Help

Table of Contents

2. Custom dataset download and visualization

4. Remotely accessible M^3DGenePages and Visualization

We provide separate files containing normalized data for all genes, and genes + intergenic regions, and all genes + intergenic regions + control probes. We also provide flat files containing the gene names, probe set names, and experimental condition information. Raw CEL files are also available upon request. Click the Download Data tab for more information.

Custom dataset download and visualization

Custom datasets are created and visualized in the analysis section (click on the Analysis tab above). On most pages you will find bracketed question mark [?] that you can mouse over for context specific help. Below is a general help description of the analysis section of the M^3D website.

To begin creating a custom dataset, click the Analysis tab at the top of the webpage. You begin by choosing a compendium. Higher build numbers for a species indicate more recent builds. Typically, you'll want to use the compendium with the highest build number for your species of interest. Older databases are maintained so that analyses performed on these data can be repeated if necessary (this is important, because some of the normalization types use the data from all of the chips to determine an expression value for a gene, so as arrays are added to the dataset the value for past experiments change a little).

After choosing a database, you are presented with a small table that allows you to change to a new compendium. This table also contains statistics describing your current dataset including the number of genes and experiments in your current dataset. In this table, you can click the links to add genes or experiments. If you currently have 0 genes or 0 experiments in your dataset, you will automatically be taken to pages for adding genes and experiments.

Experiments can be selected individually or as projects. Projects are groups of experiments run together. Typically projects are the data used for one scientific publication. An experiment represents one specific condition and may have replicates. Currently, it is not possible to select individual chips.

Once you have a dataset with at least one gene and at least one experiment, you can visualize or download the dataset. M^3D provides several different visualizations. The best way to see what they do is to try them with small datasets. Visualization of large datasets (> 500 genes) is rather slow due to the time required to read all of the expression information from the database for each analysis.

Structured experimental metadata

Structured experimental metadata is available for compedia with version four or later (currently S. cerevisiae is the only species without a version four compendium). The amount of metadata can be overwhelming for many experiments, particularly for those experiments with minimal medias and nutrient supplements. We are working on ways to display this metadata so that it can be efficiently scanned by eye in a web environment.

For commonly used media, we have defined aggregates that represent the constituents of the media. Often rather than displaying the detailed chemical components, we simply display the aggregate name to reduce clutter. If you mouseover the aggregate name, you will be presented with the constituents of that particular aggregate (e.g. sf minimal media, LB Miller).

Experimental metadata is also available in the bulk normalized data download for each species. See the README file on the bulk download page for details.

Remotely accessible M^3DGenePages and Visualization

M^3DGenePages
M^3DGenePages contain a basic set of plots for each gene. An example M^3DGenePage link:

http://m3d.bu.edu/cgi-bin/web/array/index.pl?genepage=YFL039C&species=S_cerevisiae

You can replace the YFL039C with your gene name. Both common names and standard names should work (e.g. with S. cerevisiae you can use either YFL039C or ACT1). The currently available species are E_coli, S_cerevisiae, and S_oneidensis. You must include the species name. Other examples:

http://m3d.bu.edu/cgi-bin/web/array/index.pl?genepage=lexA&species=E_coli

http://m3d.bu.edu/cgi-bin/web/array/index.pl?genepage=fdhE&species=S_oneidensis

Remote visualization

The plots on M^3D can be embedded on any website by including the appropriate information in an image url. Below is an example url to create a histogram of recA expression in E. coli:

http://m3d.bu.edu/cgi-bin/web/arrayPlotter/arrayPlotter?db=E_coli_v3_Build_2&analysis=hist&allExp=1&width=200&height=200&method=1&gene_name_list=recA&title=test%20recA

the parameters for this query are:

db	what compendium do you want to use?
analysis	what type of plot do you want to generate?
allExp	this parameter just lets the image drawing program know to use all experiments for the selected compendium. there is current no way to select individual experiments as doing so would quickly exceed the maximum URL length for most browsers
width	image width in pixels
height	image height in pixels
method	determines the normalization method to use; most compendia in M^3D only have RMA normalized data. RMA is the default, so you can leave out method parameter if you like.
gene_name_list	is an asterisk delimited list of gene names; you can use gene names, probe set names, or locus ids (i.e. standard ids like the blattner ids in E. coli. To get a list of all possible gene names for a particular compendium, you can download the normalized data for each compendium from the Download Data tab in the main menu. The normalized data contains a list of all genes in each compendium.
title	is the title displayed at the top of the image; make sure to url encode your title

Note that if you use too many genes in your plot, you will begin to bump up against the url length limit set by a few browsers (around 2000 characters).

Additional examples:

plot of araB transcription factor expression versus one of its targets expression
http://m3d.bu.edu/cgi-bin/web/arrayPlotter/arrayPlotter?db=E_coli_v3_Build_2&title=test%20tf-vs-gene&analysis=oneToMany&width=400&height=300&method=1&gene_name_list=araC*araB&allExp=1

(with scatterplots, the first gene in your list will be used as the xaxis)

histogram of many arabinose genes showing their switch-like behaviour
http://m3d.bu.edu/cgi-bin/web/arrayPlotter/arrayPlotter?db=E_coli_v3_Build_2&title=test%20many%20gene%20histogram&analysis=hist&width=400&height=300&method=1&gene_name_list=araC*araB*araD*araE&allExp=1

heat plot of arabinose genes
http://m3d.bu.edu/cgi-bin/web/arrayPlotter/arrayPlotter?db=E_coli_v3_Build_1&title=test%20heat&analysis=heat&width=1500&height=200&method=1&gene_name_list=araC*araB*araD*araE&allExp=1&avgRep=1&rescale=2.0&colormap=rwb

heat plot of arabinose genes using the classic red/green color scheme
http://m3d.bu.edu/cgi-bin/web/arrayPlotter/arrayPlotter?db=E_coli_v3_Build_1&title=test%20heat&analysis=heat&width=1500&height=200&method=1&gene_name_list=araC*araB*araD*araE&allExp=1&avgRep=1&rescale=2.0&colormap=rbg

Remote visualization with mouseovers

The gene expression scatterplots on M^3D is interactive. If you mouseover the points on the plot, you can learn the experimental condition information about each point. If you use the method of embedding your image described above, you lose this interactivity. However, you can embed an iframe in your page to obtain this interactivity (try it on the image below; here is a short explanation of how this remote visualization with mouseover support works):

<iframe scrolling="no" frameborder="0" marginheight="0" marginwidth="0" height=450 width=800 border=0 src='http://m3d.bu.edu/cgi-bin/web/arrayPlotter/arrayPlotter?db=E_coli_v4_Build_3&title=mouseoverplot%20plot%20example&analysis=oneToMany&width=450&height=450&method=1&html=1&iframe=1&gene_name_list=araC*araB&allExp=1'></iframe>

Caveats:

Unlike on the M^3D website, we currently don't allow the remotely visualized heat plots to be subtracted by a reference condition. We hope to allow this in the future.
The maximum length of a url in some browsers is around 2000 characters, so you don't have space to add more than 100-200 genes to your plot.