FAANG List Archived Post

From apache@animalgenome.org  Thu Aug 31 08:42:44 2017
From: "Kasimanickam, Vanmathy" <vkasiman@vetmed.wsu.edu>
Subject: RE: FAANG Integrative Genomics and Network Biology analysis
Date: Thu, 31 Aug 2017 13:26:55 +0000
To: FAANG Members <faang@animalgenome.org>

Hi Robert,

How do I join to the sub-group? I have lot of information to share and I also
come across problems when I use the data for animal species (other than mice
and human). I have a lot of data from real-time PCR profiling arrays and I
need to find a way to use Ct values instead of using normalized counts from
RNA seq or small RNA seq data when I integrate to biological pathways or
upstream or downstream variables.

Thanks, Vanmathy

Vanmathy Kasimanickam DVM, MS, DACVPM


________________________________
From: Robert Schaefer [schae234umn.edu]Sent: Monday, August 28, 2017 12:33 PM
To: Kasimanickam, Vanmathy; FAANG Members
Subject: Re: FAANG Integrative Genomics and Network Biology analysis sub-group

Hello Vanmathy,

Thanks for the question.

The group wont try to replace or specifically implement tools such as IPA,
rather it will focus on forming guidelines around how to approach network
analysis given the data being generated by FAANG. This is likely to include
recommendations using existing tools, i.e. if a group is successful doing
analysis using IPA (or some other tool) in one FAANG species, how do we
generalize it to be used in another species. Likewise, if a network or
integrative approach fails to work, we would like to catalog why this is so
(is it because its in an agricultural vs laboratory animal).

As we are just forming, we are first looking for research groups who are
asking integrative and network based questions so we can form a community
that is supportive and collaborative.

Thanks, Rob

On Mon, Aug 28, 2017 at 1:45 PM Kasimanickam, Vanmathy
vetmed.wsu.edu> wrote:
Hello Rob,

Will the subgroup be developing something similar to the software "ingenuity
pathway analysis" to integrate biological functions and others, but with the
specific focus on various animals species (from lab animal to large animal
species)?

Vanmathy

Vanmathy Kasimanickam DVM, MS, DACVPM

________________________________________
From: Robert Schaefer [schae234umn.edu]Sent: Monday, August 28, 2017 8:13 AM
To: FAANG Members
Subject: FAANG Integrative Genomics and Network Biology analysis sub-group

Dear FAANG community members and friends,

After seeing many posters and talks on data generation, collection, and
curation from the animal genetics community at the recent ISAG meeting it has
become clear that much progress has been made to achieve the aims set out by
FAANG. Many of the relevant data sets (e.g. RNA-Seq, Chip-Seq, DNase-Seq etc)
are currently being generated and some data sets are already available.

As such, we have seen groups starting to analyze these data and developing
pipelines that integrate and compare data across different data types,
especially in the form of biological networks. To comply with the goals of
FAANG, we are proposing to form a sub-group within the current Bioinformatics
and Data Analysis working group that will focus on Integrative Genomics and
Network Biology.

This new sub-group would complement the current Bioinformatics and Data
Analysis group and would have several specific goals:

   - Generate a panel of recommended methods and software tools that robustly
   integrate different data types with a focus on network analysis and to
   provide feedback on the quality of and feasibility of integrated/network
   approaches.


   - Define community standards for statistical methods that make inferences
   from integrated  data and to develop recommended methods for establishing
   statistical significance (e.g. making sense of correlations and profiles).


   - The group would discuss and evaluate database and storage methods for
   large biological networks using FAANG data.


   - The group would advise other FAANG groups on experimental design issues
   relevant to downstream integrative genomics and network biology analyses
   (e.g. minimum sample sizes required for correlation-based network
   approaches).


   - The group would establish an active, inclusive and friendly community
   for animal scientists interested in the application of integrative genomics
   and network biology.

To start, current FAANG members can simply join the Integrative Genomics
and Network Biology mailing list (faang-analysis-networkanimalgenome.org)at http://www.faang.org/. 
Anyone who is not currently a member of FAANG is
welcome to join the community via the above website.

Additionally, we have started a GitHub page that will be used to to
contribute code or discuss computational pipelines. Visit
https://github.com/FAANG/faang-network-biology to get started. Information
on how to contribute as well as community guidelines are specified in the
repository.

Sincerely,

Rob Schaefer, University of Minnesota, schae234umn.edu Molly McCue,University of Minnesota,
mccu0173umn.edu Carolina Correia,
UniversityCollege Dublin, carolina.correiaucdconnect.ie Thomas Hall, UniversityCollege
Dublin, thomas.hallucdconnect.ie
David MacHugh, University CollegeDublin, david.machughucd.ie
--
____________________________
Rob Schaefer, PhD

USDA-NIFA Postdoctoral Fellow Equine Genetics and Genomics Lab University of
Minnesota

@CSciBio 
____________________________

Rob Schaefer, PhD

USDA-NIFA Postdoctoral Fellow Equine Genetics and Genomics Lab University of
Minnesota @CSciBio