From listmaster animalgenome.org Tue Jan 3 11:36:35 2023
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From: "Hu, Zhiliang [ANS]" <zhuiastate.edu>
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To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#1,
2023)
Date: Tue, 03 Jan 2023 11:36:35 -0600
What's new on the NAGRP animal genome web site (#1, 2023)
o Animal QTLdb and CorrDB updates -- Announcing a joint release of the QTLdb
(Release 49) and CorrDB (Release 17):
(Dec 28, 2022): A sum of 3,979 new QTL/associations have been curated into
the database. (New additions less obsolete/retracted ones: Catfish: 0;
Cattle: 425; Chicken: 1,657; Goat: 1; Horse: 13; Pig: 879; Sheep: 88;
Rainbow trout: 916 -- Net increase: 3,979). To date, the current total
number of QTL in the database: 258,290 [Breakdown by species: Cattle:
193,641 (on 686 traits); Chicken: 18,313 (on 370 traits); Goat: 129 (on 26
traits); Horse: 2,649 (on 65 traits); Pig: 36,725 (on 698 traits); Sheep:
4,504 (on 267 traits); Rainbow trout: 2,329 (on 47 traits)]. In addition,
updates have been made to 395 previously curated QTL/associations as part
of our data quality control efforts.
URL: https://www.animalgenome.org/QTLdb
(Dec 28, 2022): A sum of 584 new correlations [Breakdown by species --
Pig: 1,119; Cattle: 353; Chicken: 90; Sheep: 140] and a sum of 211 new
heritability data [Breakdown by species -- Pig: 78; Cattle: 51; Chicken:
28; Sheep: 54] have been curated into the CorrDB. To date, the total
number of correlation data in the database: 26,839 [Breakdown by species
-- Cattle: 13,471 (on 352 traits); Chicken: 1,835 (on 80 traits); Horse:
209 (on 27 traits); Pig: 8,902 (on 241 traits); Sheep: 2,111 (on 74 traits);
Goat: 311 (on 32 traits)], and total heritability data: 4,778 [Breakdown by
species -- Cattle: 2,330 (on 405 traits); Chicken: 377 (on 106 traits);
Horse: 123 (on 53 traits); Pig: 1,607 (on 280 traits); Sheep: 336 (on 104
traits); Goat: 5 (on 2 traits)] curated from 480 publications.
In addition, data updates have been made to previously curated data (244
QTL/associations, 384 correlations, 395 heritability, and 977 traits data)
as part of our data quality control efforts.
URL: https://www.animalgenome.org/CorrDB
Database developments:
(1) Genomic marker types were added as a curation parameter to Animal QTLdb
curation pipelines in early 2016. We have retrospectively updated marker
type information for data curated prior to that time. Subsequently, we have
added this parameter for data downloads. The marker type data counts can be
found on the "data summary" pages of each species. (Choose "5. Number of
QTL/associations by marker types" from the option list.)
(2) The Animal CorrDB web portal has been updated with additions and/or
modifications of its correlation network visualization options. Now there
are two ways to visualize a correlation network: Graphviz dot graph and
Cytoscape web tools. These tools are available in subpages on various data
summary or search result page views.
(3) Developmental work has continued on data pipeline automation to
streamline the processes bridging QTL/association information across
different genome builds and dbSNP releases.
o Ontology developments:
The following data releases were made since our last "what's new" updates:
(1) Two new version releases to the Vertebrate Trait (VT) Ontology data
(versions 12.9 and 12.10).
(2) Three new version releases to the Livestock Product Trait (LPT)
ontology data (versions 4.1, 4.2, and 4.3).
(3) Two new version releases to the Livestock Breed Ontology (LBO,
versions 7.14 and 7.15).
In addition, version 2.171 of Clinical Measurement Ontology (CMO) data from
Bioportal with 3,847 terms was updated to the local QTLdb/CorrDB curation
environment and for ontology hierarchy browsers and viewers on the site.
o ANGENMAP Listserv:
A final switch was made as an endpoint of our transition from using
interactive email subscribe/unsubscribe listserv service to use of
web-based user profile management tools. After October 12, the AnGenMap
subscriber list has been completely refreshed as an automated routine from
user profiles.
URL: https://www.animalgenome.org/community/angenmap/
o Tool developments:
(1) A Cytoscape web tool for visualizing complex networks has been
successfully implemented at AnimalGenome.org to facilitate presentation
of entity relationships for research projects and as a database tool. An
example of its application was to show "phenotypically related cattle
traits by their underlining gene interactions discovered via functional
genomics through integration of multi-omics data" (see Hamid Beiki et al.
"Functional genomics of cattle through integration of multi-omics data",
bioRxiv 2022.10.05.510963).
URL: https://www.animalgenome.org/host/reecylab/a
(2) As part of our efforts linking genotypes to phenotypes, we made
efforts to visualize data profiles from the genotype-tissue expression
(GTEx) analysis. Our initial success was to use data from a CattleGTEx
study (https://www.nature.com/...22-01155-3; data downloaded
from https://cgtex.roslin.ed.ac.uk/downloads/) to show permutated p-values
for gene expression patterns across tissues with linear Manhattan plots
as a JBrowse2 plug-in, developed by Colin Diesh of MIT, originally
designed for plotting GWAS data (https://jbrowse.org/jb2/plugin_store/).
In addition, multiple JBrowse2 instances have also been deployed for
different species. Preliminary JBrowse2 views of both CattleGTEx and
PigGTEx data (Lingzhao Fang's group; private communications) can be seen at
the URLs below. QTL/association data tracks are also included for each
species.
URL: https://www.animalgenome.org/gtex/cattle
https://www.animalgenome.org/gtex/pig
Check out the daily "what's new" (https://www.animalgenome.org/news/) items
for more up-to-date information on this site. Thanks in advance for kindly
reporting broken links/errors, or suggesting corrections on our site.
Your input is always appreciated. Feel free to contact us at any time with
your needs, requests, and/or suggestions: Jim Reecy (jreecyiastate.edu),
James Koltes (jekoltesiastate.edu), Fiona McCarthy (fionamccarizona.edu).
Or talk to us using our Helpdesk (https://www.animalgenome.org/helpdesk).
--
NAGRP Bioinfo Team
bioinfo-teamanimalgenome.org
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