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, 11 (3), 216-224

Celiac Disease Microarray Analysis Based on System Biology Approach


Celiac Disease Microarray Analysis Based on System Biology Approach

Mostafa Rezaei Tavirani et al. Gastroenterol Hepatol Bed Bench.


Aim: Aim of this study is screen of the large numbers of related genes of CD to find the key ones.

Background: Celiac disease (CD) is known as a gluten sensitive and immune system dependent disease. There are several high throughput investigations about CD but it is necessary to clarify new molecular aspects mechanism of celiac.

Methods: Whole-genome profile (RNA) of the human peripheral blood mononuclear cells (PBMCs) as Gene expression profile GSE113469 was retrieved Gene Expression Omnibus (GEO) database. The significant genes were selected and analyzed via protein-protein interaction (PPI) network by Cytoscape software. The key genes were introduced and enriched via ClueGO to find the related biochemical pathways.

Results: Among 250 significant genes 47 genes with expressed change above 2 fold change (FC) were interacted and the constructed network were analyzed. The network characterized by poor connections so it was promoted by addition 50 related nodes and 18 crucial nodes were introduced. Two clusters of biochemical pathways were identified and discussed.

Conclusion: There is an obvious conflict between microarray finding and the well-known related genes of CD. This problem can be solve by more attention to the interpretation of PPI ntwork analysis results.

Keywords: Celiac disease; ClueGO.; Crucial genes; Cytoscape; System biology.

Conflict of interest statement

The authors declare that they have no conflict of interest.


Figure 1
Figure 1
The numbers of 20 control RNA profiles of human PBMCs (blue colored bars) vs. 17 PBMCs of celiac patients on gluten free diet (pink colored bars) are matched via box plot illustration
Figure 2
Figure 2
The numbers of 23 up-regulated (blue color) and 24 down-regulated (red color) DEGs of celiac samples vs. controls based on Student’s t test statistical p-values less than 0.05 and adjusted p-values considering FC≥2 were identified. The vertical axis is corresponded to logFC based on 2. The Gene expression was differentially between the GFP patients and control samples
Figure 3
Figure 3
The 41 DEGs and added 50 relate genes characterized by poor connections (the nodes were linked by only 24 edges). After addition 50 related genes (the genes were extracted from STRING database), the network including a main connected component, a component counting 4 nodes, and 8 isolated nodes was designed. The main connected component including 79 nodes and 1243 edges is illustrated
Figure 4
Figure 4
The 18 central nodes of the celiac network are organized in a sub-network. Network is characterized by 117 edges and density equal to 0.765. The nodes are layout by degree value and color from blue to orange corresponds to decrease of degree.
Figure 5.
Figure 5.
Numbers of 47 DEGs related to celiac disease are interacted. Six genes were not recognized by STRING database and 20 isolated nodes were determined. Two double components and one tetrad were identified. The main connected component included 13 nodes and 16 edges. The nodes are layout by degree value (The bigger size refers to higher degree value.

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