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Relative expression levels with regard to sample and tumor characteristics are depicted in Table 3. SD = standard deviation, N+ = lymph node metastasis, M+ = organ metastasis.
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However, further bisulfite sequencing of 8 clones from tumor sample 1 and tumor sample 4 did not detect any methylated CpGs (data not shown).
Blood samples and tumor biopsies were analyzed for evidence of transgene activity, virus replication, and immune stimulation.
We have also applied our MixHMM algorithm with real tumor samples, both pure tumor samples and tumor samples 'contaminated' with stromal cells.
Second, we analyzed common families of genes between the samples and tumor groups for significant functions.
The data set is composed in total of 409 human samples, including normal, primary tumor samples and tumor derived cell lines.
Tumors were collected from surgical samples, and tumor content verified by histopathology.
Web-interactive heatmaps are used to explore gene and pathway alterations across samples and tumor types.
With each patient's consent, peripheral blood samples and tumor tissue were collected during the operation.
AB DNA isolation from the patient blood samples and tumor specimens.
Methylation differences between tumor and normal samples and tumor subgroups were analyzed using a linear model in limma v3.2.1 [ 32].
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