Heyi Xiao: /* Gene level analysis */

Heyi Xiao — Wed, 16 Nov 2011 01:09:13 GMT

Gene level analysis

←Older revision		Revision as of 01:09, 16 November 2011
Line 35:		Line 35:
	==Gene level analysis==		==Gene level analysis==

-	Analysis procedure is similar to traditional gene expression arrays, i.e. summarize ~~signal~~ of an probe set (probes mapping to the same gene) into a whole-gene expression index [http://www.affymetrix.com/support/technical/whitepapers/exon_genesummary_whitepaper.pdf].	+	Analysis procedure is similar to traditional gene expression arrays, i.e. summarize signals of a probe set (probes mapping to the same gene) into a whole-gene expression index [http://www.affymetrix.com/support/technical/whitepapers/exon_genesummary_whitepaper.pdf].

	==Exon level analysis==		==Exon level analysis==

Heyi Xiao at 01:08, 16 November 2011

Heyi Xiao — Wed, 16 Nov 2011 01:08:10 GMT

←Older revision		Revision as of 01:08, 16 November 2011
Line 34:		Line 34:

	==Gene level analysis==		==Gene level analysis==
		+
		+	Analysis procedure is similar to traditional gene expression arrays, i.e. summarize signal of an probe set (probes mapping to the same gene) into a whole-gene expression index [http://www.affymetrix.com/support/technical/whitepapers/exon_genesummary_whitepaper.pdf].
		+
	==Exon level analysis==		==Exon level analysis==

Torsten Waldminghaus: add tag

Torsten Waldminghaus — Wed, 27 Feb 2008 11:28:05 GMT

add tag

←Older revision		Revision as of 11:28, 27 February 2008
Line 77:		Line 77:

	--->		--->
		+
		+
		+	[[Category:Protocol]] [[Category:In silico]] [[Category:Data analysis]]

Bill Flanagan: 1 revision(s)

Bill Flanagan — Tue, 20 Nov 2007 04:00:29 GMT

1 revision(s)

←Older revision

Revision as of 04:00, 20 November 2007

130.88.233.248: /* Data visualization */

130.88.233.248 — Wed, 25 Jul 2007 09:55:50 GMT

Data visualization

New page

{{Stub}}

=Technology overview=

Overview of the '''GeneChip® Exon and Gene Array''' Systems:
http://www.affymetrix.com/products/arrays/exon_application.affx

Affymetrix '''White Papers''':
# Alternative Transcript Analysis Methods for Exon Arrays v1.1 (pdf, 79 KB)]: [http://www.affymetrix.com/support/technical/whitepapers/exon_alt_transcript_analysis_whitepaper.pdf]
# Exon Array Background Correction v1.0 (pdf, 78 KB): [http://www.affymetrix.com/support/technical/whitepapers/exon_background_correction_whitepaper.pdf]
# Exon Probeset Annotations and Transcript Cluster Groupings v1.0 (pdf, 87 KB): [http://www.affymetrix.com/support/technical/whitepapers/exon_probeset_trans_clust_whitepaper.pdf]
# Exon Related Changes FAQ (pdf, 268 KB):[http://www.affymetrix.com/support/technical/whitepapers/exon_FAQ_related_changes_whitepapers.pdf]
# Gene Level Summarization on Exon Arrays (pdf, 747 KB):[http://www.affymetrix.com/support/technical/whitepapers/exon_genesummary_whitepaper.pdf]
# Gene Signal Estimates from Exon Arrays v1.0 (pdf, 428 KB): [http://www.affymetrix.com/support/technical/whitepapers/exon_gene_signal_estimate_whitepaper.pdf]
# Quality Assessment of Exon and Gene Arrays (pdf, 180 KB):[http://www.affymetrix.com/support/technical/whitepapers/exon_gene_arrays_qa_whitepaper.pdf]

'''Web-based seminars''', including several archived events specific for the Exon arrays can be found at:
# http://www.affymetrix.com/corporate/events/archive.affx

=Quality control=

Affymetrix Whitepaper on exon array QA:
http://www.affymetrix.com/support/technical/whitepapers/exon_gene_arrays_qa_whitepaper.pdf

'''A Core Lab Case Study''': Exon Array Challenges and Opportunities:
http://www.affymetrix.com/support/technical/appnotes/exonarray_challenge_appnote.pdf

=Array normalization=
=Data analysis=

'''Exonmap''' is a BioConductor package, currently under development, that uses the underlying data from [[X:MAP]] to support fine grained analysis of Exon array data.
http://bioinf.picr.man.ac.uk/

==Gene level analysis==
==Exon level analysis==

=Gene annotation=
=Analysis tools=

Affymetrix support pages for the human, mouse and rat Exon arrays provide '''library files''', '''annotation files''' and '''demonstration data''':
* http://www.affymetrix.com/support/technical/byproduct.affx?product=huexon-st
* http://www.affymetrix.com/support/technical/byproduct.affx?product=moexon-st
* http://www.affymetrix.com/support/technical/byproduct.affx?product=raexon-st

The Affymetrix '''Expression Console''' is avaialble to download at:
* http://www.affymetrix.com/products/software/specific/expression_console_software.affx

This page also includes a link to '''Affymetrix Power Tools''' (APT), which provides additional functionality.

Information about GeneChip compatible '''3rd party software''' for the various applications is available at:
* http://www.affymetrix.com/products/software/compatible/index.affx

'''exonmap''' - BioConductor package to analyse Exon arrays:
* http://bioconductor.org/packages/2.0/bioc/html/exonmap.html

'''dChip''' - Exon and tiling array analysis:
* http://biosun1.harvard.edu/complab/dchip/exon.htm

=Data visualization=

'''X:MAP''' - is an interactive, real-time scrollable, genome browser that shows the location of individual exon probes with respect to their target genes, transcripts and exons.

http://xmap.picr.man.ac.uk/

=References=

Wikiomics:Exon microarrays - Revision history

Heyi Xiao: /* Gene level analysis */

Heyi Xiao at 01:08, 16 November 2011

Torsten Waldminghaus: add tag

Bill Flanagan: 1 revision(s)

130.88.233.248: /* Data visualization */