selecting the members in Arabidopsis thaliana for
HOM04D000569, the family in which ABI3 is located,
under Data Settings and Species Selection, and using default
settings under Program Settings.
3.2.3 PANTHER
The PANTHER platform is possibly the most extensive online
resource for the study of genes and proteins on a genome-wide
scale. Initially aimed at classifying gene function using GO terms, it
now provides a plethora of tools and data for studying gene function, evolutionary relationships, biochemical pathways, and/or
analysis of gene expression or proteomics data [16]. PANTHER
has the additional advantage of being an active project that is
updated monthly. Recently, a revised and detailed protocol on
how to use PANTHER was published by its developers and we
highly recommend consulting it [17].
3.3 Epigenomic
Tools
3.3.1 EPIC-CoGe
Browser for Arabidopsis
Epigenomic Data
The EPIC-CoGe Browser [18], built on JBrowse, is CoGe’s visualization system for various types of genomic data. CoGe itself is
short for “comparative genomics” and tens of thousands of genomes have been loaded into the system for easy comparison. EPIC
is an acronym for the “Epigenomes of Plants International Consortium,” a U.S. National Science Foundation-funded research coordination network [19]. The power behind EPIC-CoGe is that it
also functions as a massive data repository for hundreds of Arabidopsis sequencing experiments. If you choose to, you can upload
your own data for visualization, add new genomes, share data easily
with collaborators, as well as integrate your own data with publicly
available experiments. To aid utility, searching for data sets of
interest only requires knowing a keyword, such as “H3K4me3”
or “Arabidopsis.” You can also overlay several genomic data types
by creating a notebook, as we will do in the steps below. For
additional tutorials using EPIC-CoGe, please refer to https://
genomevolution.org/wiki/index.php/EPIC-CoGe_Tutorial .
1. Log in to https://genomevolution.org/CoGe/User.pl using a
free CyVerse account (instructions are given on the first page).
After logging in, click on “My Data” on the left hand of page.
Next, click on “Notebooks.” At the top of this page, click on
the plus sign, “+,” to create a new notebook and name the
notebook something informative. For this tutorial, we have
named the notebook “ABI3 regulatory features.” After designating a notebook name, click “Create Notebook.” If you
wish, you can also make the notebook publicly available by
doing the following: double click on the notebook name to
see a page describing the notebook and its attributes. Click on
“Make public.” Because notebooks can be shared publicly, all
notebook names should be unique across all CoGe notebooks.
That said, notebook names can be reused; however they will be
assigned a unique ID number.
Arabidopsis Bioinformatics
33
HOM04D000569, the family in which ABI3 is located,
under Data Settings and Species Selection, and using default
settings under Program Settings.
3.2.3 PANTHER
The PANTHER platform is possibly the most extensive online
resource for the study of genes and proteins on a genome-wide
scale. Initially aimed at classifying gene function using GO terms, it
now provides a plethora of tools and data for studying gene function, evolutionary relationships, biochemical pathways, and/or
analysis of gene expression or proteomics data [16]. PANTHER
has the additional advantage of being an active project that is
updated monthly. Recently, a revised and detailed protocol on
how to use PANTHER was published by its developers and we
highly recommend consulting it [17].
3.3 Epigenomic
Tools
3.3.1 EPIC-CoGe
Browser for Arabidopsis
Epigenomic Data
The EPIC-CoGe Browser [18], built on JBrowse, is CoGe’s visualization system for various types of genomic data. CoGe itself is
short for “comparative genomics” and tens of thousands of genomes have been loaded into the system for easy comparison. EPIC
is an acronym for the “Epigenomes of Plants International Consortium,” a U.S. National Science Foundation-funded research coordination network [19]. The power behind EPIC-CoGe is that it
also functions as a massive data repository for hundreds of Arabidopsis sequencing experiments. If you choose to, you can upload
your own data for visualization, add new genomes, share data easily
with collaborators, as well as integrate your own data with publicly
available experiments. To aid utility, searching for data sets of
interest only requires knowing a keyword, such as “H3K4me3”
or “Arabidopsis.” You can also overlay several genomic data types
by creating a notebook, as we will do in the steps below. For
additional tutorials using EPIC-CoGe, please refer to https://
genomevolution.org/wiki/index.php/EPIC-CoGe_Tutorial .
1. Log in to https://genomevolution.org/CoGe/User.pl using a
free CyVerse account (instructions are given on the first page).
After logging in, click on “My Data” on the left hand of page.
Next, click on “Notebooks.” At the top of this page, click on
the plus sign, “+,” to create a new notebook and name the
notebook something informative. For this tutorial, we have
named the notebook “ABI3 regulatory features.” After designating a notebook name, click “Create Notebook.” If you
wish, you can also make the notebook publicly available by
doing the following: double click on the notebook name to
see a page describing the notebook and its attributes. Click on
“Make public.” Because notebooks can be shared publicly, all
notebook names should be unique across all CoGe notebooks.
That said, notebook names can be reused; however they will be
assigned a unique ID number.
Arabidopsis Bioinformatics
33