table heading style}}~~ \|Link/URL:		!align=left \|Link/URL:
	\|\|		\|\|
	[http://www.phosida.de/ www.phosida.de/]		[http://www.phosida.de/ www.phosida.de/]
	\|-		\|-
	!align=left ~~{{table heading style}}~~ \|What:		!align=left \|What:
	\|\|		\|\|
	Phosida - Phosphorylation Site Database		Phosida - Phosphorylation Site Database
	\|-		\|-
	!align=left ~~{{table heading style}}~~ \|Who:		!align=left \|Who:
	\|\|		\|\|
	*Florian Gnad		*Florian Gnad
	*Matthias Mann		*Matthias Mann
	\|-		\|-
	!align=left ~~{{table heading style}}~~ \|Updates:		!align=left \|Updates:
	\|\|		\|\|
	Genome Annotation Section		Genome Annotation Section
	\|-		\|-
	!align=left ~~{{table heading style}}~~ \|Upcoming events:		!align=left \|Upcoming events:
	\|\|		\|\|
	Inclusion of additional phosphoproteomes of various organisms		Inclusion of additional phosphoproteomes of various organisms
	\|-		\|-
	!align=left ~~{{table heading style}}~~ \|Web Services:		!align=left \|Web Services:
	\|\|		\|\|


	\|-class=~~'sortbottom'~~		\|- class="tableEdit_footer"
	\|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.114326.Q4a26971c93b4a&page=114326&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] \|\|		\|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.114326.Q4a26971c93b4a&page=114326&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table]</span> \|\|
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	****************************************************************************************** -->		****************************************************************************************** -->
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	\|-		\|-
	!\|[[Template:Organism]] not found		!\|[[Template:Organism]] not found
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	Bacillus subtilis (78 phosphoproteins, 78 phosphosites)		Bacillus subtilis (78 phosphoproteins, 78 phosphosites)

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Amandasupak: add home page jpg

2009-06-09T21:41:04Z

add home page jpg

← Older revision		Revision as of 21:41, 9 June 2009
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	{{Database_table_help}}		{{Database_table_help}}
	==About {{PAGENAME}} {{HelpIcon\|Help:Databases}}==		==About {{PAGENAME}} {{HelpIcon\|Help:Databases}}==
			[[Image:PHOSIDA_home.jpg\|right\|Home Page\|thumb\|350px]]
	''Add general information here''		''Add general information here''

Amandasupak: Table edited by Amandasupak via TableEdit

2009-06-03T15:35:02Z

Table edited by Amandasupak via TableEdit

← Older revision		Revision as of 15:35, 3 June 2009
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	\|-		\|-
	!align=left {{table heading style}} \|Link/URL:		!align=left {{table heading style}} \|Link/URL:
			\|\|
			[http://www.phosida.de/ www.phosida.de/]
	\|-		\|-
	!align=left {{table heading style}} \|What:		!align=left {{table heading style}} \|What:
			\|\|
			Phosida - Phosphorylation Site Database
	\|-		\|-
	!align=left {{table heading style}} \|Who:		!align=left {{table heading style}} \|Who:
			\|\|
			*Florian Gnad
			*Matthias Mann
	\|-		\|-
	!align=left {{table heading style}} \|Updates:		!align=left {{table heading style}} \|Updates:
			\|\|
			Genome Annotation Section
	\|-		\|-
	!align=left {{table heading style}} \|Upcoming events:		!align=left {{table heading style}} \|Upcoming events:
			\|\|
			Inclusion of additional phosphoproteomes of various organisms
	\|-		\|-
	!align=left {{table heading style}} \|Web Services:		!align=left {{table heading style}} \|Web Services:
			\|\|


	\|-class='sortbottom'		\|-class='sortbottom'
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Amandasupak at 15:30, 3 June 2009

2009-06-03T15:30:39Z

← Older revision		Revision as of 15:30, 3 June 2009
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	[[Category:Databases]]		[[Category:Databases]]

