midterm project

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midterm project

• Course Statistics in Bioinformatics
• Date20070430
• ???? ???
• ?? ???

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midterm project

• Course Statistics in Bioinformatics
• Date20070507
• ???? ???
• ?? ???

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GEO

• In National Center for Biotechnology Information
  (NCBI)

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Figure 4

• Schematic overview of the query workflow, and how
  the various features and tools are interlinked.

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Figure 4
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GEO Database

• www.ncbi.nlm.nih.gov/geo
• The Gene Expression Omnibus (GEO) is a public
  repository(database) that archives and freely
  distributes highthroughput
• gene expression data submitted by the scientific
  community.

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Figure 1

• Schematic diagram of the relations between GEO
  Platform, Sample, DataSet, and Profiles. For each
  gene on a Platform, multiple Sample measurement
  values are generated. Related Samples constitute
  a DataSet, from which multiple gene expression
  profile entities are generated.

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Figure 2

• Screenshot of a typical DataSet record GDS877
  (Gonzalez et al., 2005). The record includes a
  summary of the experiment, links to related
  records and publications, subset designations and
  classifications, download options, and access to
  mining features such as cluster heat maps and
  Query group A vs B tool.

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Figure 3
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Figure 3

• Screenshot of Entrez GEO Profiles retrieval
  results each entity includes sequence identifier
  and DataSet information, and a tiny profile
  image. Links to other Entrez databases or related
  profiles are provided above the thumbnail image.
  The expanded profile chart depicts values (bars)
  and rank (squares) information for the crystallin
  gene across each Sample in GEO DataSet GDS877
  (Gonzalez et al., 2005). Experimental subset
  groupings are reflected in labels at foot of
  chart.

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Who can use GEO data?

• Anybody can access and download public GEO data.
  There are no login requirements. All data are in
  the public domain, but please read our data
  disclaimer.

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How can I query and analyze GEO data?

• Several features are provided to assist with the
  exploration, visualization, and analysis of GEO
  data. These include individual gene expression
  profile charts, DataSet hierarchical and
  K-means/median clusters, DataSet value
  distribution charts, a 'Query mean group A vs B'
  tool, and profile and sequence neighbor searches.
  Alternatively, full text, tab-delimited value
  data tables provided with DataSet downloads
  (available on the DataSet record, or via FTP) may
  prove suitable for upload into your favorite
  microarray analysis software package. Please see
  the overview or recent publications for more
  information.