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iPlant Omics Data Analysis and
Visualization System
iPlant Viz Team,
Lecong Zhou, demo, 7-8-10
GenAV
--Analysis & Visualization of Affymetrix Gene Expression Data
G
AffyGen
Analyser ®
input
U
User
output
I
GO®
Analyser
BiNGO
(Cytoscape
plugin)
Enriched
GOterms
Output
(text files,
graphs)
GeneMANIA
(Cytoscape
plugin)
Gene
List(s)
GenAV
--Analysis & Visualization of Affymetrix Gene Expression Data
G
AffyGen
Analyser ®
input
U
User
output
I
GO®
Analyser
BiNGO
(Cytoscape
plugin)
Enriched
GOterms
Output
(text files,
graphs)
GeneMANIA
(Cytoscape
plugin)
Gene
List(s)
AffyGenAnalyser
•GEO #
(or alternatives)
R
CEL files
•Design file
QC
PMAcalls
RMA
present genes
QCreport(.pdf)
expr values of
present genes
Summary(.txt)
limma
summarizing
DEG
sets(.txt
files)
GOanalyser
ViVA
GOanalyser
DEG sets
Goanalyser.R(GO
hyperGAll)
Args:
Idtype, FDR, cutoff
•Design file
Outputs (.txt, with
GOid, At#s, p-values,
etc)
Multi-lists
organisor.pl
Heatmap.R
•Added FDR option
“qvalue”.
•Heatmap uses converted
p-values (cPval, negative
log10). Show the top 50
terms with highest sum
of cPvals of all the listed
contrasts.
heatmaps(.pdf)
Args:
GOterm(s)
DEGs [At#]
GeneMANIA
Notes:
• Goanalyser is based on
GOhyperGAll package,
which is for “Global
Hypergeometric Test
Using Custom Gene-toGO Mappings Plus GO
Slim Analysis” (Thomas
Girke, UC Riverside)
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