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E-GEOD-12630.idf

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					            Gene
Investigation Title expression profiles of poorly differentiated, undifferentiated and metastatic cancers
            Gene expression
Comment[Submitted Name] profiles of poorly differentiated, undifferentiated and metastatic cancers
            transcription profiling by array
Experimental Design
            EFO
Experimental Design Term Source REF
Comment[SecondaryAccession]
            GSE12630
Comment[SecondaryAccession]
            2009-03-28
Comment[ArrayExpressReleaseDate]
            4
Comment[AEMIAMESCORE]
            10.1200/JCO.2008.17.9762
Comment[Publication DOI]
            E-GEOD-12630
Comment[ArrayExpressAccession]
            2010-09-10 06:21:08 Last Changed Rev: 13833
Comment[MAGETAB TimeStamp_Version]
            ANATOMICAL   AGE
Experimental Factor NameSITES GENDER TNM
            Anatomical age
Experimental Factor Type  sites      gender      TNM
Experimental Factor Term Source REF
            Buturovic
Person Last Name
            Ljubomir
Person First Name
Person Mid Initials
Person Email
Person Phone
Person Fax
            Application Development, Pathwork Diagnostics, 1196 Borregas Avenue, Sunnyvale, CA, USA
Person Address
            Pathwork Diagnostics
Person Affiliation
Person Rolessubmitter
            The MGED Ontology
Person Roles Term Source REF
Quality Control Type
Quality Control Term Source REF
Replicate Type
Replicate Term Source REF
Normalization Type
Normalization Term Source REF
Date of Experiment
            2009-03-28
Public Release Date
PubMed ID19332734
            DOI
Publication 19332734
            Author List
Publication Monzon FA, Lyons-Weiler M, Buturovic LJ, Rigl CT, Henner WD, Sciulli C, Dumur CI, Medeiros F, Anderson GG
            Title
Publication Multicenter validation of a 1,550-gene expression profile for identification of tumor tissue of origin.
            Status
Publication journal_article
            Status Term Source
Publication The MGED OntologyREF
             Description
ExperimentThe tissue of origin form metastatic tumors is sometimes difficult to identify from clinical and histologic information.
            P-GSE12630-3
Protocol Name            P-GSE12630-4P-GSE12630-5P-GSE12630-6 P-GSE12630-7P-GSE12630-2P-GSE12630-1
            nucleic_acid_extraction
Protocol Type            labeling                image_aquisition
                                     hybridization                        bioassay_data_transformation
                                                              feature_extraction      bioassay_data_transformation
            Qiagen RNEasy kit        Affymetrix GeneChip labeling protocol synthesis
                                                 Affymetrix GeneChip standard = <br>VALUEet normalized normalized No. 1)
                                                              Pathwork standardization (Dumur = al., JMD = signal
                                                                           cDNA       ID_REF
Protocol Description Affymetrix GeneChip 1-cycle IVT standardand ID_REFprotocol kits= <br>VALUE2008, Vol. 10, values
Protocol Parameters
Protocol Hardware
Protocol Software
Protocol Contact
            The MGED The  Ontology Ontology                                Ontology Ontology
Protocol Term Source REF MGED The MGED Ontology The MGED The MGED The MGED Ontology
SDRF File E-GEOD-12630.sdrf.txt
            ncbitax
Term Source Name The MGED ArrayExpressOntology                mo          EFO         The MGED Ontology
            http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html
Term Source File                     http://www.ebi.ac.uk/arrayexpress http://www.ebi.ac.uk/efo/
                                                              http://mged.sourceforge.net/ontologies/MGEDontology.php
                         http://mged.sourceforge.net/ontologies/MGEDontology.php      http://mged.sourceforge.net/ontologies/MGED
Term Source Version
 yvale, CA, USA




mur CI, Medeiros F, Anderson GG
mor tissue of origin.


m clinical and histologic information. Gene expression signatures are one potential method for identifying the tissue of origin. In the developm

 data_transformation
 <br>VALUE = normalized values




 d.sourceforge.net/ontologies/MGEDontology.php
g the tissue of origin. In the development of algorithms to identify tissue of origin, a collection of human tumor metastatic specimens with kno
tumor metastatic specimens with known primary sites or primary tumors with poor differentiation are very useful in identifying gene expressio
y useful in identifying gene expressions signatures that can classify unknown specimens as to the tissue of origin. Here we describe a serie
e of origin. Here we describe a series of 276 such tumor specimens used for this purpose. The specimens are poorly differentiated, undiffere
ns are poorly differentiated, undifferentiated and metastatic specimens from tumors of the following types/tissues of origin: breast, liver, non
es/tissues of origin: breast, liver, non-Hodgkin's lymphoma, non-small cell lung cancer, ovary, testicular germ cell, thyroid, kidney, pancreas,
germ cell, thyroid, kidney, pancreas, colorectal cancer, soft tissue sarcoma, bladder, gastric cancer, prostate and melanoma. This data com
state and melanoma. This data combined with other series (GSE2109) was used to validate a proprietary

				
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