title: The Stanford Tissue Microarray Database.
abstract: The Stanford Tissue Microarray Database (TMAD; http://tma.stanford.edu) is a public resource for disseminating annotated tissue images and associated expression data. Stanford University pathologists, researchers and their collaborators worldwide use TMAD for designing, viewing, scoring and analyzing their tissue microarrays. The use of tissue microarrays allows hundreds of human tissue cores to be simultaneously probed by antibodies to detect protein abundance (Immunohistochemistry; IHC), or by labeled nucleic acids (in situ hybridization; ISH) to detect transcript abundance. TMAD archives multi-wavelength fluorescence and bright-field images of tissue microarrays for scoring and analysis. As of July 2007, TMAD contained 205 161 images archiving 349 distinct probes on 1488 tissue microarray slides. Of these, 31 306 images for 68 probes on 125 slides have been released to the public. To date, 12 publications have been based on these raw public data. TMAD incorporates the NCI Thesaurus ontology for searching tissues in the cancer domain. Image processing researchers can extract images and scores for training and testing classification algorithms. The production server uses the Apache HTTP Server, Oracle Database and Perl application code. Source code is available to interested researchers under a no-cost license.
authors.affiliation: Department of Biochemistry, Stanford University School of Medicine, Howard Hughes Medical Institute, Stanford, CA, USA. bobm@stanford.edu
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Marinelli
authors.forename: Kelli
authors.initials: K
authors.lastname: Montgomery
authors.forename: Chih Long
authors.initials: CL
authors.lastname: Liu
authors.forename: Nigam H
authors.initials: NH
authors.lastname: Shah
authors.forename: Wijan
authors.initials: W
authors.lastname: Prapong
authors.forename: Michael
authors.initials: M
authors.lastname: Nitzberg
authors.forename: Zachariah K
authors.initials: ZK
authors.lastname: Zachariah
authors.forename: Gavin J
authors.initials: GJ
authors.lastname: Sherlock
authors.forename: Yasodha
authors.initials: Y
authors.lastname: Natkunam
authors.forename: Robert B
authors.initials: RB
authors.lastname: West
authors.forename: Matt
authors.initials: M
authors.lastname: van de Rijn
authors.forename: Patrick O
authors.initials: PO
authors.lastname: Brown
authors.forename: Catherine A
authors.initials: CA
authors.lastname: Ball
mesh_terms: D030541:Databases, Genetic; D006801:Humans; D007150:Immunohistochemistry; D017403:In Situ Hybridization; D020407:Internet; D011506:Proteins / Q000032:analysis; D012333:RNA, Messenger / Q000032:analysis; D012984:Software; D046888:Tissue Array Analysis; D014584:User-Computer Interface
chemical_list: D011506:Proteins; D012333:RNA, Messenger