Systems Biology Tools
In this section you will find the link and general concepts of different tools that we are developing to help advance (Plant) Systems Biology.
Available
5) TransDetect has been released in Plant Physiology [link]. From transcriptomic data TransDetect tries to identify a set of TFs that may interact in the control of a given gene.
4) Our algorithm named FRANK has been released in NPJ systems biology.
FRANK is a large Gene Regulatory Network (GRNs) simulator that helped us to define some potential emerging properties of GRNs, and to understand rules to learn them using transcriptomics and prior knowledge on GNR (here).
FRANK output. Simulated gene expression and Large GRN:
A "click and go"online version of the FRANK algorithm (GRN simulator) written by Clement Carre is available here --> [M2SB.org]
3) Our algorithm named GeneCloud has been released in Molecular Plant.
GeneCloud explores semantic enrichments in your gene lists. It is provided through a web platform enabling click and go analysis. This platform generates data compatible with Virtual Plant formats [Katari et al. 2009].
Go play with it! --> [M2SB.org]
GeneCloud output:
2) You can also download the code [here] developed by Dr Piotr Mirowski in collaboration with Pr Shasha and Pr Lecun, that modeled GRNs responding to Nitrate. This correspond to State Space Modeling techniques described in our Genome Biol paper [here].
1) I developed a program named GeneSect, in collaboration with Pr Dennis Shasha, that determines whether the overlap between two gene lists is higher/lower than expected by chance.
The procedure is described in this paper [here] and is very useful to study signal convergence. GeneSect is available through the Virtual Plant Platform hosted at NYU (Pr Gloria Coruzzi lab) [Katari et al. Plant Phys 2009, the link to Virtual Plant is here, chose Analysis/Genesect].
GeneSect has been extensivelly used in order to probe NLP7 and CHL1/NRT1.1 effect on Primary Nitrate Response in a meta-analysis published here.
GeneSect output:
