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In this study, we observed that greater stemness, as defined by microarray similarity, was inversely associated with brain tumor malignancy (Fig. S1C).
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No sequence similarity was detected with mammalian transcripts as checked by BLAST search, and no cross-hybridization was observed in microarray hybridization experiments with RNAs from mammalian tissues (Yadetie et al., in preparation).
Although similarity is measured by the marks as entities, similarities weigh more heavily than differences.
Similarity is measured by Dali Z-scores.
Comparing gene expression profiles from multiple experiments is notoriously difficult and typically any true similarities are swamped by technical differences in microarray vendor, normalization strategies and analytical approach.
Linear regressions between hybridization intensities and actual nucleotide similarities were done for each microarray while excluding nonhybridized probe noises (empirically determined to be below 80% genomic DNA-probe match) by using the stats R package (R Development Core Team 2009).
The similarities are by design.
Nevertheless, microarray profile similarity effectively distinguished all GSC samples from non-fractionated GBM (Fig. S1B), whereas CD133 expression failed to distinguish any GSCs from GBM, indicating relative superiority in defining CSC lines by microarray profile similarity.
Some of the DEGs detected by the microarray analysis were also analyzed by RT-PCR, and the gene responses detected by the microarray analysis were confirmed by the RT-PCR results (Additional file 2: Figure S1). Figure 1 Similarity of gene responses across different fog treatments.
The similarities were many.
Self-similarities were ignored.
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