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AnGenMap Archived Post

From  Mon May  2 22:38:56 2016
From: "Hu, Zhiliang [AN S]" <>
Postmaster: submission approved by list moderator
To: Multiple Recipients of AnGenMap <>
Subject: What's new on the NAGRP animal genome web site (#2,
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.

  Developmental updates:
  (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" ( 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
( for any routine

NAGRP Bioinfo Team



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