ONTOLOGY SOURCE REFERENCE
Term Source Name	"CHEBI"	"EFO"	"BTO"	"NCBITAXON"	"SNOMEDCT"	"DOID"	
Term Source File	"http://data.bioontology.org/ontologies/CHEBI"	"http://data.bioontology.org/ontologies/EFO"	"http://data.bioontology.org/ontologies/BTO"	"http://data.bioontology.org/ontologies/NCBITAXON"	"http://data.bioontology.org/ontologies/SNOMEDCT"	"http://data.bioontology.org/ontologies/DOID"	
Term Source Version	"78"	"111"	"20"	"2"	"7"	"399"	
Term Source Description	"Chemical Entities of Biological Interest Ontology"	"Experimental Factor Ontology"	"BRENDA Tissue and Enzyme Source Ontology"	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"Systematized Nomenclature of Medicine - Clinical Terms"	"Human Disease Ontology"	
INVESTIGATION
Investigation Identifier	""
Investigation Title	""
Investigation Description	""
Investigation Submission Date	""
Investigation Public Release Date	""
Comment [Created with configuration]	""
Comment [Last Opened With Configuration]	""
Comment[Created With Configuration]	""
Comment[Last Opened With Configuration]	""
INVESTIGATION PUBLICATIONS
Investigation PubMed ID	""
Investigation Publication DOI	""
Investigation Publication Author List	""
Investigation Publication Title	""
Investigation Publication Status	""
Investigation Publication Status Term Accession Number	""
Investigation Publication Status Term Source REF	""
INVESTIGATION CONTACTS
Investigation Person Last Name	""
Investigation Person First Name	""
Investigation Person Mid Initials	""
Investigation Person Email	""
Investigation Person Phone	""
Investigation Person Fax	""
Investigation Person Address	""
Investigation Person Affiliation	""
Investigation Person Roles	""
Investigation Person Roles Term Accession Number	""
Investigation Person Roles Term Source REF	""
STUDY
Study Identifier	"E-GEOD-12021"
Study Title	"Transcription profiling of human rheumatoid arthritis patients to identify inter-individual and gene-specific variance in the synovial membrane"
Study Description	"Background. Rheumatoid arthritis (RA) is a chronic inflammatory and destructive joint disease, characterized by overexpression of pro-inflammatory/-destructive genes and other activating genes (e.g., proto-oncogenes) in the synovial membrane (SM). The gene expression in disease is often characterized by significant inter-individual variances via specific synchronization/desynchronization of gene expression. To elucidate the contribution of the variance to the pathogenesis of disease, expression variances were tested in SM samples of RA patients, osteoarthritis (OA) patients, and normal controls (NC). Results. For the comparison between RA and NC, 568 genes with significantly different variances in the 2 groups (p < 0.05; Bonferroni/Holm corrected Brown-Forsythe version of the Levene-Test) were selected. For the comparison between RA and OA, 333 genes were selected. Using the Kyoto encyclopedia of genes and genomes (KEGG), 10 pathways/complexes significantly affected by higher gene expression variances were identified in RA compared to NC, including cytokine-cytokine receptor interactions, the TGF-pathway, and anti-apoptosis. Compared to OA, 3 pathways with significantly higher variances were identified in RA (e.g., B cell receptor signaling, VEGF signaling). Functionally, the majority of the identified pathways is involved in the regulation of inflammation, proliferation, cell survival, and angiogenesis. Conclusion. In RA, a number of disease-relevant or even disease-specific pathways/complexes are characterized by broad intra-group, inter-individual expression variances. This indicates that RA pathogenesis in different individuals may depend to a lesser extent on common alterations of the expression of specific key genes, but on individual-specific alterations of different genes resulting in common disturbances of key pathways. Experiment Overall Design: Expression variances were tested in synovial membrane samples of rheumatoid arthritis patients, osteoarthritis patients, and normal controls (see publication for further details)."
Comment[Study Grant Number]	""
Comment[Study Funding Agency]	""
Study Submission Date	""
Study Public Release Date	"2008-10-25"
Study File Name	"s_E-GEOD-12021_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"unknown_experiment_design_type"	"transcription profiling by array"
Study Design Type Term Accession Number	""	""
Study Design Type Term Source REF	""	""
STUDY PUBLICATIONS
Study PubMed ID	"18721452"
Study Publication DOI	"18721452"
Study Publication Author List	"Hummert Huber, Pohlers Gausmann, Guthke Koczan,  Kinne"
Study Publication Title	"Identification of intra-group, inter-individual, and gene-specific variances in mRNA expression profiles in the rheumatoid arthritis synovial membrane."
