Functional Prediction of Hypothetical Proteins from and Validation of the Predicted Models by Using ROC Curve Analysis
Shigella spp. constitutes some of the key pathogens responsible for the global burden of diarrhoeal disease. With over 164 million reported cases per annum, shigellosis accounts for 1.1 million deaths each year. Majority of these cases occur among the children of the developing nations and the emerg...
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BioMed Central
2018-12-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gi-2018-16-4-e26.pdf |
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| author | Md. Amran Gazi Sultan Mahmud Shah Mohammad Fahim Mohammad Golam Kibria Parag Palit Md. Rezaul Islam Humaira Rashid Subhasish Das Mustafa Mahfuz Tahmeed Ahmeed |
| author_facet | Md. Amran Gazi Sultan Mahmud Shah Mohammad Fahim Mohammad Golam Kibria Parag Palit Md. Rezaul Islam Humaira Rashid Subhasish Das Mustafa Mahfuz Tahmeed Ahmeed |
| author_sort | Md. Amran Gazi |
| collection | DOAJ |
| description | Shigella spp. constitutes some of the key pathogens responsible for the global burden of diarrhoeal disease. With over 164 million reported cases per annum, shigellosis accounts for 1.1 million deaths each year. Majority of these cases occur among the children of the developing nations and the emergence of multi-drug resistance Shigella strains in clinical isolates demands the development of better/new drugs against this pathogen. The genome of Shigella flexneri was extensively analyzed and found 4,362 proteins among which the functions of 674 proteins, termed as hypothetical proteins (HPs) had not been previously elucidated. Amino acid sequences of all these 674 HPs were studied and the functions of a total of 39 HPs have been assigned with high level of confidence. Here we have utilized a combination of the latest versions of databases to assign the precise function of HPs for which no experimental information is available. These HPs were found to belong to various classes of proteins such as enzymes, binding proteins, signal transducers, lipoprotein, transporters, virulence and other proteins. Evaluation of the performance of the various computational tools conducted using receiver operating characteristic curve analysis and a resoundingly high average accuracy of 93.6% were obtained. Our comprehensive analysis will help to gain greater understanding for the development of many novel potential therapeutic interventions to defeat Shigella infection. |
| format | Article |
| id | doaj-art-31f6a90f0215428b87eee9bf157cef7b |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2018-12-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-31f6a90f0215428b87eee9bf157cef7b2025-02-02T05:29:04ZengBioMed CentralGenomics & Informatics2234-07422018-12-0116410.5808/GI.2018.16.4.e26526Functional Prediction of Hypothetical Proteins from and Validation of the Predicted Models by Using ROC Curve AnalysisMd. Amran Gazi0Sultan Mahmud1Shah Mohammad Fahim2Mohammad Golam Kibria3Parag Palit4Md. Rezaul Islam5Humaira Rashid6Subhasish Das7Mustafa Mahfuz8Tahmeed Ahmeed9 Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh International Max Planck Research School, Grisebachstraße 5, 37077 Göttingen, Germany Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, Bangladesh Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka 1212, BangladeshShigella spp. constitutes some of the key pathogens responsible for the global burden of diarrhoeal disease. With over 164 million reported cases per annum, shigellosis accounts for 1.1 million deaths each year. Majority of these cases occur among the children of the developing nations and the emergence of multi-drug resistance Shigella strains in clinical isolates demands the development of better/new drugs against this pathogen. The genome of Shigella flexneri was extensively analyzed and found 4,362 proteins among which the functions of 674 proteins, termed as hypothetical proteins (HPs) had not been previously elucidated. Amino acid sequences of all these 674 HPs were studied and the functions of a total of 39 HPs have been assigned with high level of confidence. Here we have utilized a combination of the latest versions of databases to assign the precise function of HPs for which no experimental information is available. These HPs were found to belong to various classes of proteins such as enzymes, binding proteins, signal transducers, lipoprotein, transporters, virulence and other proteins. Evaluation of the performance of the various computational tools conducted using receiver operating characteristic curve analysis and a resoundingly high average accuracy of 93.6% were obtained. Our comprehensive analysis will help to gain greater understanding for the development of many novel potential therapeutic interventions to defeat Shigella infection.http://genominfo.org/upload/pdf/gi-2018-16-4-e26.pdfhypothetical protein NCBIROC curve |
| spellingShingle | Md. Amran Gazi Sultan Mahmud Shah Mohammad Fahim Mohammad Golam Kibria Parag Palit Md. Rezaul Islam Humaira Rashid Subhasish Das Mustafa Mahfuz Tahmeed Ahmeed Functional Prediction of Hypothetical Proteins from and Validation of the Predicted Models by Using ROC Curve Analysis Genomics & Informatics hypothetical protein NCBI ROC curve |
| title | Functional Prediction of Hypothetical Proteins from and Validation of the Predicted Models by Using ROC Curve Analysis |
| title_full | Functional Prediction of Hypothetical Proteins from and Validation of the Predicted Models by Using ROC Curve Analysis |
| title_fullStr | Functional Prediction of Hypothetical Proteins from and Validation of the Predicted Models by Using ROC Curve Analysis |
| title_full_unstemmed | Functional Prediction of Hypothetical Proteins from and Validation of the Predicted Models by Using ROC Curve Analysis |
| title_short | Functional Prediction of Hypothetical Proteins from and Validation of the Predicted Models by Using ROC Curve Analysis |
| title_sort | functional prediction of hypothetical proteins from and validation of the predicted models by using roc curve analysis |
| topic | hypothetical protein NCBI ROC curve |
| url | http://genominfo.org/upload/pdf/gi-2018-16-4-e26.pdf |
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