Protein Interaction Networks, Volume 131 in the Advances in Protein Chemistry and Structural Biology series, highlights new advances in the field, with this new volume presenting interesting chapters written by an international board of authors.
1. Cover image - p. i 2. Title page - p. ii 3. Table of Contents - p. iii 4. Copyright - p. iii 5. Contributors - p. iii 6. Chapter One: On the current failure—but bright future—of topology-driven biological network alignment - p. 27 7. Chapter Two: From single-omics to interactomics: How can ligand-induced perturbations modulate single-cell phenotypes? - p. 67 8. Chapter Three: A review of bioinformatics tools and web servers in different microarray platforms used in cancer research - p. 105 9. Abstract - p. 86 10. Abbreviations - p. 86 11. 1 Microarray and bioinformatics - p. 89 12. 2 Application of microarray data - p. 88 13. 3 Classification of microarray data in cancer - p. 92 14. 4 Microarray data expression repositories - p. 95 15. 5 Gene expression profiling (GEP) - p. 98 16. 6 Tools available to analyze microarray data - p. 100 17. 7 Biological networks - p. 104 18. 8 Pathway databases and analysis - p. 118 19. 9 Gene and transcriptional regulatory networks - p. 119 20. 10 Metabolic networks - p. 123 21. 11 Drug-drug interaction networks - p. 123 22. 12 Clustering, classification, and comparison of microarray data - p. 124 23. 13 Methodology and results - p. 126 24. 14 Limitations - p. 138 25. 15 Conclusion and future perspectives - p. 137 26. References - p. 140 27. Further reading - p. 158 28. Chapter Four: Fusion proteins mediate alternation of protein interaction networks in cancers - p. 165 29. Chapter Five: Integrative ontology and pathway-based approach identifies distinct molecular signatures in transcriptomes of esophageal squamous cell carcinoma - p. 177 30. Chapter Six: Protein interaction networks of the mammalian core clock proteins - p. 207 31. Chapter Seven: Investigation of differentially expressed genes and dysregulated pathways involved in multiple sclerosis - p. 235 32. Chapter Eight: Viral hijacking mechanism in humans through protein–protein interactions - p. 261 33. Chapter Nine: Glycoprotein molecular dynamics analysis: SARS-CoV-2 spike glycoprotein case study - p. 277 34. Chapter Ten: Exploring COVID-19 pathogenesis on command-line: A bioinformatics pipeline for handling and integrating omics data - p. 311
Protein Interaction Networks, Volume 131 in the Advances in Protein Chemistry and Structural Biology series, highlights new advances in the field, with this new volume presenting interesting chapters written by an international board of authors.
1. Cover image - p. i 2. Title page - p. ii 3. Table of Contents - p. iii 4. Copyright - p. iii 5. Contributors - p. iii 6. Chapter One: On the current failure—but bright future—of topology-driven biological network alignment - p. 27 7. Chapter Two: From single-omics to interactomics: How can ligand-induced perturbations modulate single-cell phenotypes? - p. 67 8. Chapter Three: A review of bioinformatics tools and web servers in different microarray platforms used in cancer research - p. 105 9. Abstract - p. 86 10. Abbreviations - p. 86 11. 1 Microarray and bioinformatics - p. 89 12. 2 Application of microarray data - p. 88 13. 3 Classification of microarray data in cancer - p. 92 14. 4 Microarray data expression repositories - p. 95 15. 5 Gene expression profiling (GEP) - p. 98 16. 6 Tools available to analyze microarray data - p. 100 17. 7 Biological networks - p. 104 18. 8 Pathway databases and analysis - p. 118 19. 9 Gene and transcriptional regulatory networks - p. 119 20. 10 Metabolic networks - p. 123 21. 11 Drug-drug interaction networks - p. 123 22. 12 Clustering, classification, and comparison of microarray data - p. 124 23. 13 Methodology and results - p. 126 24. 14 Limitations - p. 138 25. 15 Conclusion and future perspectives - p. 137 26. References - p. 140 27. Further reading - p. 158 28. Chapter Four: Fusion proteins mediate alternation of protein interaction networks in cancers - p. 165 29. Chapter Five: Integrative ontology and pathway-based approach identifies distinct molecular signatures in transcriptomes of esophageal squamous cell carcinoma - p. 177 30. Chapter Six: Protein interaction networks of the mammalian core clock proteins - p. 207 31. Chapter Seven: Investigation of differentially expressed genes and dysregulated pathways involved in multiple sclerosis - p. 235 32. Chapter Eight: Viral hijacking mechanism in humans through protein–protein interactions - p. 261 33. Chapter Nine: Glycoprotein molecular dynamics analysis: SARS-CoV-2 spike glycoprotein case study - p. 277 34. Chapter Ten: Exploring COVID-19 pathogenesis on command-line: A bioinformatics pipeline for handling and integrating omics data - p. 311
