This site is dedicated to the network analyses of cancer transcriptomics data. In particular we provide pre-analysed network graphs of a number of publically available transcriptomics studies derived from a diverse range of cancers and the meta-analysis thereof. The initial datasets provided here have been described in a paper by Doig et al (submitted)*. Also provided here are the results of the meta-analyses of this data which has identified the expression signature of the major "stromal components" common to all tumours regardless of their histogenesis.

Doig T.N., Hume D.A., Theocharidis T., Goodlad, J.R., Gregory C.D. and Freeman T.C. 3D Network Analysis of the Cellular and Pathway Signatures in Cancer Transcriptomics Data (2013)

Analysis makes use of the tool Biolayout Express3D to lay out networks of co-expressed genes in a 3D graph format allowing exploration of the transcriptional signatures in a wide variety of cancers.

Meta-analysis of 6 cancer datasets
Six cancer datasets comprising gene expression date from more than a thousand individual patients were used to create a network of common signatures conserved across all datasets examined. Clusters within the graph have been assigned names based on analysis of the genes contained within the clusters. In this meta-analysis the main classes of clusters identified relate to "Housekeeping" functions, cell cycle and related functions and the tumour stroma. Start BioLayout Express 3D
Database
Reference
Reference
(PMID)
Tumor
Types
Cases
Analysed
Affymetrix
U133
Platforms
Graph
Size
(nodes)
Graph
Size
(edges)
GSE11318Lenz et al.
(18765795)
DLBCL19,850Plus 2.019,850614,273
 

A dataset consisting of 194 cases of Diffuse Large B cell lymphoma. These are stratified by tumour subtype (Activated B cell (ABC)-like, Germinal Centre B cell (GCB)-like, Primary mediastinal B cell lymphoma (PMBL) and unclassifiable) and by sex and patient outcome. Annotation from the clusters derived in the meta-analysis has been overlaid on the graph.

GSE1456Pawitan et al.
(16280042)
Breast carcinoma19,246A & B19,246559,761
 

A dataset of 134 cases of primary breast carcinoma derived from a single hospital over a 3 year period. The data is stratified by tumour type, grade and noverlaid with the annotation derived from the meta-analysis.

GSE9891Tothill et al.
(18698038)
Ovarian (epithelial) carcinoma19,415Plus 2.019,415268,471
 

A dataset of 256 cases of Ovarian epithelial carcinoma and the closely related Fallopian tube and primary peritoneal carcinomas from the Australian Ovarian Cancer Study. These were stratified by malignant potential (malignant vs low malignant potential), histological type, grade, stage and primary site. Annotation from the meta-analysis was overlaid on the graph.

GSE3218Korkola et al.
(16424014)
Testicular germ cell tumours18,934A & B18,934954,082
 

A dataset of 86 Testicular germ cell tumours from the Memorial Sloan-Kettering Cancer Center. These were stratified on the basis of pure or mixed histological types, then by the individual tumour subtypes using the WHO classification. Annotation from the meta-analysis was overlaid on the graph.

GSE13294Jorissen et al.
(19088021)
Colorectal carcinoma22,687Plus 2.022,687725,467
 

Data from 150 patients with colorectal carcinoma which was stratified into microsatellite stable and microsatellite unstable cancers. Annotation from the meta-analysis was overlaid on the the graph.

caArray/rembr-00037REMBRANT – Repository for Molecular Brain Neoplasia DataPrimary CNS tumours23,015Plus 2.023,015623,591
 

Data from 253 primary CNS tumours available from REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT). These were stratified by tumour subtype, WHO grade and sex. The graph was overlaid with annotation from the meta-analysis.

GSE7553Riker et al.
(18442402)
Skin tumours19,623A & B19,623600,143
 

Seventy-seven cases of skin cancer, mostly primary melanomas, but also including squamous cell carcinoma, basal cell carcinoma and a small number of metastatic melanomas. These were stratified by primary tumour type and primary or metastatic disease. This independent dataset was not used in the generation of the “conserved signatures” in the meta-analysis. The annotation from the meta-analysis overlaid on this dataset demonstrates that these represent true conserved signatures.

GSE17920Steidl et al.
(20220182)
Hodgkin lymphoma13,846Plus 2.013,846521,593
 

A dataset of 131 cases of Hodgkin Lymphoma which were stratified by treatment success or failure. Again, this dataset was not used in generating the conserved signatures in the meta-analysis and the annotation from the meta-analysis is overlaid on the graph.

GSE15459Ooi et al.
(19798449)
Gastric cancer15,747Plus 2.015,747719,884
 

A dataset of 200 cases of gastric cancer from a Singaporean cohort. These were not stratified on the basis of clinical data. This dataset was not used in the meta-analysis and the annotation from that analysis is overlaid on the graph.

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