cross-species expression viewing New for 2009 – ePl - iPlant Pods

bricklayerbelchedInternet και Εφαρμογές Web

5 Φεβ 2013 (πριν από 4 χρόνια και 6 μήνες)

117 εμφανίσεις

Overview of Bio
-
Array Resource DataViz Tools


Framework


Webservices



Expression Browser


eFP Browser


ePlant

BAR Framework


The Bio
-
Array Resource consists of numerous MySQL DBs. There is also
associated code written in Perl, Python, Ruby, and some Java for exploring
gene expression data, protein
-
protein interactions, subcellular localization,
orthologs, and protein structure


Expression data are from in
-
house or public DBs, such as GEO or the PDB,
and are stored in a MIAME
-
compliant format. Details on experimental setup,
genetic background (whether the material is from a mutant plant), etc. are
captured.


In general, we try to capture such details using standardized ontologies,
such a the Boyes system for describing the age of plants, GO etc.
Unfortunately not all of these ontologies are suitable for our needs (e.g.
Plant Ontology for now). MinSeq may be suitable for NGS data…



The BAR runs off on a Dell webserver with 2 Dual Core Xeon Processors
(2.33GHz), 4 GB of RAM, and ~80 GB of redundant disk storage.

Webservices


Many older BAR tools use direct SQL queries within the code to retrieve
data


More recently, we have implemented BioMoby based webservices to e.g.
return eFP Browser images to remote clients


We are also finding it convenient to implement lighter weight JSON
(Javascript Object Notation) webservices for internal use


this makes
development a lot faster and as a bonus provides others with direct,
computer
-
readable access to our data (expression data, protein
-
protein
interaction data, orthologs etc.)


The Bio
-
Array Resource: e
-
Northerns w. Expression Browser



Toufighi
et al.
(2005), Plant J
43
(1): 153
-
163

Experiment Identifier

Experiment Category

Control/Treatment Flag

black=treatment, white=control

Expression Levels

red=higher expression level

AGI IDs, My Gene Categories

colouring as specified by user

Functional Classification

’Barcode’
indicates GO category

Cluster Tree

co
-
expressed genes are grouped

Growth Stage
darker=older

Tissue type
e.g. green=leaf

Mutant/WT Flag

white=WT, blue=mutant

Timecourse
darker=later

Protein Interactions
if present

Looking at
DHS3

response with the eFP Browser



Data Source
to choose different
AtGenExpress projects and other

projects, e.g. Birnbaum set.

Expression Level scale

red=higher expression level

Expression Level distribution

shows how maximum level
compares with all other genes,
and maximum level in any set

Clickable tissues
hyperlink to
the NASCArrays, GEO or
literature record for the sample

Mode
allows viewing in Absolute,
Relative, and Compare modes

Signal Threshold
to set a
maximum for colour scale

Winter et al. (2007) PLoS One
2
(8): e718




AtGenExpress

data


Browser

array_element_name locus

(from affy_ATH1_array_elements
-
2006
-
01
-
06.txt at TAIR)

261585_at AT1G01010

261568_at AT1G01030

261584_at AT1G01040

261579_at AT1G01050

261569_at AT1G01060

261576_at AT1G01070

261577_at AT1G01080

261583_at AT1G01090

261578_at AT1G01100

261580_at AT1G01110

261570_at AT1G01120

261575_at AT1G01130



At
-
TAX

data from

Tuebingen w.


webservices

New for 2008


cross
-
species expression viewing







New for 2009


ePl : seamless viewing of km
-

to nm
-
scale data

David Di Biase, Geoff Fucile, Shokoufeh Kohdabandeh, Hardeep Nahal

3DDI.org

BAR.utoronto.ca/ePlant

NGS mRNA
-
seq data could be displayed with BAR tools