SGD Newsletter, Summer 2023 - Revision history

Stacia at 22:18, 22 June 2023

2023-06-22T22:18:12Z

Stacia: /* Alliance of Genome Resources - Releases 5.3 & 5.4 */

2023-06-22T21:35:30Z

‎Alliance of Genome Resources - Releases 5.3 & 5.4

Stacia: /* CoSMoS.c. - Conserved Sequence Motif in Saccharomyces cerevisiae */

2023-06-22T21:34:25Z

‎CoSMoS.c. - Conserved Sequence Motif in Saccharomyces cerevisiae

Stacia: /* GENETICS Knowledgebase and Database Resources */

2023-06-22T21:32:44Z

‎GENETICS Knowledgebase and Database Resources

Stacia at 21:18, 22 June 2023

2023-06-22T21:18:03Z

Stacia: /* Alliance of Genome Resources - Releases 5.3 & 5.4 */

2023-06-22T21:17:34Z

‎Alliance of Genome Resources - Releases 5.3 & 5.4

Stacia: /* Alliance of Genome Resources - Releases 5.3 & 5.4 */

2023-06-22T21:17:12Z

‎Alliance of Genome Resources - Releases 5.3 & 5.4

Stacia: /* Alliance of Genome Resources - Releases 5.3 & 5.4 */

2023-06-22T21:16:59Z

‎Alliance of Genome Resources - Releases 5.3 & 5.4

Stacia: /* Alliance of Genome Resources - Releases 5.3 & 5.4 */

2023-06-22T21:16:51Z

‎Alliance of Genome Resources - Releases 5.3 & 5.4

Stacia: /* Alliance of Genome Resources - Releases 5.3 & 5.4 */

2023-06-22T21:16:35Z

‎Alliance of Genome Resources - Releases 5.3 & 5.4

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 [[Category: Newsletter]]
-'''About this newsletter:''' <br> This is the Summer 2023 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community. You can view this [https://wiki.yeastgenome.org/index.php/SGD_Newsletter,_Summer_2023 newsletter] as well as previous newsletters, on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].
+'''About this newsletter:''' <br> This is the Summer 2023 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community. You can view this [https://wiki.yeastgenome.org/index.php/SGD_Newsletter,_Summer_2023 newsletter] as well as previous newsletters, on the SGD [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].
 ==Biochemical Pathways added to SGD Search==

@@ Line 89: / Line 89: @@
 The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released version 5.3 last October and [https://www.alliancegenome.org/release-notes version 5.4] this past April.
-'''Version 5.3''' saw the release of ''Xenopus'' data from Xenbase. These amphibians are an important tetrapod model, spanning the evolutionary gap between the mammalian (human, mouse, and rat) and zebrafish data already included in the Alliance. ''Xenopus'' have long been used in developmental and cell biology, and two species are widely studied. The African clawed frog, ''X. laevis'' is an allotetraploid (2n = 36) of hybrid origin. The resulting ''X. laevis'' genome has a set of ‘long’ and ‘short’ chromosomes and gene symbols are therefore appended with ‘.L’ or ‘.S’ denoting on which chromosome pair they reside. The second ''Xenopus'' species, the Western clawed frog ''X. tropicalis'', is a conventional diploid (2n=20), and is increasingly used in human disease modeling.
+'''Version 5.3''' saw the addition of ''Xenopus'' data from Xenbase. These amphibians are an important tetrapod model, spanning the evolutionary gap between the mammalian (human, mouse, and rat) and zebrafish data already included in the Alliance. ''Xenopus'' have long been used in developmental and cell biology, and two species are widely studied. The African clawed frog, ''X. laevis'' is an allotetraploid (2n = 36) of hybrid origin. The resulting ''X. laevis'' genome has a set of ‘long’ and ‘short’ chromosomes and gene symbols are therefore appended with ‘.L’ or ‘.S’ denoting on which chromosome pair they reside. The second ''Xenopus'' species, the Western clawed frog ''X. tropicalis'', is a conventional diploid (2n=20), and is increasingly used in human disease modeling.
 Data for both ''Xenopus'' species are organized on individual gene pages that feature data such as gene descriptions, orthology to human and other species, disease associations for orthologs, an expression ribbon view, and a Sequence Feature Viewer.

