ONTOLOGY SOURCE REFERENCE
Term Source Name	"HP"	"CHEBI"	"BTO"	"EFO"	"NCBITAXON"	"OMIM"	"PR"	"SNOMEDCT"	"DOID"	
Term Source File	"http://data.bioontology.org/ontologies/HP"	"http://data.bioontology.org/ontologies/CHEBI"	"http://data.bioontology.org/ontologies/BTO"	"http://data.bioontology.org/ontologies/EFO"	"http://data.bioontology.org/ontologies/NCBITAXON"	"http://data.bioontology.org/ontologies/OMIM"	"http://data.bioontology.org/ontologies/PR"	"http://data.bioontology.org/ontologies/SNOMEDCT"	"http://data.bioontology.org/ontologies/DOID"	
Term Source Version	"408"	"78"	"20"	"111"	"2"	"4"	"56"	"7"	"399"	
Term Source Description	"Human Phenotype Ontology"	"Chemical Entities of Biological Interest Ontology"	"BRENDA Tissue and Enzyme Source Ontology"	"Experimental Factor Ontology"	"National Center for Biotechnology Information (NCBI) Organismal Classification"	"Online Mendelian Inheritance in Man"	"Protein Ontology"	"Systematized Nomenclature of Medicine - Clinical Terms"	"Human Disease Ontology"	
INVESTIGATION
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INVESTIGATION PUBLICATIONS
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STUDY
Study Identifier	"E-GEOD-8650"
Study Title	"Transcription profiling of PBMCs from patients with several autoimmune inflammatory diseases or similar disorders and healthy controls. Some patients are on Celebrex or steroids. [original title: Transcription profiling of human blood leukocytes to diagnose systemic onset juvenile idiopathic arthritis and follow IL-1 blockade]"
Study Description	"123 patients, duplicate samples. [original description: Systemic onset Juvenile Idiopathic Arthritis (SoJIA) represents up to 20% of Juvenile Idiopathic Arthritis (JIA). We have previously reported that this disease is Interleukin 1 (IL1)-mediated, and that IL-1 blockade results in clinical remission in the majority of patients. The diagnosis of SoJIA, however, still relies on clinical findings as no specific diagnostic tests are available, which leads to delays in the initiation of specific therapy. To identify specific diagnostic markers, we analyzed gene expression profiles in 19 pediatric patients with SoJIA during the systemic phase of the disease (fever and/or arthritis), 25 SoJIA patients with no systemic symptoms (arthritis only or no symptoms), 39 healthy controls, 94 pediatric patients with acute viral and bacterial infections (available under GSE6269), 38 pediatric patients with Systemic Lupus Erythematosus (SLE), and 6 patients with a second IL-1 mediated disease known as PAPA syndrome. Statistical group comparison and class prediction identified genes differentially expressed in SoJIA patients compared to healthy children. These genes, however, were also changed in patients with acute infections and SLE. By performing an analysis of significance across all diagnostic groups, we generated a list of 88 SoJIA-specific genes (p<0.01 in SoJIA and >0.5 in all other groups). A subset of 12/88 genes permitted us to accurately classify an independent test set of SoJIA patients with systemic disease. We were also able to identify a group of transcripts that changed significantly in patients undergoing IL-1 blockade. Thus, analysis of transcriptional signatures from SoJIA blood leukocytes can help distinguishing this disease from other febrile illnesses and assessing response to therapy. Availability of accurate diagnostic markers for SoJIA patients may allow prompt initiation of effective therapy and prevention of long-term disabilities. Experiment Overall Design: 123 RNA samples extracted from PBMCs were studied. For more details on the clinical information, please refer to the paper (PudMed ID 17724127).]"
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Study Public Release Date	"2008-06-16"
Study File Name	"s_E-GEOD-8650_study_samples.txt"
STUDY DESIGN DESCRIPTORS
Study Design Type	"unknown_experiment_design_type"	"transcription profiling by array"
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STUDY PUBLICATIONS
Study PubMed ID	"17724127"
Study Publication DOI	"10.1084/jem.20070070"
Study Publication Author List	"Allantaz F, Chaussabel D, Stichweh D, Bennett L, Allman W, Mejias A, Ardura M, Chung W, Smith E, Wise C, Palucka K, Ramilo O, Punaro M, Banchereau J, Pascual V."
Study Publication Title	"Blood leukocyte microarrays to diagnose systemic onset juvenile idiopathic arthritis and follow the response to IL-1 blockade."
Study Publication Status	"Published"
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STUDY FACTORS
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STUDY ASSAYS
Study Assay File Name	"a_E-GEOD-8650_GeneChip_assay.txt"
Study Assay Measurement Type	"transcription profiling"
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Study Assay Technology Type	"DNA microarray"
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STUDY PROTOCOLS
Study Protocol Name	"P-G8650-2"	"P-G8650-1"	"Affymetrix:Protocol:Hybridization-Unknown"	"P-AFFY-6"
Study Protocol Type	"nucleic_acid_extraction"	"labeling"	"hybridization"	"feature_extraction"
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Study Protocol Description	"RNeasy Mini"	"Biotinylated cRNA were prepared according to the standard Affymetrix protocol."	"Title: Affymetrix Generic Hybridization. Description: "	"Title: Affymetrix CEL analysis. Description: "
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Study Protocol Components Name	""	""	"MicroArraySuite 5.0"	"MicroArraySuite 5.0"
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STUDY CONTACTS
Study Person Last Name	"Allantaz"
Study Person First Name	"Florence"
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Study Person Email	"florenca@baylorhealth.edu"
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Study Person Address	"Baylor Institute for Immunology Research, 3434 Live Oak Street, Dallas, 75204, USA"
Study Person Affiliation	"Baylor Institute for Immunology Research"
Study Person Roles	"submitter"
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