Open Access Research article

Correlation analyses of clinical and molecular findings identify candidate biological pathways in systemic juvenile idiopathic arthritis

Xuefeng B Ling1, Claudia Macaubas2, Heather C Alexander3, Qiaojun Wen1, Edward Chen1, Sihua Peng1, Yue Sun2, Chetan Deshpande2, Kuang-Hung Pan4, Richard Lin4, Chih-Jian Lih4, Sheng-Yung P Chang3, Tzielan Lee5, Christy Sandborg5, Ann B Begovich3, Stanley N Cohen4 and Elizabeth D Mellins25*

Author Affiliations

1 Department of Surgery, Stanford University, Stanford, CA 94305, USA

2 Program in Immunology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA

3 Celera Corporation, Alameda, CA 94502, USA

4 Department of Genetics, Stanford, CA 94305, USA

5 Division of Pediatric Rheumatology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA

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BMC Medicine 2012, 10:125  doi:10.1186/1741-7015-10-125

Published: 23 October 2012

Additional files

Additional file 1:

Supplementary Figure 1. Unsupervised hierarchical clustering analysis of a subset of differentially expressed genes from SJIA flare and quiescence samples studied by microarray. Paired samples from 14 subjects at flare (red) and quiescence (green) were studied. Independent samples from the same individual are indicated by *. Each column represents a separate sample; each row represents a separate gene.

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Additional file 2:

Supplementary Table 1. The 181 immune-related genes analyzed in this study.

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Additional file 3:

Supplementary Table 2. Annotation of the 181 analyzed genes into different functional categories using PANTHER software.

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Additional file 4:

Supplementary Table 3. SJIA ESR, SJIA JC and POLY ESR related gene lists.

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Additional file 5:

Supplementary Figure 2. The fold changes in expression of the genes that differ between groups and between quartiles of ESR or JC. (A) The probability density of fold changes with the selected ESR-related genes between F1 + Q and F2 of SJIA; (B) The probability density of fold changes with the selected ESR-related genes between quartiles (the first quartile to the third quartile) of SJIA; (C) The probability density of fold changes with the selected JC-related genes between Q and F of SJIA; (D) The probability density of fold changes with the selected JC- related genes between quartiles (the first quartile to the third quartile) of SJIA; (E) The probability density of fold changes with the selected ESR-related genes between F2 and F1 + Q of POLY; (F) The probability density of fold changes with the selected ESR-related genes between quartiles (the first quartile to the third quartile) of POLY.

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