Study Publication Status	"journal_article"
Study Publication Status Term Accession Number	""
Study Publication Status Term Source REF	""
STUDY FACTORS
Study Factor Name	"disease"	"Current NSAID"	"Current NSARD"	"current steroid"	"current drug"
Study Factor Type	"disease"	"drug"	"drug"	"drug"	"drug"
Study Factor Type Term Accession Number	""	""	""	""	""
Study Factor Type Term Source REF	""	""	""	""	""
STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-12021_GeneChip_assay.txt"
Study Assay Measurement Type	"transcription profiling"
Study Assay Measurement Type Term Accession Number	""
Study Assay Measurement Type Term Source REF	""
Study Assay Technology Type	"DNA microarray"
Study Assay Technology Type Term Accession Number	""
Study Assay Technology Type Term Source REF	""
Study Assay Technology Platform	""
STUDY PROTOCOLS
Study Protocol Name	"P-G12021-11"	"P-G12021-1"	"P-G12021-6"	"P-G12021-12"	"P-G12021-5"	"P-G12021-7"	"P-G12021-14"	"P-G12021-8"	"P-G12021-10"	"P-G12021-13"	"P-G12021-9"	"P-G12021-4"	"P-G12021-3"	"P-G12021-2"
Study Protocol Type	"specified_biomaterial_action"	"specified_biomaterial_action"	"specified_biomaterial_action"	"specified_biomaterial_action"	"specified_biomaterial_action"	"specified_biomaterial_action"	"specified_biomaterial_action"	"specified_biomaterial_action"	"specified_biomaterial_action"	"specified_biomaterial_action"	"specified_biomaterial_action"	"specified_biomaterial_action"	"nucleic_acid_extraction"	"labeling"
Study Protocol Type Term Accession Number	""	""	""	""	""	""	""	""	""	""	""	""	""	""
Study Protocol Type Term Source REF	""	""	""	""	""	""	""	""	""	""	""	""	""	""
Study Protocol Description	"NSARD, prednisolone"	"none"	"NSARD"	"COX-2 inhibitor, prednisolone, quensyl"	"NSARD, azulfidine, prednisolone"	"NSARD, prednisolone, MTX"	"NSAID, prednisolone, Tilidin"	"NSARD, azulfidine, prednisolone, MTX"	"prednisolone, MTX"	"NSAID"	"NSARD, prednisolone, azulfidine, MTX"	"NSARD, azulfidine, prednisolone,"	"according RNeasy Kit, Qiagen"	"according to supplier's instructions, Affymetrix"
Study Protocol URI	""	""	""	""	""	""	""	""	""	""	""	""	""	""
Study Protocol Version	""	""	""	""	""	""	""	""	""	""	""	""	""	""
Study Protocol Parameters Name	""	""	""	""	""	""	""	""	""	""	""	""	""	""
Study Protocol Parameters Name Term Accession Number	""	""	""	""	""	""	""	""	""	""	""	""	""	""
Study Protocol Parameters Name Term Source REF	""	""	""	""	""	""	""	""	""	""	""	""	""	""
Study Protocol Components Name	""	""	""	""	""	""	""	""	""	""	""	""	""	""
Study Protocol Components Type	""	""	""	""	""	""	""	""	""	""	""	""	""	""
Study Protocol Components Type Term Accession Number	""	""	""	""	""	""	""	""	""	""	""	""	""	""
Study Protocol Components Type Term Source REF	""	""	""	""	""	""	""	""	""	""	""	""	""	""
STUDY CONTACTS
Study Person Last Name	"Huber"
Study Person First Name	"René"
Study Person Mid Initials	""
Study Person Email	"Rene.Huber@med.uni-jena.de"
Study Person Phone	""
Study Person Fax	""
Study Person Address	"Research, Institute for Clinical Chemistry, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, 30625, Germany"
Study Person Affiliation	"Hannover Medical School"
Study Person Roles	"submitter"
Study Person Roles Term Accession Number	""
Study Person Roles Term Source REF	""
Comment[Study Person REF]	""