From zhuiastate.edu Mon May 2 22:38:56 2016
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
Postmaster: submission approved by list moderator
To: Multiple Recipients of AnGenMap <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#2, 2016)
Date: Mon, 02 May 2016 22:38:56 -0500
What's new on the NAGRP animal genome web site (#2, 2016)
o Animal QTLdb updates:
Announcing Release 29 of the Animal QTLdb. A sum of 30,421 new QTL have
been added to the database less 10 chicken QTL retracted, representing
the largest curated data increase in the database during a 4-month
release period. The current total number of QTL in the database: 94,457
[Break down: Cattle: 71,448; Chicken: 5,462; Horse: 1,139; Pig: 15,108;
Sheep: 1,173; Rainbow trout: 127] (New additions: Cattle: 29,429;
Chicken: 266; Horse: 14; Pig: 629; Sheep: 83; Rainbow trout: 0). We thank
Angelica Van Goor from Susan Lamont's group at Iowa State University for
her curation of data and Daniel Ciobanu from University of Nebraska-
Lincoln for helping to provide data and input regarding implementation
of a new supplementary data structure for the QTLdb.
(1) A new structure is being developed for the QTLdb to allow
supplementary data from a publication to be uploaded "as is". These
data include original genotypes, phenotypes, near-significant or other
association/QTL data from the same experiment, supplementary to the
curated data. We are still in the process of developing schemes where
the use of these data by the public or third parties can best be managed.
(2) The QTLdb was developed to allow two sets of genome maps for cattle.
As the genome assemblies of multiple species are being improved, we are
working to revamp the structure to allow alternative genome maps to show
association/QTL data. Stay tuned for further details to come. (3) We
continue to improve processes and tools for post-curation data debugging
and data release procedures to ensure good data quality. (4) Now the
QTLdb can "retract" data once the paper is retracted by the journal.
(5) Five new curators have signed up for a curator account, adding the
total number of QTLdb curators to 91. (6) A new species - catfish was
added to the QTLdb for its QTL/association data curations. Catfish curator
account sign up is open to accept volunteer applications in order for
them to add new catfish data.
o New tool for querying genes that are associated with known expressed
genes in cattle:
In collaboration with Hamid Beiki from James Reecy's group at Iowa State
University, we have set up an online tool for querying genes from a data
set obtained from analysis of "related" cattle genes based on GEO archive
data using weighted correlation network analysis, using a method called
"Topological Overlap Measure (TOM)" (Langfelder P, Horvath S. WGCNA: an
R package for weighted correlation network analysis. BMC bioinformatics
2008, 9:559). The data set contains 137,887,921 connectivities identified
among 16,608 probe sets representing 11,125 genes.
o EpiDB goes online:
The development of EpiDB is a collaboration between James Koltes of
University of Arkansas, Matt Vaughn of Texas Advanced Computing Center,
and James Reecy of Iowa State University, to provide gene and epigenetics
expression data useful for dissecting quantitative trait data in
o NAGRP Data Repository:
We have developed a scheme within the NAGRP Data Repository to allow
individual labs to have their own area for private data sharing, i.e. to
have the ability to control access to their data by giving permissions to
those they wish to share with. The first user of this utility is Huaijun
Zhou's group at University of California-Davis. Any PI/lab who is
interested in having this set up, please let us know.
NAGRP Host of Supplementary Data to Publications is continually being
used. Supplementary data for two recent publications have been added
since last update.
o Virtual Machine recovery/re-setup:
Due to an earlier storage disk failure, two of the NAGRP hosted virtual
machines experienced a recovery process. Thanks to Matthew Hobbs from
Australia and Shane McCoy of North Carolina State University, the Online
Mendelian Inheritance in Animals database (OMIA) and Striped Bass Genome
Database are back to life again. A better VM backup/recovery mechanism
is being implemented.
o New hardware:
The NAGRP Bioinformatics Coordination program has acquired a new computer
server that is more powerful in terms of CPU speed and disk space. The
new server is configured to better survive disk failures and allow
improved data safety plans to be implemented with increased computational
Check out the daily "what's new" (http://www.animalgenome.org/news/) items
for more up-to-date information on this site. Thanks in advance for kindly
reporting broken links or web errors on AnimalGenome.ORG.
Your input is always appreciated. Feel free to contact us any time with
your needs, requests, and/or suggestions. You can reach us in multiple
ways: contact Jim Reecy (+1-515-294-9269) for new projects/priorities,
email the team at the email address below, or use our online Helpdesk
(http://www.animalgenome.org:bioinfo/services/helpdesk) for any routine
NAGRP Bioinfo Team