Screenshots
Qualitative modelling of nitrogen uptake regulation in Arabidopsis (Source: Artem Lysenko)
Protein-protein interaction (PPI) data from the TAIR curated PPI and IntAct can be combined
with the co-expression data from the ATTEDII database using Ondex.
Positive co-expression by itself does not appear to be a strong indicator of interaction.
However, it is a good indicator of interacting proteins that are in the same complex.
In the graph below, these are clusters of nodes where all of them interact with each other.
Some of these clusters also have positively correlated expression between all members.
| Open databases |
TAIR curated PPI, IntAct, ATTEDII |
| Experimental dataset |
None |
| Visualisation |
Degree (concept size) and betweenness (concept colour) centralities for part of the Arabidopsis interaction network |
The colour-coded annotation used here shows how influential some concepts – proteins in this case – are within the network.
The colour legend is based on the rainbow scale, where purple is low and red is high.
Context of changes in gene expression with pathways (Source: Matthew Hindle)
An Ondex pipeline was developed for analysis of time-course microarray data on drought stress in three cultivars of durum wheat.
Ondex was used to integrate databases that contained metabolic pathways and functional protein annotations in plant model organisms
and closely related species to wheat.
Sequence alignment tools, which are closely integrated into Ondex, were used to identify putative functional orthologs to
genes on the Affymetrix microarray chip.
A combination of statistical analysis and graph visualization techniques in the Ondex Visualization Toolkit (OVTK)
was used to dissect the temporal changes in gene and pathway regulation.
| Open databases |
KEGG, AraCyc, TAIR, TIGR, GRAMENE, UniProt |
| Experimental dataset |
Wheat Affymetrix microarray chip (Dr Dimah Habash, Rothamsted Research) |
| Visualisation |
Enzymes significantly regulated within the Jasmonic acid biosynthesis pathway |
An alternative visualisation of the analysis of time-course microarray data on drought stress in three cultivars of durum wheat.
This representation shows the enzymes significantly up/down regulated within the Jasmonic acid biosynthesis pathway
after two days of stress on one of the cultivars.
Blue squares represent ortholog proteins, blue circles reactions and pink squares pathways.
Squares are target sequences, their size is proportional to expression and their colour depends on regulation since
the pre-stress point zero. Red shows up regulation, green down, while yellow means the regulation was not significant.
Black nodes indicate that the target sequence was not significantly expressed in any time point.
More screenshots available HERE
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