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. 2013:2013:263952.
doi: 10.1155/2013/263952. Epub 2013 Dec 30.

Prediction of IL4 inducing peptides

Sandeep Kumar Dhanda  1 , Sudheer Gupta  1 , Pooja Vir  1 , G P S Raghava  1
Affiliations

Prediction of IL4 inducing peptides

Sandeep Kumar Dhanda et al. Clin Dev Immunol. 2013.

Abstract

The secretion of Interleukin-4 (IL4) is the characteristic of T-helper 2 responses. IL4 is a cytokine produced by CD4+ T cells in response to helminthes and other extracellular parasites. It has a critical role in guiding antibody class switching, hematopoiesis and inflammation, and the development of appropriate effector T-cell responses. In this study, it is the first time an attempt has been made to understand whether it is possible to predict IL4 inducing peptides. The data set used in this study comprises 904 experimentally validated IL4 inducing and 742 noninducing MHC class II binders. Our analysis revealed that certain types of residues are preferred at certain positions in IL4 inducing peptides. It was also observed that IL4 inducing and noninducing epitopes differ in compositional and motif pattern. Based on our analysis we developed classification models where the hybrid method of amino acid pairs and motif information performed the best with maximum accuracy of 75.76% and MCC of 0.51. These results indicate that it is possible to predict IL4 inducing peptides with reasonable precession. These models would be useful in designing the peptides that may induce desired Th2 response.

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Figures

Figure 1
Figure 1
Box plot to represent the variation of peptide length in IL4 inducing and non-IL4-inducing dataset.
Figure 2
Figure 2
Bar plot representing the average percentage composition of residue in IL4 inducing and non-IL4-inducing datasets. ∗ here represents the significantly different residues at P value <0.05.
Figure 3
Figure 3
Representing the percentage bar plot of IL4 positive and IL4 negative epitope with corresponding MHC alleles.
Figure 4
Figure 4
Two-sample logo displaying the positional conservation of amino acid for N15 residue among positive and negative dataset.
See this image and copyright information in PMC

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