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	<!--		<!--
	******************************************************************************************		******************************************************************************************
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	\|-		\|-
	!align=left {{table heading style}} \|Link/URL:		!align=left {{table heading style}} \|Link/URL:
	\|\|
	~~[http://www.phosida.de/ http://www.phosida.de/]~~
	\|-		\|-
	!align=left {{table heading style}} \|What:		!align=left {{table heading style}} \|What:
	\|\|
	~~Phosida - Phosphorylation Site Database~~
	\|-		\|-
	!align=left {{table heading style}} \|Who:		!align=left {{table heading style}} \|Who:
	\|\|
	~~Florian Gnad and Matthias Mann~~
	\|-		\|-
	!align=left {{table heading style}} \|Updates:		!align=left {{table heading style}} \|Updates:
	\|\|
	~~Genome Annotation Section~~
	\|-		\|-
	!align=left {{table heading style}} \|Upcoming events:		!align=left {{table heading style}} \|Upcoming events:
	\|\|
	~~Inclusion of additional phosphoproteomes of various organisms~~
	\|-		\|-
	!align=left {{table heading style}} \|Web Services:		!align=left {{table heading style}} \|Web Services:
	\|\|


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	{{Database_table_help}}		{{Database_table_help}}
	==About {{PAGENAME}} {{HelpIcon\|Help:Databases}}==		==About {{PAGENAME}} {{HelpIcon\|Help:Databases}}==

imported>Wikientrybot: Fix links due to TableEditLinks.php changes.

2009-02-19T22:14:44Z

Fix links due to TableEditLinks.php changes.

← Older revision		Revision as of 22:14, 19 February 2009
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	<!--		<!--
	******************************************************************************************		******************************************************************************************
	*		*
	* PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table.		* PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table.
	*		*
	****************************************************************************************** -->		****************************************************************************************** -->
	{\|{{Prettytable}} width='30%' align=right		{\|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}} width='30%' align=right

	\|-		\|-
	!{{table heading style}} \|Link/URL:		!align=left {{table heading style}} \|Link/URL:
	\|		\|\|
	[http://www.phosida.de/ http://www.phosida.de/]		[http://www.phosida.de/ http://www.phosida.de/]
	\|-		\|-
	!{{table heading style}} \|What:		!align=left {{table heading style}} \|What:
	\|		\|\|
	Phosida - Phosphorylation Site Database		Phosida - Phosphorylation Site Database
	\|-		\|-
	!{{table heading style}} \|Who:		!align=left {{table heading style}} \|Who:
	\|		\|\|
	Florian Gnad and Matthias Mann		Florian Gnad and Matthias Mann
	\|-		\|-
	!{{table heading style}} \|Updates:		!align=left {{table heading style}} \|Updates:
	\|		\|\|
	Genome Annotation Section		Genome Annotation Section
	\|-		\|-
	!{{table heading style}} \|Upcoming events:		!align=left {{table heading style}} \|Upcoming events:
	\|		\|\|
	Inclusion of additional phosphoproteomes of various organisms		Inclusion of additional phosphoproteomes of various organisms
	\|-		\|-
	!{{table heading style}} \|Web Services:		!align=left {{table heading style}} \|Web Services:
	\|		\|\|


	\|-		\|-class='sortbottom'
	~~\|colspan~~='2'\|[{{SERVER}}{{SCRIPTPATH}}~~/index.php~~?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.M47a37e72a634a&page=0&pagename={{FULLPAGENAMEE}} edit table]		\|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.0.M47a37e72a634a&page=0&pagename={{FULLPAGENAMEE}}&type=1&template=Database_table edit table] \|\|
	\|}		\|}
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	<!--		<!--
	******************************************************************************************		******************************************************************************************
	*		*
	* PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table.		* PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table.
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	{\|class = 'sortable' {{Prettytable}} ~~id='241525'~~		{\|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
	\|-
	!
	\|-		\|-
			!\|[[Template:Organism]] not found
			\|-
	\|		\|
	Escherichia coli (79 phosphoproteins, 81 phosphosites)		Escherichia coli (79 phosphoproteins, 81 phosphosites)
	\|-		\|-
	\|		\|
	Bacillus subtilis (78 phosphoproteins, 78 phosphosites)		Bacillus subtilis (78 phosphoproteins, 78 phosphosites)

	\|-class='sortbottom'		\|-class='sortbottom'
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	\|}		\|}
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127.0.0.1: Edited by wikibot