@@ Line 57: / Line 57: @@
 The new website [https://shiny-server-dept-yeast-cosmos.apps.cloudapps.unc.edu CoSMoS.c.] - Conserved Sequence Motif in ''Saccharomyces cerevisiae'' - may be of interest to investigators who study protein modifications in budding yeast. The new web-based search algorithm scores conservation of amino acid sequences based on whole-genome sequencing of 1000+ wild and domesticated yeast isolates.
-In the [https://www.yeastgenome.org/reference/36933807 recent publication describing the method], Li and Dohlman examined each of the 550 pairs of duplicated genes in ''S. cerevisiae'', integrating 38,000+ documented post-translational modifications (PTMs), and 30,000+ reported interactions between protein kinases and substrates (all obtained from SGD!). More than 3,500 instances were identified where only one of two paralogous proteins undergoes a PTM despite having retained the same amino acid residue in both. Li and Dohlman found that the most common modifications – phosphorylation, ubiquitylation and acylation, but not N-glycosylation – occur in regions of high sequence conservation. The analysis indicates that differences in PTMs may be an important source of protein neo- or sub-functionalization, and that such differences likely account for the retention of closely related enzymes throughout evolution.
+In the [https://www.yeastgenome.org/reference/36933807 recent publication describing the method], Li and Dohlman examined each of the 550 pairs of duplicated genes in ''S. cerevisiae'', integrating 38,000+ documented post-translational modifications (PTMs), and 30,000+ reported interactions between protein kinases and substrates (all obtained from [https://www.yeastgenome.org SGD]!). More than 3,500 instances were identified where only one of two paralogous proteins undergoes a PTM despite having retained the same amino acid residue in both. Li and Dohlman found that the most common modifications – phosphorylation, ubiquitylation and acylation, but not N-glycosylation – occur in regions of high sequence conservation. The analysis indicates that differences in PTMs may be an important source of protein neo- or sub-functionalization, and that such differences likely account for the retention of closely related enzymes throughout evolution.
 You can find links to [https://shiny-server-dept-yeast-cosmos.apps.cloudapps.unc.edu CoSMoS.c.] at the bottom of your favorite protein page at SGD, in the Resources section under Post-translational Modifications.

@@ Line 20: / Line 20: @@
 Scientists from [https://www.alliancegenome.org Alliance of Genome Resources] member groups [https://www.yeastgenome.org SGD], [https://www.alliancegenome.org/members/rgd RGD], [https://www.alliancegenome.org/members/zfin ZFIN], [https://www.alliancegenome.org/members/goc Gene Ontology], and [https://www.xenbase.org/entry/ Xenbase] have provided updates on recent activities and innovations.
-Be sure to browse the issue and get acquainted with these excellent Knowledgebase and Database Resource papers at GENETICS. Cover art by [https://www.vividbiology.com Vivid Biology].
+Be sure to browse the issue and get acquainted with these excellent Knowledgebase and Database Resource papers at GENETICS.
 <br><br>
 *SGD	https://doi.org/10.1093/genetics/iyac191
@@ Line 29: / Line 29: @@
 </p><p>
 <br />
 ==SGD designated "Global Core Biodata Resource"==
 [[Image:FkAzFtQWIAExhDl.jpeg|link=https://www.yeastgenome.org/blog/global-biodata-coalition-selects-sgd-in-first-set-of-global-core-biodata-resources |thumb|left|upright=.75]]

