the maize inflorescence project website tutorial nov 7, 2014

The Maize Inflorescence Project Website Tutorial

Nov 7, 2014

To access the data, you must login firsthttp://www.maizeinflorescence.org

Click to login

Navigation panel to unrestricted pages.

To access the data, you must login firsthttp://www.maizeinflorescence.org/

Username

Password

Click to login

Click on user’s name to edit user information

Click to log out

Your name appears after your login

Access Profile page

Navigation panel changed

You may change your password

Click on “Tools” tab to see the list of

tools. Click on the buttons above to visit respective

tool page.

You can only see the list of “tools” after you login

Select experiments to be displayed for each Gene id. (default: all)

Filter the Gene ids by RPKM value in the

selected experiment. (optional)

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.Click “Search” to extract list of genes in tabular

format.

Profile Display – slide# 1

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# 2

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 Display – slide# 3

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”.

Profile Search – slide# 1

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.

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 Search – slide# 2

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# 1

Output: Cluster Dendrogram

Profile Clustering – Hierarchical Clustering Slide# 2

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# 1

Output: Heatmap

Profile Clustering – Heatmap Slide# 2

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)

Select or Unselect the tracks from the “Available Tracks”

to visualize in “Genome Browser” region.

Controls to browse through a selected Chromosome

Click on “X” to remove the track from “Genome Browser” and place it in “Available Tracks” region.

GFF track

QTL track

RNAseq tracks

Genome Browser (Jbrowse)

More info available at http://gmod.org/mediawiki/images/0/0c/JBrowse_bioit_world_apr2013.pdf

Click on the coordinates in the table to perform interval search.

QTL Regions

Data obtained regarding QTL

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

Perform BLAST.

All the genomes that are available at GRAMENE.ORG

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 fromArabidopsis 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 OrthologsSave 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)

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.

Click “Filter” to filter the RNAseq output.

A new tab called “RNAseq (filter)” appears on the top, and that tab

holds the filtered results.

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)

Ortholog gene id in black.Ortholog gene description in red.

List of available orthologs in the database

Select and click to get addional

Orthologs

Interval Query (9: Save list)

Click on “Save list” to save the gene ids into a file for further analysis.

Name the list and click on

“Save”.

Keyword search (Gene description or GO description)

The database output.

List the keywords and click “Search”

MyGene (1. List)

Lists the your files so far. Maximum limit is 10.

Upload a list of gene ids in a file. Maximum limit: 100 gene ids

Show: To see contents of the fileEdit: To change name and gene idsDelete: To delete the file.

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

Click on the “Download” link to go to data download web page

Data is categorized based on the date we received the data.Click on the links to download