2008-04-30T12:16:37Z

Edited by wikibot

← Older revision		Revision as of 12:16, 30 April 2008
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	Bacillus subtilis (78 phosphoproteins, 78 phosphosites)		Bacillus subtilis (78 phosphoproteins, 78 phosphosites)
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Flo: /* Searching */

2008-03-18T13:55:21Z

Searching

← Older revision		Revision as of 13:55, 18 March 2008
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	[[Image:Evolution_protein.jpg]]<br /><br />		[[Image:Evolution_protein.jpg]]<br /><br />
	In addition, all phosphorylation sites that have been measured in our laboratory are listed on the right side. If users click on a phosphorylation site of interest, the conservation status of the selected phosphorylation site is indicated in red or green. Green points to conservation. For conserved phosphosites, the alignment of the surrounding sequence is displayed. With alignments between the phosphorylation site of interest and protein sequences from 70 organisms, PHOSIDA enables users to check the conservation of each site of each protein of interest. Furthermore, the conservation of matching motifs can immediately be checked. This enables the user to distinguish conserved motifs around the phosphosite from other motifs that also match the phosphosite but are not conserved and may thus be less likely to be functionally important or have appeared only recently in evolution.<br />		In addition, all phosphorylation sites that have been measured in our laboratory are listed on the right side. If users click on a phosphorylation site of interest, the conservation status of the selected phosphorylation site is indicated in red or green. Green points to conservation. For conserved phosphosites, the alignment of the surrounding sequence is displayed. With alignments between the phosphorylation site of interest and protein sequences from 70 organisms, PHOSIDA enables users to check the conservation of each site of each protein of interest. Furthermore, the conservation of matching motifs can immediately be checked. This enables the user to distinguish conserved motifs around the phosphosite from other motifs that also match the phosphosite but are not conserved and may thus be less likely to be functionally important or have appeared only recently in evolution.<br />
	[[Image:Evolution_site.jpg]]		[[Image:Evolution_site.jpg]]<br /><br />
			The genome annotation section is accessible via the ‘notepad’ button located right next to the main ‘web book’ of MAPU 2.0 and PHOSIDA (Figure 8.4). At first, the user is required to select a certain species of interest. Then, the karyotype of the selected species is illustrated along with a link that connects to the EnsEMBL genome annotation webpage. If one clicks on one of the displayed chromosomes, a more detailed image of the chosen chromosome is shown along with general information such as length of the chromosome, number of known and predicted genes, quantity of occurring single nucleotide polymorphisms (SNPs), and number of gene transcripts. Besides these annotations derived from the EnsEMBL database, the number of gene transcripts that have been identified in our lab is posed.<br />
			We wished to use the proteomic data to annotate the genome. Thus, we extracted all measured peptides of each proteomic dataset and reassigned the given peptide sequences to gene transcripts that are annotated in the EnsEMBL database.<br />
			The genome annotation section is accessible via the ‘notepad’ button located right next to the main ‘web book’ of PHOSIDA. At first, the user is required to select a certain species of interest. Then, the karyotype of the selected species is illustrated along with a link that connects to the EnsEMBL genome annotation webpage. If one clicks on one of the displayed chromosomes, a more detailed image of the chosen chromosome is shown along with general information such as length of the chromosome, number of known and predicted genes, quantity of occurring single nucleotide polymorphisms (SNPs), and number of gene transcripts. Besides these annotations derived from the EnsEMBL database, the number of gene transcripts that have been identified in our lab is posed. <br />
			Furthermore, the chromosome is divided up into 93 bins: On the one hand, the number of transcripts that are annotated in EnsEMBL is displayed. If one clicks on one of the bin boxes, the EnsEMBL web page will pop up showing a detailed view of the selected chromosome region. On the other hand, the number of transcripts that have been detected in any of our uploaded projects is illustrated for each bin. Clicking on one of these bin buttons results into the listing of all identified gene transcripts along with the descriptions of the corresponding genes and exact localizations on the chromosome. Furthermore, a link is provided for each gene transcript that connects to the EnsEMBL homepage displaying the full annotation of the given transcript. In addition to the general annotation of the given gene transcript, the popped up EnsEMBL page will show all detected phosphorylation sites via the PHOSIDA DAS source. <br />
			[[Image:GenomeAnnotation.jpg]]

	===Usage examples===		===Usage examples===