← Older revision		Revision as of 21:18, 22 June 2023
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	[[Category: Newsletter]]		[[Category: Newsletter]]
−	~~<FONT COLOR=RED>THIS IS NOT THE FINAL VERSION - WE ARE STILL WORKING ON THIS DOCUMENT</FONT>~~
−
	'''About this newsletter:''' <br> This is the Summer 2023 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community. You can view this [https://wiki.yeastgenome.org/index.php/SGD_Newsletter,_Summer_2023 newsletter] as well as previous newsletters, on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].		'''About this newsletter:''' <br> This is the Summer 2023 issue of the SGD newsletter. The goal of this newsletter is to inform our users about new features in SGD and to foster communication within the yeast community. You can view this [https://wiki.yeastgenome.org/index.php/SGD_Newsletter,_Summer_2023 newsletter] as well as previous newsletters, on our [https://wiki.yeastgenome.org/index.php/SGD_Newsletter_Archives Community Wiki].

← Older revision		Revision as of 21:17, 22 June 2023
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	*The Alliance of Genome Resources has a new Facebook page: https://www.facebook.com/AllianceOfGenomeResources		*The Alliance of Genome Resources has a new Facebook page: https://www.facebook.com/AllianceOfGenomeResources
		+	</p><p>
		+	<br />

	==Upcoming Conferences and Courses==		==Upcoming Conferences and Courses==

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 ==Alliance of Genome Resources - Releases 5.3 & 5.4==
-[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.7]]
+[[Image:alliance_logo.png|link=https://www.alliancegenome.org/ |thumb|left|upright=.725]]
 The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released version 5.3 last October and [https://www.alliancegenome.org/release-notes version 5.4] this past April.

@@ Line 90: / Line 90: @@
 The [https://www.alliancegenome.org/ Alliance of Genome Resources], a collaborative effort from SGD and other model organism databases (MOD), released version 5.3 last October and [https://www.alliancegenome.org/release-notes version 5.4] this past April.
-Version 5.3 saw the release of ''Xenopus'' data from Xenbase. These amphibians are an important tetrapod model, spanning the evolutionary gap between the mammalian (human, mouse, and rat) and zebrafish data already included in the Alliance. ''Xenopus'' have long been used in developmental and cell biology, and two species are widely studied. The African clawed frog, ''X. laevis'' is an allotetraploid (2n = 36) of hybrid origin. The resulting ''X. laevis'' genome has a set of ‘long’ and ‘short’ chromosomes and gene symbols are therefore appended with ‘.L’ or ‘.S’ denoting on which chromosome pair they reside. The second ''Xenopus'' species, the Western clawed frog ''X. tropicalis'', is a conventional diploid (2n=20), and is increasingly used in human disease modeling.
+'''Version 5.3''' saw the release of ''Xenopus'' data from Xenbase. These amphibians are an important tetrapod model, spanning the evolutionary gap between the mammalian (human, mouse, and rat) and zebrafish data already included in the Alliance. ''Xenopus'' have long been used in developmental and cell biology, and two species are widely studied. The African clawed frog, ''X. laevis'' is an allotetraploid (2n = 36) of hybrid origin. The resulting ''X. laevis'' genome has a set of ‘long’ and ‘short’ chromosomes and gene symbols are therefore appended with ‘.L’ or ‘.S’ denoting on which chromosome pair they reside. The second ''Xenopus'' species, the Western clawed frog ''X. tropicalis'', is a conventional diploid (2n=20), and is increasingly used in human disease modeling.
 Data for both ''Xenopus'' species are organized on individual gene pages that feature data such as gene descriptions, orthology to human and other species, disease associations for orthologs, an expression ribbon view, and a Sequence Feature Viewer.
-Version 5.4 provides new Alliance SimpleMine and Facebook URLs:
+'''Version 5.4''' provides new Alliance SimpleMine and Facebook URLs:
 *SimpleMine allows basic batch searches of Alliance data: https://www.alliancegenome.org/agr_simplemine.cgi