3.2.2.6 Malignant peripheral nerve sheath tumor

There are 36886 genes and 10 samples in the dataset.

At least some samples or genes look not suitable for the co-expression analysis. After removing them, there remain 36199 genes and 10 samples.

##    Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1      1   0.0468  1.57          0.862 10600.0  10400.00  14300
## 2      3   0.2400 -1.37          0.874  2350.0   2160.00   4970
## 3      5   0.6340 -1.99          0.944   858.0    728.00   2520
## 4      7   0.7940 -2.20          0.972   399.0    321.00   1510
## 5      9   0.8480 -2.28          0.984   216.0    162.00   1000
## 6     11   0.8710 -2.31          0.989   130.0     91.70    709
## 7     13   0.8820 -2.30          0.993    84.2     55.90    525
## 8     15   0.8800 -2.28          0.989    58.1     36.10    405
## 9     17   0.8710 -2.23          0.978    42.1     24.30    323
## 10    19   0.8530 -2.13          0.944    31.8     17.10    264
## 11    21   0.8620 -1.92          0.899    24.9     12.40    220
## 12    23   0.8650 -1.75          0.833    20.2      9.25    188
## 13    25   0.7940 -1.81          0.739    16.7      7.05    186
## 14    27   0.2910 -2.86          0.161    14.2      5.47    183
## 15    29   0.3110 -2.88          0.182    12.3      4.32    181

Network is computed using power=11.

Here are the modules for a few genes of interest:

  • VNN1 is in the grey module.
  • PPARA is in the turquoise module.
  • PPARD is in the brown module.
  • PPARG is in the brown4 module.
  • PPARGC1A is in the green module.
  • PPARGC1B is in the pink3 module.

g:Profiler results for all modules are available here. Since there are many modules, you should expect at least 1 minute computation on the g:Profiler website for this query. Check below for faster queries focused on VNN1 module.

Pathway

Figure 3.114: Pathway

Kegg

Figure 3.115: Kegg

MSigDb Hallmarks. [readable pdf version](plots/resultsWgcnaTcgaSarcMalignantPeripheralNerveSheathTumorKnitComputeEnrichHallmarks.pdf).

Figure 3.116: MSigDb Hallmarks. readable pdf version. 

## No enriched DO term in these classes

To check that module-to-genes reattribution is working as expected, heatmap of signal for VNN1 module is produced, both as absolute values and as Z-score ones.

## VNN1 module contains more than 2000 genes. Heatmap generation is skipped

VNN1 module contains more than 2000 genes. Heatmap generation is skipped

## VNN1 module contains more than 5000 genes. Correlation analysis is skipped

More than 5000 genes in VNN1 module. Analysis skipped. You should try to reduce module size.