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| Status |
Public on Sep 02, 2008 |
| Title |
Identification of inter-individual and gene-specific variances in mRNA expression profiles in the RA SM |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
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.
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| Overall design |
Expression variances were tested in synovial membrane samples of rheumatoid arthritis patients, osteoarthritis patients, and normal controls (see publication for further details).
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| Contributor(s) |
Huber R, Hummert C, Gausmann U, Pohlers D, Koczan D, Guthke R, Kinne RW |
| Citation(s) |
18721452 |
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| Submission date |
Jul 07, 2008 |
| Last update date |
Aug 10, 2018 |
| Contact name |
René Huber |
| E-mail(s) |
huber.rene@mh-hannover.de
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| Phone |
+49 511 5322529
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| Fax |
+49 511 5328614
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| Organization name |
Hannover Medical School
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| Department |
Institute for Clinical Chemistry
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| Lab |
Research
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| Street address |
Carl-Neuberg-Str. 1
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| City |
Hannover |
| State/province |
Lower Saxony |
| ZIP/Postal code |
30625 |
| Country |
Germany |
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| Platforms (2) |
| GPL96 |
[HG-U133A] Affymetrix Human Genome U133A Array |
| GPL97 |
[HG-U133B] Affymetrix Human Genome U133B Array |
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| Samples (57)
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| GSM302859 |
Normal, synovial membrane patient EB 125 (U133A) |
| GSM302864 |
Normal, synovial membrane patient EB 184 (U133A) |
| GSM302866 |
Normal, synovial membrane patient EB188 (U133A) |
| GSM302870 |
Normal, synovial membrane patient EB228 (U133A) |
| GSM302872 |
Rheumatoid arthritis, synovial membrane patient EB20 (U133A) |
| GSM302874 |
Rheumatoid arthritis, synovial membrane patient EB20 (U133B) |
| GSM302876 |
Osteoarthrisits, synovial membrane patient EB21 (U133A) |
| GSM302878 |
Osteoarthritis, synovial membrane patient EB21 (U133B) |
| GSM302880 |
Osteoarthritis, synovial membrane patient EB24 (U133A) |
| GSM302881 |
Osteoarthritis, synovial membrane patient EB24 (U133B) |
| GSM302882 |
Rheumatoid arthritis, synovial membrane patient EB27 (U133A) |
| GSM302895 |
Rheumatoid arthritis, synovial membrane patient EB27 (U133B) |
| GSM302896 |
Rheumatoid arthritis, synovial membrane patient EB30 (U133A) |
| GSM302897 |
Rheumatoid arthritis, synovial membrane patient EB30 (U133B) |
| GSM302900 |
Rheumatoid arthritis, synovial membrane patient EB35 (U133A) |
| GSM302905 |
Rheumatoid arthritis, synovial membrane patient EB35 (U133B) |
| GSM302924 |
Rheumatoid arthritis, synovial membrane patient EB40 (U133A) |
| GSM302926 |
Rheumatoid arthritis, synovial membrane patient EB40 (U133B) |
| GSM302927 |
Rheumatoid arthritis, synovial membrane patient EB41 (U133A) |
| GSM302929 |
Rheumatoid arthritis, synovial membrane patient EB41 (U133B) |
| GSM302930 |
Osteoarthritis, synovial membrane patient EB54 (U133A) |
| GSM302932 |
Osteoarthritis, synovial membrane patient EB54 (U133B) |
| GSM302933 |
Rheumatoid arthritis, synovial membrane patient EB56 (U133A) |
| GSM302934 |
Rheumatoid arthritis, synovial membrane patient EB56 (U133B) |
| GSM302943 |
Rheumatoid arthritis, synovial membrane patient EB74 (U133A) |
| GSM302944 |
Rheumatoid arthritis, synovial membrane patient EB74 (U133B) |
| GSM303326 |
Osteoarthritis, synovial membrane patient EB90 (U133A) |
| GSM303339 |
Osteoarthritis, synovial membrane patient EB90 (U133B) |
| GSM303341 |
Osteoarthritis, synovial membrane patient EB94 (U133A) |
| GSM303355 |
Osteoarthritis, synovial membrane patient EB94 (U133B) |
| GSM303356 |
Osteoarthritis, synovial membrane patient EB97 (Affymetrx U133A) |
| GSM303357 |
Osteoarthritis, synovial membrane patient EB97 (U133B) |
| GSM303358 |
Osteoarthritis, synovial membrane patient EB99 (Affymetrx U133A) |
| GSM303359 |
Osteoarthritis, synovial membrane patient EB99 (Affymetrx U133B) |
| GSM303360 |
Osteoarthritis, synovial membrane patient EB100 (Affymetrx U133A) |
| GSM303361 |
Osteoarthritis, synovial membrane patient EB100 (Affymetrx U133B) |
| GSM303362 |
Osteoarthritis, synovial membrane patient EB104 (Affymetrx U133A) |
| GSM303363 |
Osteoarthritis, synovial membrane patient EB104 (U133B) |
| GSM303364 |
Rheumatoid arthritis, synovial membrane patient EB108 (U133A) |
| GSM303365 |
Rheumatoid arthritis, synovial membrane patient EB108 (U133B) |
| GSM303366 |
Rheumatoid arthritis, synovial membrane patient EB110 (U133A) |
| GSM303367 |
Rheumatoid arthritis, synovial membrane patient EB110 (U133B) |
| GSM303368 |
Rheumatoid arthritis, synovial membrane patient EB124 (U133A) |
| GSM303369 |
Rheumatoid arthritis, synovial membrane patient EB124 (U133B) |
| GSM303370 |
Osteoarthritis, synovial membrane patient EB140 (U133A) |
| GSM303377 |
Osteoarthritis, synovial membrane patient EB140 (U133B) |
| GSM303520 |
Rheumatoid arthritis, synovial membrane patient EB141 (U133A) |
| GSM303521 |
Rheumatoid arthritis, synovial membrane patient EB141 (U133B) |
| GSM303522 |
Normal, synovial membrane patient J19 (U133A) |
| GSM303523 |
Normal, synovial membrane patient J2 (U133A) |
| GSM303524 |
Normal, synovial membrane patient J2 (U133B) |
| GSM303525 |
Normal, synovial membrane patient J6 (U133A) |
| GSM303530 |
Normal, synovial membrane patient J6 (U133B) |
| GSM303531 |
Normal, synovial membrane patient J7 (U133A) |
| GSM303532 |
Normal, synovial membrane patient J7 (U133B) |
| GSM303533 |
Normal, synovial membrane patient J12 (U133A) |
| GSM303534 |
Normal, synovial membrane patient J12 (U133B) |
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| Relations |
| BioProject |
PRJNA113297 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE12021_RAW.tar |
200.3 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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