General Information

Number of samples

3388

Number of groups

9

Number of genes

48106

ID type of genes

illumina_humanht_12_v4

Dimension of the SOM

100 x 100

Date

Di Aug 14 12:36:31 2018 CEST

Analyst

henry

oposSOM version

Results

General

• Data Distribution (PDF)
• Chromosome-wise gene expression heatmap (PDF)

SOM Analysis

These reports comprise the SOM portraits in standard and alternative color scales, as well as supporting maps and profiles which provide supplementary information about the 1st level SOM.

• Supporting Maps (PDF)

• Entropy Profiles (PDF)
• Topology Profiles (PDF)

Geneset Enrichment Analysis

Functional analyses using predefined gene sets. The results are visualized in terms of heatmaps, profile plots and population maps.

• Functional Analysis (HTML)

Sample Similarity Analyses

Sample similarity analyses based on expression module data and metagene data using different metrics and algorithms.

Euclidean Distance based approaches:

• Sample SOM (PDF)
• Phylogenetic clustering using neighbor joining algorithm and clustering heatmaps (PDF)

Correlation based approaches:

• Correlation spanning tree connecting all samples (PDF)
• Correlation backbone, a 2-nearest-neighbor graph (PDF)
• Pairwise correlation maps (supervised & clustered orderings) (PDF)

Component Analysis:

• Independent Component Analysis: 2d-ICA, 3d-ICA (PDF)

Expression Module Analysis

Different criteria of spot module definition such as overexpression or mutual correlations between the metagenes where applied. The reports comprise integrated portraits, functional analyses.

• Spot Reports (HTML)

Analyses based on PAT-wise aggregated data, including clustering dendrogram, portraits and assotiation to the sample groups.
PATs were defined using dmap approach.

• PAT Report (PDF)