By comparing expression data between amplified and non-amplified material, we have observed that the ratios were significantly different for a number of genes, in addition to a set of genes whose ratios were neither conserved nor rejected.
A ratio of averaged normalized gene expression value for each gene was generated by comparing expression in HEPG2 to hES-MSC cells.
Furthermore, we have integrated expression data from both transcriptomic and proteomic profiling to analyze the gene regulation across two porcine tissues by comparing tissue expression ratios of transcripts and proteins.
To take into account the genetic background differences, we measured allele-specific gene expression of 18- and 4-bp sfl alleles in 15 different "controlled" genetic backgrounds, but keeping the background the same for the two alleles by comparing their expression ratios in heterozygotes.
Microarray data were validated by comparing the expression ratio of 14 genes (adhE, clpB, dnaK, hfq, kpdE, marR, minD, nfrB, ompW, soxS, trxC, wzxE, zntA and znuA) with the results of expression determined by real-time PCR (Additional file 3: Figure S1).
Microarray data were validated by qRT-PCR on 11 differentially expressed genes with different functions and by comparing their average expression ratios (DS/controls) with those of the array (Additional file 3).
While this is valid, the approach described here more accurately reproduces the standard experimental conditions for two-color microarray expression analysis by comparing the ratio of gene expression between two different samples.
To achieve this purpose, we assigned a co-expression (or co-changing) score to a protein protein interaction by comparing the expression-change ratios of the two genes in a sample with representative values.
By comparing the ratio of expression, we found that PTPN22 expression in RA cases is significantly different compared with that in controls (P = 6 × 10-9), whish is a result of significantly higher expression of PTPN22-long isoforms and simultaneously slightly lower expression of PTPN22_v4 in patients (Table 1).
