Comparative Analysis of Glycogene Expression in Different Mouse Tissues Using RNA-Seq Data
Glycogenes regulate a wide array of biological processes in the development of organisms as well as different diseases such as cancer, primary open-angle glaucoma, and renal dysfunction. The objective of this study was to explore the role of differentially expressed glycogenes (DEGGs) in three major...
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| Format: | Article |
| Language: | English |
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Wiley
2014-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2014/837365 |
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| author | Ahmad Firoz Adeel Malik Sanjay Kumar Singh Vivekanand Jha Amjad Ali |
| author_facet | Ahmad Firoz Adeel Malik Sanjay Kumar Singh Vivekanand Jha Amjad Ali |
| author_sort | Ahmad Firoz |
| collection | DOAJ |
| description | Glycogenes regulate a wide array of biological processes in the development of organisms as well as different diseases such as cancer, primary open-angle glaucoma, and renal dysfunction. The objective of this study was to explore the role of differentially expressed glycogenes (DEGGs) in three major tissues such as brain, muscle, and liver using mouse RNA-seq data, and we identified 579, 501, and 442 DEGGs for brain versus liver (BvL579), brain versus muscle (BvM501), and liver versus muscle (LvM442) groups. DAVID functional analysis suggested inflammatory response, glycosaminoglycan metabolic process, and protein maturation as the enriched biological processes in BvL579, BvM501, and LvM442, respectively. These DEGGs were then used to construct three interaction networks by using GeneMANIA, from which we detected potential hub genes such as PEMT and HPXN (BvL579), IGF2 and NID2 (BvM501), and STAT6 and FLT1 (LvM442), having the highest degree. Additionally, our community analysis results suggest that the significance of immune system related processes in liver, glycosphingolipid metabolic processes in the development of brain, and the processes such as cell proliferation, adhesion, and growth are important for muscle development. Further studies are required to confirm the role of predicted hub genes as well as the significance of biological processes. |
| format | Article |
| id | doaj-art-369dab1977e84d2aadb3d05ee592e44d |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2014-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-369dab1977e84d2aadb3d05ee592e44d2025-08-20T03:55:02ZengWileyInternational Journal of Genomics2314-436X2314-43782014-01-01201410.1155/2014/837365837365Comparative Analysis of Glycogene Expression in Different Mouse Tissues Using RNA-Seq DataAhmad Firoz0Adeel Malik1Sanjay Kumar Singh2Vivekanand Jha3Amjad Ali4School of Chemistry and Biochemistry, Thapar University, Patiala, Punjab 147004, IndiaSchool of Biotechnology, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongbuk 712-749, Republic of KoreaBiomedical Informatics Center of ICMR, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, IndiaBiomedical Informatics Center of ICMR, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, IndiaSchool of Chemistry and Biochemistry, Thapar University, Patiala, Punjab 147004, IndiaGlycogenes regulate a wide array of biological processes in the development of organisms as well as different diseases such as cancer, primary open-angle glaucoma, and renal dysfunction. The objective of this study was to explore the role of differentially expressed glycogenes (DEGGs) in three major tissues such as brain, muscle, and liver using mouse RNA-seq data, and we identified 579, 501, and 442 DEGGs for brain versus liver (BvL579), brain versus muscle (BvM501), and liver versus muscle (LvM442) groups. DAVID functional analysis suggested inflammatory response, glycosaminoglycan metabolic process, and protein maturation as the enriched biological processes in BvL579, BvM501, and LvM442, respectively. These DEGGs were then used to construct three interaction networks by using GeneMANIA, from which we detected potential hub genes such as PEMT and HPXN (BvL579), IGF2 and NID2 (BvM501), and STAT6 and FLT1 (LvM442), having the highest degree. Additionally, our community analysis results suggest that the significance of immune system related processes in liver, glycosphingolipid metabolic processes in the development of brain, and the processes such as cell proliferation, adhesion, and growth are important for muscle development. Further studies are required to confirm the role of predicted hub genes as well as the significance of biological processes.http://dx.doi.org/10.1155/2014/837365 |
| spellingShingle | Ahmad Firoz Adeel Malik Sanjay Kumar Singh Vivekanand Jha Amjad Ali Comparative Analysis of Glycogene Expression in Different Mouse Tissues Using RNA-Seq Data International Journal of Genomics |
| title | Comparative Analysis of Glycogene Expression in Different Mouse Tissues Using RNA-Seq Data |
| title_full | Comparative Analysis of Glycogene Expression in Different Mouse Tissues Using RNA-Seq Data |
| title_fullStr | Comparative Analysis of Glycogene Expression in Different Mouse Tissues Using RNA-Seq Data |
| title_full_unstemmed | Comparative Analysis of Glycogene Expression in Different Mouse Tissues Using RNA-Seq Data |
| title_short | Comparative Analysis of Glycogene Expression in Different Mouse Tissues Using RNA-Seq Data |
| title_sort | comparative analysis of glycogene expression in different mouse tissues using rna seq data |
| url | http://dx.doi.org/10.1155/2014/837365 |
| work_keys_str_mv | AT ahmadfiroz comparativeanalysisofglycogeneexpressionindifferentmousetissuesusingrnaseqdata AT adeelmalik comparativeanalysisofglycogeneexpressionindifferentmousetissuesusingrnaseqdata AT sanjaykumarsingh comparativeanalysisofglycogeneexpressionindifferentmousetissuesusingrnaseqdata AT vivekanandjha comparativeanalysisofglycogeneexpressionindifferentmousetissuesusingrnaseqdata AT amjadali comparativeanalysisofglycogeneexpressionindifferentmousetissuesusingrnaseqdata |