Author: Josset, Laurence; Zeng, Hui; Kelly, Sara M.; Tumpey, Terrence M.; Katze, Michael G.
Title: Transcriptomic Characterization of the Novel Avian-Origin Influenza A (H7N9) Virus: Specific Host Response and Responses Intermediate between Avian (H5N1 and H7N7) and Human (H3N2) Viruses and Implications for Treatment Options Document date: 2014_2_4
ID: uz0m1o0q_28
Snippet: Transcriptomic distance analysis. To visualize transcriptional similarity between samples in a 2-dimensional space, Euclidian distances were calculated with transcriptomic normalized data, and nonmetric multidimensional scaling (MDS) was performed using the MASS software package in the R Bioconductor program (44) to map the distances into the 2-dimensional space with minimal loss of information (evaluated by Kruskal's stress). Biological replicat.....
Document: Transcriptomic distance analysis. To visualize transcriptional similarity between samples in a 2-dimensional space, Euclidian distances were calculated with transcriptomic normalized data, and nonmetric multidimensional scaling (MDS) was performed using the MASS software package in the R Bioconductor program (44) to map the distances into the 2-dimensional space with minimal loss of information (evaluated by Kruskal's stress). Biological replicates from the same condition were linked in convex hulls (i.e., polygons) using the function "chull" in R. Pearson correlation coefficients, Spearman correlation coefficients, total Euclidean distances, or total Manhattan distances were used to estimate similarities in the gene expression profiles between Anhui01-infected and other IAV-or mock-infected samples. The average distance between conditions was calculated as the arithmetic mean of distances between all biological replicates.
Search related documents:
Co phrase search for related documents- arithmetic mean and correlation coefficient: 1, 2
- average distance and correlation coefficient: 1, 2, 3
- average distance and euclidean distance: 1, 2, 3, 4, 5, 6
- average distance and gene expression: 1, 2
- average distance and Manhattan distance: 1
- biological replicate and condition biological replicate: 1
- biological replicate and gene expression: 1, 2
- correlation coefficient and euclidean distance: 1
- correlation coefficient and euclidian distance: 1
- correlation coefficient and gene expression: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12
- correlation coefficient and gene expression profile: 1
- correlation coefficient and Manhattan distance: 1
- distance map and euclidean distance: 1
- euclidean distance and gene expression: 1, 2
- euclidean distance and Manhattan distance: 1, 2
- euclidian distance and gene expression: 1
- euclidian distance and Manhattan distance: 1
- gene expression and Manhattan distance: 1
Co phrase search for related documents, hyperlinks ordered by date