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ULBP1-5 expression was also found to be expressed in many tumor samples of colorectal and ovarian cancer [ 9, 10, 15].
qRT-PCR confirmed de novo expression of the short TCF12 isoform (exon 1B) in many tumor samples and showed strong correlation to the exon array data (RS = 0.82, Spearman correlation).
While the roles of both Tie-1 and Tie-2 in AGASACA and TC are currently unknown, further investigation is warranted given the observed phosphorylation of both receptors in many tumor samples in this study.
To leverage our mechanistic understanding, and to link multigene expression changes to outcomes, we performed individualized computational simulations of competitive VEGF and Sema receptor binding across many tumor samples.
Only the recent hierarchical hidden Markov model (H-HMM) (Shah et al., 2007) and fused SVM (Rapaport et al., 2008) models demonstrate the benefits of supervised sequential array-CGH analysis over many tumor samples for identifying clinically important regions of aneuploidy, but identifying the causal genes within these amplicons remains an open challenge.
First, we observed that many tumor samples (approximately 20% on average across all cancer types and hallmarks), which lacked mutations in SFM genes that were linked to hallmarks, had mutations in other genes that were linked to hallmarks and could potentially play a role in enabling them (Additional file 9: Figure S7).
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The efficiency of cDNA synthesis was also examined with conventional PCR for the PBGD gene with primers provided by the kit: the same intensity of a 151 bp band was obtained each time for the RNA+ control (also many tumor cDNA samples were run alongside as an additional control of quality and purity of the RNA samples).
Our histological analyses showed that tumor cells containing incorporated, nonapoptotic tumor cells are commonly observed in many tumor tissue samples.
However, the sensitivity of Sanger sequencing is suboptimal for many clinical tumor samples.
The limitation of conventional methods of LOH analysis is that many archived tumor samples are not accompanied by patient-matched control tissue resulting in the under-utilization of these potentially valuable resources for interrogation of LOH.
Further, the protocol applied for the assay was the same as for using the in situ PLA on ethanol fixed cells, i.e. not optimized, but the observation of signals is an important step in the development since it opens up for fast investigation of many clinical tumor samples available on TMAs in the future.
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