T-REx results of Brinsmade_annotation

     Tutorial for Interpretation of T-REx Results
Global analysis
DATA Table
Factors Table
Contrasts
Class data
Download results

Library size

PCA of Experiments

PCA of Factors

PCA of Genes

Box plot of normalized signals
Library size data Data table Data table
Data table Library size data

Individual Contrasts analysis

AdMiRE: Volcano plots
Interactive mining

Volcano plots

Significant Changed Genes

MA plots

Differential Expression
Each Contrast

Differential Expression
All Contrasts

Heatmap
TopHits

Heatmap
TopHits, High Fold
Data table Data table -Heatmap TopHits data
-Heatmap Cluster data
-Heatmap High Fold data
-Heatmap Cluster data

Experiment Analysis

Correlation matrix
of Experiments

Heatmap
of Experiments

Gene Network
Significant Changed Genes

Gene Network
High Fold Changed Genes
Correlation data Heatmap data Gene Network data Gene Network High FC data

Contrasts Cohesion
Genes overlap of Contrasts

Contrasts Cohesion
Gene list

Contrasts Cohesion
High Fold Change

Contrasts Cohesion
Gene List
Matrix data Matrix data

Clustering
Median FOLD k-means

Clustering
High FOLD k-means

Clustering
Mean SIGNALS k-means

Dendrogram
Median Fold k-means

Dendrogram
High Fold k-means
ClusterIDs and data ClusterIDs and data ClusterIDs and data

Analysis of the Classes

k-means RATIO
Class TopHits

k-means SIGNAL
Class TopHits

Mean SIGNAL Plots
Each Class

Correlation matrix
All Classes

Correlation matrices
Each Class
ClusterIDs and data ClusterIDs and data Mean SIGNAL data Correlation data

Heatmap
Class TopHits

Heatmap
Class Signals

Heatmaps
Each Class Ratio

Heatmaps
Each Class Signals

MDS plot of k-means
of ClassTophits
- Heatmap data
- ClusterIDs
- Heatmap Signal data
- ClusterIDs
Link to ClusterIDs Link to ClusterIDs

Data tables
Link to fileDescription
Class TopHits ClusterIDsTable of Class TopHits and there ClusterID
Class TopHits High FoldTable of Class HighFold: Fold Change > 5, p-value < 0.01
Class TopHits logFCTable of Class and Log2 Fold Change values. TopHits= Fold Change > 5 and p-value<0.05
Class TopHits mean signalsTable of Class TopHits Signals
Contrasts OverviewOverview of COntrasts and link to TopHits tables of each Contrast
Correlation Matrix ClassesCorrelation between Class members over Experiments
Correlation Matrix ExperimentsCorrelation between Experiments
Differential Expression all ContrastsDE table, all values
Differential Expression all Contrasts logFCDE table TopHits= Fold Change > 2 and p-value<0.05
Differential Expression all Contrasts logFC High FoldDE table High Fold: Fold Change > 5, p-value < 0.01
Filenames in JSON formatSummery JSON formmated file with filenames for downstream processing
Filenames of Class TopHits k-meansOverview of k-means clusters
Filenames of Correlation Matrix of ClassesFilenames
Filenames of Heatmaps Class TopHitsFile with filenames of all heatmaps of each Class group
Filenames of MA PlotsFilenames
Filenames of Mean Signals ClassesMean Signals of Genes
Filenames of Mean Signals Classes log2Filenames
Filenames of Mean signals Classes TopHitsMean Signals of Genes
Filenames of Significant changed GenesComplete table with Significant changed genes
Filenames of Volcano Plot dataFilenames
Filenames of k-means High FoldFilenames
Filenames of k-means on Fold changeFilenames
Gene Network EdgesGene network for Cytoscape of Changed genes
Gene Network Edges High FoldGene network for Cytoscape of HighFold Changed genes
Heatmap of Class SignalsHeatmap of Class Signals
Heatmap of Class TophitsHeatmap of Class TopHits
Heatmap of ExperimentsHeatmap of Experiments
Heatmap of High Fold TophitsHeatmap of HighFold TopHits of all Contrasts
Heatmap of TophitsHeatmap of TopHits of all Contrasts
Mean signals log2Log2 Signals normalized
Mean signals log2 ScaledLog2 Signals Global scaled
Mean signals log2 Scaled per ClassLog2 Signals Scaled per Class
Mean signals log2 Scaled per GeneLog2 Signals Scaled per Gene
Mean signals of replicatesMean Signal of replicates
Normalised Data TableNormalized data
k-means High Fold ClusterIDsk-means Cluster IDs
k-means on Fold change ClusterIDsTable with Cluster IDs