Download Tutorial - Maize Inflorescence

The Maize Inflorescence Project
Website Tutorial
Nov 7, 2014
To access the data, you must login first
http://www.maizeinflorescence.org
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Navigation panel to
unrestricted pages.
To access the data, you must login first
http://www.maizeinflorescence.org/
Username
Password
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Your name appears after your login
Click on user’s name to
edit user information
Access Profile page
Navigation panel changed
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You may change your password
You can only see the list of “tools” after you login
Click on “Tools” tab
to see the list of
tools.
Click on the buttons
above to visit respective
tool page.
Profile Display – slide# 1
Select experiments to be displayed for
each Gene id. (default: all)
Filter the Gene ids by
RPKM value in the
selected experiment.
(optional)
Click “Search” to
extract list of genes in
tabular format.
Specify a list of gene
ids or gene
description in each
line of the query
box. (default: none)
Click on “sample text” to fill the query
box with a small set of gene ids and
description as shown.
Profile Display – slide# 2
Information on count of entries present in the database.
To navigate to the next 20 entries and previous 20 entries
Self descriptive table with Gene id, Gene description and RPKM values.
Click anywhere within the row of the first
Gene id “GRMZM2G176394”.
The RPKM values for this gene is plotted
against the selected experiments.
The plot is at the bottom of the table.
NOTE: The checkboxes in the table and “Combine Graph”
button above the plot is explained on next slide.
Profile Display – slide# 3
Use checkbox to select two or more Gene ids to merge their
profile in a single chart.
Click “Combine graph” to generate the chart.
Profile Search – slide# 1
Provide a gene id for profile search. (required)
Select correlation method “Pearson”,
“Spearman” and “Kendall”. (default: pearson)
Set the cutoff value for the correlation
method. (default: >= 0.9)
Select the experiments for consideration.
(default: all experiments)
Click on “Search”.
The profile search takes considerable amount of time, an
URL link to search results page will be emailed to you.
This is the email sent to the user, providing link to search
results page.
Profile Search – slide# 2
Table of Gene ids whose profile correlates with
query gene “GRMZM2G32875”
Select all the genes. Click on “Combine
graph” to merge the profiles of selected
genes. The chart is shown below the
table.
Profile Clustering – Hierarchical Clustering Slide# 1
Select experiments to be
considered while performing
cluster analysis.
Provide a list of Gene ids to be clustered.
Select the Agglomeration method e.g. ward,
single, complete, average, mcquitty, median
and centroid. (default: complete).
Click on “Run” to execute
clustering analysis.
Profile Clustering – Hierarchical Clustering Slide# 2
Output: Cluster Dendrogram
Profile Clustering – Heatmap Slide# 1
Select experiments to be
considered while performing
cluster analysis.
Provide a list of Gene ids to be clustered.
Click on “Run” to execute
clustering analysis.
Profile Clustering – Heatmap Slide# 2
Output: Heatmap
Genome Browser (Jbrowse)
This part of the webpage is for
available tracks.
This part of the webpage is for visualizing the
Chromosome along with the tracks.
Genome Browser (Jbrowse)
Controls to browse through a selected Chromosome
GFF track
QTL track
RNAseq tracks
Select or Unselect the tracks
from the “Available Tracks”
to visualize in “Genome
Browser” region.
Click on “X” to remove the track from “Genome Browser”
and place it in “Available Tracks” region.
More info available at http://gmod.org/mediawiki/images/0/0c/JBrowse_bioit_world_apr2013.pdf
QTL Regions
Data obtained regarding QTL
Click on the coordinates in the table
to perform interval search.
Promoter Analysis (Query)
Select the upstream
basepairs for the gene ids.
Use sample text to insert
a sample list, or list them
in the box
Promoter Analysis(Gene list)
Select the Gene ids and
click on “Get Motifs”
This button appears after
generation MEME output.
Click on it to see MEME
output.
Promoter Analysis(Meme Output)
Gene Ontology Term Enrichment (goatools)
Gene Ontology Term Enrichment (goatools)
Select from the gene list files
and lookup for GO terms
Use the text box to list the
ids to get GO terms.
Minimum ids: 25
Gene Ontology Term Enrichment (goatools)
The output from goatools tool, in
tabular format. The “e” in
enrichment column means
“enriched”.
BLAST search
All the genomes that are available
at GRAMENE.ORG
Perform BLAST.
Gene Network
Search Results
Select gene ids of interest and take
carry these ids to Profile Display page.
Interval Query (1. Search)
Use drop down to select the Chromosome and enter the start
and end coordinates. Now click “Search”
Interval Query (2. Genes)
The genes are linked to JBrowse for visualization.
Ortholog information from
Arabidopsis thaliana and
Setaria italica. The gene in black
and gene description in dark red
Interval Query (2. Genes)
Profile Display: To load the gene ids onto “Profile Display” tool input box.
RNAseq: To know whether the selected genes are differentially expressed.
ChIPseq: To query for presence of Peak summits within 2kb of the gene.
SNPs: To know if there is any SNPs within 2kb of the gene.
Orthologs: To get the Orthologs
Save list: To save list of gene ids in a file
Interval Query (3. RNAseq results)
On mouseover on the column header, a
tooltip with detailed description of the
column headers appear. In this example,
“log fold change” appears on mouse over
column header “ln_fc”
RNAseq results can be filtered by
selecting a series “Tassel
development”, “Ear
development” or “Mutant”
The subject 1 and subject 2
comparisons update based on the
series selected.
Interval Query (4. Filter RNAseq results)
A new tab called “RNAseq (filter)”
appears on the top, and that tab
holds the filtered results.
Click “Filter” to filter the RNAseq
output.
RNAseq results can be filtered by selecting a
series “Tassel development”, “Ear
development” or “Mutant”
The subject 1 and subject 2
comparisons update based on the
series selected.
Interval Query (4. Filter RNAseq results)
Interval Query (6. ChIPseq search)
Default is 2000 bp, define the interval and click
“Change Interval”. Results will appear in a new tab.
At the end of above table is a column called “Summit
difference”. It is the difference between Peak summit
and start position of gene.
Interval Query (7. SNPs)
Distance from start position of
the gene to position of SNP.
Interval Query (8: Orthologs)
List of available orthologs in the database
Select and click
to get addional
Orthologs
Ortholog gene id in black.
Ortholog gene description in red.
Interval Query (9: Save list)
Name the list
and click on
“Save”.
Click on “Save list” to save the gene
ids into a file for further analysis.
Keyword search (Gene description or GO description)
List the keywords and click
“Search”
The database output.
MyGene (1. List)
Upload a list of gene ids in a file.
Maximum limit: 100 gene ids
Show: To see contents of the file
Edit: To change name and gene ids
Delete: To delete the file.
Lists the your files so far.
Maximum limit is 10.
MyGene (2. Upload)
MyGene (3. Show)
Clicked “Show” and the
contents are listed.
To perform further analysis on
the given list of gene ids.
MyGene (4. Edit)
Click on the “Edit” link to access the list
and click “Update” to save the changes
to the list.
MyGene (5. Delete)
Click on “Delete” the list and it has to
confirmed before deleting.
Data Download
Data is categorized based on
the date we received the data.
Click on the links to download
Click on the “Download” link to go to
data download web page