Table 2 Fold-changes between thrombin-treated samples and control samples (SRA: SRP008482).
From: Assessing the impact of human genome annotation choice on RNA-seq expression estimates
| Â | RNA-seq data with TPM Expression Estimates (OSA Pipeline) | ||||||
|---|---|---|---|---|---|---|---|
Gene | RT-qPCR | AceView | H-InvDB | Ensembl | Vega | UCSC | RefSeq |
TRAF1 | 2.862 | 3.029 | 3.034 | 3.025 | 2.998 | 2.934 | 2.922 |
FANCD2 | -1.050 | -0.782 | -0.687 | -0.888 | -0.856 | -0.840 | -0.840 |
CELF1 | -0.202 | -0.138 | -0.202 | -0.098 | -0.098 | -0.239 | -0.275 |
Average Absolute Deviation from RT-qPCR | 0.166 | 0.178 | 0.143 | 0.145 | 0.106 | 0.114 | |
| Â | RNA-seq data with FPKM Expression Estimates (TopHat/Cufflinks Pipeline) | ||||||
Gene | RT-qPCR | AceView | H-InvDB | Ensembl | Vega | UCSC | RefSeq |
TRAF1 | 2.862 | 3.874 | 3.845 | 3.797 | 3.719 | 3.677 | 3.674 |
FANCD2 | -1.050 | 0.057 | 0.057 | -0.345 | -0.322 | -0.202 | -0.151 |
CELF1 | -0.202 | 0.642 | 0.516 | 0.595 | 0.585 | 0.390 | 0.356 |
Average Absolute Deviation from RT-qPCR | 0.987 | 0.936 | 0.812 | 0.791 | 0.751 | 0.756 | |