GEOMI

GEOMI is a network visualisation and analysis platform originally developed at National ICT Australia (NICTA). The program and its source code are released under the LGPL licence. For more information, please click here.

geomi_network

The SBI version of GEOMI enables visualisation of protein-protein interaction data in four-dimensions, and mapped with proteomic data as described in:

  • Li SS, Xu K, Wilkins MR (2011). Visualisation and analysis of the complexome network of Saccharomyces cerevisiae. Journal of Proteome Research, 10: 4744-56. [abstract]
  • Goel A, Li SS, Wilkins MR (2010). Four-Dimensional Visualisation and Analysis of Protein-Protein Interaction Networks. Proteomics, 11: 2672-82. [abstract]
  • Ho E, Webber R, Wilkins MR (2008). Interactive three-dimensional visualization and contextual analysis of protein interaction networks. Journal of Proteome Research, 7: 104-12. [abstract]

Download GEOMI (SBI version) [zip]
Requires Java and at least Java 3D 1.5.

GEOMI User Guide [pdf]

4-D Visualisation of Protein-Protein Interaction Networks

More videos can be viewed on our Youtube channel.

DNA mismatch repair proteins

Cell cycle gene expression data has been mapped onto DNA mismatch repair proteins MLH1, MSH2, MSH6, PMS1 and nearby interacting proteins in yeast. Green: down regulation, Red: up regulation, Black: no change in expression. Colour intensity indicates level of expression change.

Histones in the cell cycle

Cell cycle expression data mapped onto histone proteins and nearby interacting partners in yeast. Green: down regulation, Red: up regulation, Black: no change in expression. Colour intensity indicates level of expression change.

XWG Files

The XWG (XML Wilma Graph) file format is used by GEOMI to visualise networks. To view these files, move the downloaded files to the data directory in GEOMI. Make sure the directory also contains the WilmaGraph.dtd file.

YEAST (SACCHAROMYCES CEREVISIAE) REFERENCES
CMnetwork.xwg complexome network of Gavin et al. (2006) dataset [abstract]
 CMnetwork_GOprocess.xwg  complexome network, with mapped putative function
 4D_Histones.xwg  4D network of histone proteins
 4D_MLC1.xwg  4D network of hub protein MLC1
 4D_DNAMismatchRepair.xwg 4D network of DNA mismatch repair proteins
 4D_YPT52.xwg  4D network of hub protein YPT52
 4D_CentralCarbon.xwg 4D network of central carbon network metabolism proteins
 all.xwg interactome of Bertin et al. (2007) dataset [abstract]
 all_bcc.xwg biggest connected component of the above
 cytoplasm.xwg interactome within the cytoplasm
 cytoplasm_bcc.xwg biggest connected component of the cytoplasmic interactome
 mitochondria.xwg interactome within the mitochondria
 nucleus.xwg interactome within the nucleus
 nucleus_bcc.xwg biggest connected component of the nuclear interactome
HUMAN (HOMO SAPIENS) REFERENCES
cell_membrane_and_secreted.xwg interactome of cell membrane and secreted proteins
cytoskeleton.xwg interactome of cytoskeleton proteins
ER_to_Golgi.xwg interactome of ER and Golgi proteins
mitochondria.xwg interactome of mitochondria proteins
HELICOBACTER PYLORI REFERENCES
hpylori_all_annotated.xwg interactome of Rain et al. (2001) dataset [abstract]
ESCHERICHIA COLI
E_coli_protein_interaction_networks_database.zip E. coli protein interaction networks database
ecoli_all.xwg interactome of Hu et al. (2009) dataset [abstract]