BioLayout Express3D

Example Datasets

For more information see Input Formats or BioLayout Express^3D Manual.

Gene Expression (.expression)

Dataset Name	Dataset Description
GNF1M Mouse Tissue Atlas	Expression profiling of 61 mouse tissues. Data originating from Su et al., A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A. (2004). See also Genome Novartis Foundation BioGPS site and BioLayout Express^3D paper.
HGMP Mouse Tissue Atlas	Small tissue atlas dataset (26 tissues) generated in Tom Freeman’s laboratory at the HGMP-RC, Hinxton on the Affymetrix U74A chips. Some interesting tissues including good coverage of the GI tract. Published in Freilich et al., Relationship between the tissue-specificity of metazoa gene expression and the evolutionary origin and function of the proteins. Genome Biol. 6:R56 (2005).

Correlation (.matrix)

Dataset Name	Dataset Description
GNF1M Mouse tissue atlas sample-to-sample correlation	New to Update 5 and newer versions, matrix file support. Sample-to-sample Log2 correlation matrix for the GNF1M Mouse tissue atlas

Protein Interaction (.layout / .tgf / .txt)

Dataset Name	Dataset Description
Response regulators	Plot of protein families involved in transcription, that are connected together due to similarity relationships arising from promiscuous and multi-domain proteins. Generated by Dr Anton Enright, this was the original proof of concept graph that started the BioLayout development.

RNAi Phenotype Graph (.layout)

Dataset Name	Dataset Description
RNAi Phenotype Graph	Fuchs et al. performed a genome-wide RNAi screen in human cells and used quantitative descriptors derived from high-throughput imaging to generate multiparametric phenotypic profiles. They showed that profiles predicted functions of genes by phenotypic similarity. This graph represents their scores of similarity whereby genes that induce a similar cellular phentotype upon knockdown cluster together. Multiparametric phenotyping by automated imaging and computational annotation is a powerful method for functional discovery and mapping the landscape of phenotypic responses to cellular perturbations.

Dataset Name

Dataset Description

RNAi Phenotype Graph

Fuchs et al. performed a genome-wide RNAi screen in human cells and used quantitative descriptors derived from high-throughput imaging to generate multiparametric phenotypic profiles. They showed that profiles predicted functions of genes by phenotypic similarity. This graph represents their scores of similarity whereby genes that induce a similar cellular phentotype upon knockdown cluster together. Multiparametric phenotyping by automated imaging and computational annotation is a powerful method for functional discovery and mapping the landscape of phenotypic responses to cellular perturbations.

mEPN Pathway (.graphml / .mEPN)

Dataset Name	Dataset Description
Macrophage activation pathway version 1	A logic-based diagram of signalling pathways central to macrophage activation. This logically represented pathway diagram attempts to integrate these four pathways central to innate (toll-like receptor, interferon, NF-kB and apoptotic pathways) immunity using a modified version of the Edinburgh Pathway Notation. See also Raza et al., BMC Systems Biology, v.2; 2008.
Macrophage activation pathway version 2	A large scale integrated map of macrophage pathogen recognition and effector systems. The diagram includes detailed views of the toll-like receptor (TLR) pathways, other pathogen recognition systems, NF-kappa-B, apoptosis, interferon signalling, MAP-kinase cascades, MHC antigen presentation and proteasome assembly, as well as selected views of the transcriptional networks they regulate. The integrated pathway includes a total of 496 unique proteins, the complexes formed between them and the processes in which they are involved. This produces a network of 2,170 nodes connected by 2,553 edges See also BMC Systems Biology 4:63, 2010.

Dataset Name

Dataset Description

Macrophage activation pathway version 1

A logic-based diagram of signalling pathways central to macrophage activation. This logically represented pathway diagram attempts to integrate these four pathways central to innate (toll-like receptor, interferon, NF-kB and apoptotic pathways) immunity using a modified version of the Edinburgh Pathway Notation. See also Raza et al., BMC Systems Biology, v.2; 2008.

Macrophage activation pathway version 2

A large scale integrated map of macrophage pathogen recognition and effector systems. The diagram includes detailed views of the toll-like receptor (TLR) pathways, other pathogen recognition systems, NF-kappa-B, apoptosis, interferon signalling, MAP-kinase cascades, MHC antigen presentation and proteasome assembly, as well as selected views of the transcriptional networks they regulate. The integrated pathway includes a total of 496 unique proteins, the complexes formed between them and the processes in which they are involved. This produces a network of 2,170 nodes connected by 2,553 edges See also BMC Systems Biology 4:63, 2010.

Data Analysis Services

Fios Genomics Ltd. is a data analysis service company that has been founded with the help of the developers of BioLayout Express^3D. They provide cutting edge analysis of microarray data as well as data derived from other genomics platforms using conventional and network-based approaches. For more details click on the icon or contact: info@fiosgenomics.co.uk.