Many Microbe Microarrays Database (M3D): Difference between revisions

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{{Pagetop}}
{{Pagetop}}
[[Category:Databases]]
[[Category:Databases]]
{|{{Prettytable}} width='30%' align = 'right'
[[Category:Gene Expression Databases]]
|- align='center' bgcolor = '#ddddff'
[[Category:IECA Portal]]
|  colspan = '2' | '''{{PAGENAME}}'''
<protect><!--box uid=63ce1649aab8b3180235b0af7618f667.1700.W4817f1007b40d-->
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{| {{Prettytable}} width='30%' align="right"  id="W4817f1007b40d"  class=" tableEdit Database_table" 
 
|-
|-
| width='30%' | Who:
!align=left {{table heading style}} |Link/URL:
| ''proprietor''
||
[http://m3d.bu.edu/cgi-bin/web/array/index.pl?section=home Many Microbe Microarrays Database]
 
Mirror site: http://cgs.wustl.edu/~faithj/m3d_mirror/
|-
|-
| width='30%' | What:
!align=left {{table heading style}} |What:
| ''short description''
||
Affymetrix data for ''E. coli'' and other bacteria
|-
|-
| Where:
!align=left {{table heading style}} |Who:
| [http://ASAP {{PAGENAME}}]
||
Tim Gardner http://gardnerlab.bu.edu/
 
Boston University
 
|-
|-
| Updates
!align=left {{table heading style}} |Updates:
|
||
 
|-
|-
| Upcoming events
!align=left {{table heading style}} |Upcoming events:
| ''link to event calendar, if applicable''
||
 
|-
|-
| Web Services
!align=left {{table heading style}} |Web Services:
|
||
 
 
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=About {{PAGENAME}}=
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[http://ASAP {{PAGENAME}}] is...
==About {{PAGENAME}}==
=Content=
[[Image:Mmm_home.jpg|300px|thumb|right|Home Page]]
=Using {{PAGENAME}}=
[http://m3d.bu.edu/cgi-bin/web/array/index.pl?section=home {{PAGENAME}}] is a resource for analyzing and retrieving gene expression data for microbes. The database currently contains affymetrix expression profiles for Escherichia coli. In the future, Shewanella oneidensis affymetrix data will be available as well.<ref name='PMID:17932051'/>
==Browsing==
 
==Searching==
==Content==
==Usage examples==
Experiments: 189
Arrays: 445
 
==Using {{PAGENAME}}==
===Browsing===
===Searching===
Users can query M3D by choosing a project and a list of genes. 
Data can be normalized (scaling by gene) prior to analysis. 
 
http://m3d.bu.edu/cgi-bin/web/array/index.pl?db=E_coli_v3_Build_1
 
Presentation formats include:
*Heat Plot (genes vs experiments)
*Histogram of individual gene expression (one plot per gene)
*Histogram of all gene expression (one plot for N genes)
*Plot Expression of many genes as a function of one gene
*Link to download expression data
 
Average Array Replicates by:
*RMA
*GCRMA
*DchipPM
*DchipMM
*MAS5
 
Heat Plot Parameters:
*rescale data to within stddev of mean
*Order Genes By Correlation
*Order Experiments By Correlation
 
Heat Map coloring:
*Red/Blue 
*Red/Green
 
 
M3D provides a meatalink to execute queries on N-browse, which is described as  an interactive graphical browser for molecular interaction networks
 
http://nematoda.bio.nyu.edu:8080/NBrowse/N-Browse.jsp?last=false
 
===Usage examples===
''Add links to additional pages describing success stories here.''
''Add links to additional pages describing success stories here.''


=Other sites with related content=
==Other sites with related content==
=Technology=
==Technology==
==Web Services/API==
The following free software and libraries were used for array normalization and to develop M3D: dChip, Bioconductor (for GCRMA and RMA), gd, cgic, Cluster 3.0, and MySQL.
=Discussion=
===Web Services/API===
 
==Discussion==
 
==References==
{{BacktoTop}}
{{RefHelp}}
<references />


=References=
==External Links==
=External Links=
[http://m3d.bu.edu/cgi-bin/web/array/index.pl?section=home {{PAGENAME}}]
[http://ASAP {{PAGENAME}}]
==Discussion of {{PAGENAME}} on other websites==
==Discussion of {{PAGENAME}} on other websites==

Latest revision as of 18:44, 23 January 2013

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Link/URL:

Many Microbe Microarrays Database

Mirror site: http://cgs.wustl.edu/~faithj/m3d_mirror/

What:

Affymetrix data for E. coli and other bacteria

Who:

Tim Gardner http://gardnerlab.bu.edu/

Boston University

Updates:
Upcoming events:
Web Services:


edit table


About Many Microbe Microarrays Database (M3D)

Home Page

Many Microbe Microarrays Database (M3D) is a resource for analyzing and retrieving gene expression data for microbes. The database currently contains affymetrix expression profiles for Escherichia coli. In the future, Shewanella oneidensis affymetrix data will be available as well.[1]

Content

Experiments: 189 Arrays: 445

Using Many Microbe Microarrays Database (M3D)

Browsing

Searching

Users can query M3D by choosing a project and a list of genes. Data can be normalized (scaling by gene) prior to analysis.

http://m3d.bu.edu/cgi-bin/web/array/index.pl?db=E_coli_v3_Build_1

Presentation formats include:

  • Heat Plot (genes vs experiments)
  • Histogram of individual gene expression (one plot per gene)
  • Histogram of all gene expression (one plot for N genes)
  • Plot Expression of many genes as a function of one gene
  • Link to download expression data

Average Array Replicates by:

  • RMA
  • GCRMA
  • DchipPM
  • DchipMM
  • MAS5

Heat Plot Parameters:

  • rescale data to within stddev of mean
  • Order Genes By Correlation
  • Order Experiments By Correlation

Heat Map coloring:

  • Red/Blue
  • Red/Green


M3D provides a meatalink to execute queries on N-browse, which is described as an interactive graphical browser for molecular interaction networks

http://nematoda.bio.nyu.edu:8080/NBrowse/N-Browse.jsp?last=false

Usage examples

Add links to additional pages describing success stories here.

Other sites with related content

Technology

The following free software and libraries were used for array normalization and to develop M3D: dChip, Bioconductor (for GCRMA and RMA), gd, cgic, Cluster 3.0, and MySQL.

Web Services/API

Discussion

References

[back to top]


See Help:References for how to manage references in EcoliWiki.

  1. ↑ Faith, JJ et al. (2008) Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Res. 36 D866-70 PubMed

External Links

Many Microbe Microarrays Database (M3D)

Discussion of Many Microbe Microarrays Database (M3D) on other websites

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