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Figure 2 | BMC Bioinformatics

Figure 2

From: IsoformEx: isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data

Figure 2

RPKM values of transcript isoforms of ZNF580 and ZNF581. RPKM values of transcript isoforms of ZNF580 and ZNF581 in the breast normal cell line (HME) and cancer cell line (MCF-7). The total number of exon slices in this transcript block having six overlapping transcripts was eight, and approximated RPKM values of the exon slices in MCF-7 cell line were α(s1) ≈ 10, α(s2) ≈ 8, α(s3) ≈ 14, α(s4) ≈ 30, α(s5) ≈ 20, α(s6) ≈ 0, α(s7) ≈ 45, and α(s8) ≈ 60, where α(·) is the RPKM value of an exon slice (for example, α(s1) and α(s8) are the RPKM values of the first and the eighth exon slices). Although the sixth exon slice can be expressed from uc002qln.1 and uc002qlq.1, the observed value was close to 0 due to its very small exon slice size. In order to handle this small exon effect (observed RPKM of very small exon slices is usually not reliable), we applied a lower weight.

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