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© 2004, 2005 by
Chih Long Liu

Explore Combined Datasets

Combined Datasets

The Stanford Tissue Microarray Consortium has published a number of TMA datasets that have made use of the TMA-Combiner. Here, one can access Stainfinder through the CaseXplorer web application to access the multiple replicate core images used to construct the combined dataset.


GeneXplorer is a web application written by Christian Rees that allows the exploration of large bodies of gene expression data generated by DNA microarray experiments using a web browser as its interface. GeneXplorer is based on the Windows program TreeView written by Michael Eisen. For more information on GeneXplorer, refer to the publication in BMC Bioinformatics (2004) 5:141. The PubMed listing is here.

CaseXplorer is a version of GeneXplorer that has been modified by Chih Long Liu and updated in Feb. 2005 to work with Stainfinder, an on-line program by Wijan Prapong that retrieves the corresponding spot images from an on-line digital image database.

The Combined Datasets

Below is a listing of combined datasets available, as of Feb. 2005, that have been published in the web portal of the Stanford TMA consortium. For those of you unfamiliar with CaseXplorer or its predecesor, GeneXplorer, please browse the Demonstration Dataset that was published online with our original TMA paper.

Follow the links below to explore the respective, TMA-Combined datasets. An instance of CaseXplorer will open in a new window. Clicking on the "SF" button for a given case's row will take you to Stainfinder. Upon selecting available antibodies to display, the core images from the corresonding row in CaseXplorer, along with the selected antibody stains, will display, in replicate if available. Note that not all cases represented in these datasets were combined from multiple replicates.

Tissue microarray validation of epidermal growth factor receptor and SALL2 in synovial sarcoma with comparison to tumors of similar histology.
CaseXplorer TMA Portal Site

Apo D in Soft Tissue Tumors: A Novel Marker for Dermatofibrosarcoma Protuberans
CaseXplorer TMA Portal Site

The novel marker, DOG1, is expressed ubiquitously in GI Stromal Tumors irrespective of KIT or PDGFA mutation status
CaseXplorer TMA Portal Site

Last edited by Chih Long Liu on August 15, 2005