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For samples that did not have matching normal data (n = 15), a pooled normal baseline from all the other normal samples was used.
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However, the matched normal data from the same individual are often unavailable in clinical situation.
Clinical importance of the method is providing pathway interpretation of single cancer, even though its matched normal data are unavailable.
Members can specify one or more values for a variety of search parameters spanning participant, tumor specimen and matched normal data elements.
Therefore, we suggest a new approach for the personalized identification of altered pathways, making special use of accumulated normal data in cases when a patient's matched normal data are unavailable.
This group consists of 53 TSCC cases and 22 matching normal tissues where the microarray data were either generated from our previous study [ 8] or downloaded from GEO database [ 9- 11].
Gene and miRNA expression data sets of matching normal samples from GBM, KIRC, and OvCa were also extracted from the TCGA database.
Except for the FGFR2 and PIK3CA mutations that affected human tumour cell lines, the remaining 8 mutations were found in samples derived from primary tumours and were somatic in origin as assessed by the sequencing of the matched normal DNA (data not shown).
In a large study (98 cases), we confirmed by real-time quantitative PCR (RT-QPCR) that its expression level remains relatively constant between HNSCC tumours and matched normal tissues (data not shown).
An important clinical aspect of our methods is that it enables the interpretation of a cancer case in a single patient, even if matched normal tissue data from the same individual are unavailable.
Only GSE21124 data set was analyzed by matching normal samples.
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