Results: Functional Pathway Analysis
Zymo Research Corporation
1 Heatmaps
The abundance heatmap with sample clustering is a quick way to help identify patterns of functional profiling among samples. Heatmaps with or without sample clustering can be found by clicking the links below the figure.
1.1 Gene Family
The following heatmap shows top 75 most abundant gene families detected in all the samples. Each row represents the abundance for each gene family along with the species information, with the gene family ID shown on the right. Each column represents the abundance for each sample, with the sample ID shown at the bottom. If available, group information is indicated by the colored bar located on the top of each column. Hierarchical clustering was performed on samples based on Bray-Curtis dissimilarity. Hierarchical clustering was also performed on the gene families so that gene families with similar distributions are grouped together.
Heatmaps with Sample Clustering: Category1
Heatmaps without Sample Clustering: Category1
1.2 Functional Pathway
The following heatmap shows top 75 most abundant functional pathways detected in all the samples. Each row represents the abundance for each pathway, with the pathway ID shown on the right. Each column represents the abundance for each sample, with the sample ID shown at the bottom. If available, group information is indicated by the colored bar located on the top of each column. Hierarchical clustering was performed on samples based on Bray-Curtis dissimilarity. Hierarchical clustering was also performed on the pathways so that pathways with similar distributions are grouped together.
Heatmaps with Sample Clustering: Category1
Heatmaps without Sample Clustering: Category1
1.3 Functional Pathway with Species Identification
The following heatmap shows top 75 most abundant functional pathways detected (with species information) in all the samples. Each row represents the abundance for each pathway, with the pathway ID shown on the right. Each column represents the abundance for each sample, with the sample ID shown at the bottom. If available, group information is indicated by the colored bar located on the top of each column. Hierarchical clustering was performed on samples based on Bray-Curtis dissimilarity. Hierarchical clustering was also performed on the pathways so that pathways with similar distributions are grouped together.
Heatmaps with Sample Clustering: Category1
Heatmaps without Sample Clustering: Category1
2 LEfSe Analysis
LEfSe analysis helps to identify biomarkers whose distributions are significantly and statistically different among pre-defined groups.
LEfSe uses statistical analysis to identify biomarkers whose distributions among pre-defined groups is significantly different. It also utilizes the concept of effect size to allow researchers to focus on the taxa of dramatic differences. By default, LEfSe identifies biomarkers whose distributions among different groups are statistically different with p-value <0.05 and the effect size (LDA score) higher than 2. LEfSe analysis is only possible if group information is given. It can conveniently help researchers identify biomarkers among/between groups (e.g. control group vs. disease group). Major outputs from LEfSe analysis includes the following:
1. Interactive Biomarkers Plot: This plot shows the distribution of the abundance of identified biomarkers among all samples. Click on the bars of biomarkers on the Interactive Biomarkers Plot to access the abundance distribution profile among groups.
2. Biomarkers Plot: This plot lists biomarkers by group definition and effect size.
3. Cladogram Plot: This plot illustrates identified biomarkers (colored based on groups) in a context of phylogenetic tree.
4. LEfSe Statistics Table(Output): This excel file stores the raw data of effect size (4th column/ column D) and P-values (5th column/ column E) from statistical analysis. The group in which the biomarkers was more abundant is in the 3rd column/column C.
2.1 Functional Pathway
Pathway LEfSe analysis helps to identify functional pathways whose distributions are significantly and statistically different among pre-defined groups.
Interactive Biomarkers Plot: Category1
Biomarkers Plot (PDF): Category1
Cladogram Plot (PDF): Category1
LEfSe Statistics Table (Output File): Category1