---
# System prepended metadata

title: IFIH1 gene ontology analysis

---

# IFIH1 gene ontology analysis

The *Homo sapiens* interferon-induced helicase C domain-containing protein 1 (IFIH1) gene codes for the melanoma differentiation-associated protein 5 (MDA5). This plays an important role in the innate immunity being a pattern recognition receptor. MDA5 can recognize double-stranded (ds) RNA, a molecule that is not normally present in humans and other animals' cells. The ds-RNA is present in certain pathogens such as reovirus, rotavirus, birnavirus, etc. When the ds-RNA is detected, a signal mediated by the mitochondrial antiviral-signaling protein (MAVS) initiates the cytokines (interferons) clearing the virus by killing the infected host cells and participating in inflammation regulation.

By using gene ontology (GO) analysis a network model of the IFIH1 gene.

![](https://i.imgur.com/Y8bvy1z.png)
Figure 1. IFIH1 gene network created using Cytoscape Software with STRING layout. The yellow nodes and red edges represent a cluster of the first neighbor selected.

In order to visualize the GO of significantly over-represented categories within the selected gene, a GO enrichment analysis was created by using BiNGO tools (Figure 1 and Table 1). 

![](https://i.imgur.com/ZUht0qX.png =2000x)
Figure 2. Pathway of biological process related to the IFIH1 gene in the *Homo sapiens*. The yellow nodes shows the proteins that are over-represented (p>0.05) in biological proceses related with IFIH1 gene.

**Table 1. IFIH1 enriched GO terms**
| GO ID |               description_MDA5              | pValue_MDA5 | adjustedPValue_MDA5 | N_MDA5 | nn_MDA5 | X_MDA5_ | xx_MDA5 | Degree |
|:-----:|:-------------------------------------------:|:-----------:|:-------------------:|:------:|:-------:|:-------:|:-------:|:------:|
| 51260 | protein homooligomerization                 | 1.56E-04    | 1.59E-02            | 14305  | 104     | 3       | 2       | 1      |
| 51259 | protein oligomerization                     | 5.22E-04    | 2.14E-02            | 14305  | 190     | 3       | 2       | 2      |
| 10815 | bradykinin catabolic process                | 6.29E-04    | 2.14E-02            | 14305  | 3       | 3       | 1       | 1      |
| 50435 | beta-amyloid metabolic process              | 1.05E-03    | 2.57E-02            | 14305  | 5       | 3       | 1       | 1      |
| 43171 | peptide catabolic process                   | 1.26E-03    | 2.57E-02            | 14305  | 6       | 3       | 1       | 3      |
| 42447 | hormone catabolic process                   | 1.89E-03    | 3.21E-02            | 14305  | 9       | 3       | 1       | 2      |
| 6461  | protein complex assembly                    | 3.67E-03    | 4.68E-02            | 14305  | 507     | 3       | 2       | 3      |
| 70271 | protein complex biogenesis                  | 3.67E-03    | 4.68E-02            | 14305  | 507     | 3       | 2       | 2      |
| 65003 | macromolecular complex assembly             | 6.48E-03    | 6.01E-02            | 14305  | 676     | 3       | 2       | 3      |
| 43933 | macromolecular complex subunit organization | 7.42E-03    | 6.30E-02            | 14305  | 724     | 3       | 2       | 2      |
| 6518  | peptide metabolic process                   | 1.15E-02    | 6.39E-02            | 14305  | 55      | 3       | 1       | 2      |
| 22607 | cellular component assembly                 | 1.17E-02    | 6.39E-02            | 14305  | 913     | 3       | 2       | 3      |
| 44085 | cellular component biogenesis               | 1.49E-02    | 7.25E-02            | 14305  | 1035    | 3       | 2       | 3      |
| 42445 | hormone metabolic process                   | 2.29E-02    | 1.02E-01            | 14305  | 110     | 3       | 1       | 3      |
| 10817 | regulation of hormone levels                | 3.17E-02    | 1.35E-01            | 14305  | 153     | 3       | 1       | 2      |
| 9100  | glycoprotein metabolic process              | 4.01E-02    | 1.55E-01            | 14305  | 194     | 3       | 1       | 2      |
| 16043 | cellular component organization             | 8.48E-02    | 2.07E-01            | 14305  | 2563    | 3       | 2       | 3      |
| 44260 | cellular macromolecule metabolic process    | 1.51E-01    | 2.53E-01            | 14305  | 3507    | 3       | 2       | 3      |
| 44248 | cellular catabolic process                  | 1.54E-01    | 2.53E-01            | 14305  | 776     | 3       | 1       | 3      |
| 43170 | macromolecule metabolic process             | 1.92E-01    | 2.76E-01            | 14305  | 4016    | 3       | 2       | 2      |
| 9056  | catabolic process                           | 1.97E-01    | 2.78E-01            | 14305  | 1006    | 3       | 1       | 3      |
| 44237 | cellular metabolic process                  | 2.80E-01    | 3.76E-01            | 14305  | 4989    | 3       | 2       | 5      |
| 65008 | regulation of biological quality            | 2.90E-01    | 3.79E-01            | 14305  | 1542    | 3       | 1       | 2      |
| 8152  | metabolic process                           | 3.76E-01    | 4.51E-01            | 14305  | 5958    | 3       | 2       | 5      |
| 65007 | biological regulation                       | 4.78E-01    | 5.30E-01            | 14305  | 6943    | 3       | 2       | 2      |
| 9987  | cellular process                            | 7.25E-01    | 7.32E-01            | 14305  | 9369    | 3       | 2       | 2      |
| 8150  | biological_process                          | 1           | 1                   | 14305  | 14305   | 3       | 3       | 5      |


By using the enrichment network analysis I learned that MDA5, the protein encoded by IFIH1, plays a role in the different interconnected biological processes. In the center of the network is the biological process node that generates sub nodes. There are eight processes that are over-represented (yellow nodes in figure 2) and they are listed in table 1 based on their hierarchy. Interestingly, all of these processes are not directly interconected with each other. There are four connected over-represented nodes:  protein homooligomerization;  protein oligomerization;  protein complex assemby and protein complex biogenesis, that are part of cellular component biogenesis and macromolecular complex assembly. There are two connected over-represented nodes: peptide and bradykinin catabolic processes that belong to a cellular metabolic process which generates a cellular macromolecule metabolic process that gives origin to another over-represented node: the beta-amyloid metabolic process. Finally the hormone catabolic process is part of a metabolic process that is related with hormone regulation. In conclusion, the MDA5 protein encoded by IFIH1 gene plays diverse roles in biological processes not only limited to the immune system.


### References
Maere S, Heymans K, Kuiper M (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. Bioinformatics 21, 3448-3449
The UniProt Consortium (2019). UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 47: D506-515 
Doncheva NT, Morris JH, Gorodkin J, Jensen LJ. (2019) Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data. J Proteome Res. 18(2):623-632






