Fig. 2

Selected events of tumor-specific APA regulations that indicate clear 3’ UTR length modulations in cancer. (a) FGF2 in LUAD, a 3’ UTR shortening event. (b) CCNE1 in LUAD, a 3’ UTR lengthening event. (c, d) RNF43 in KIRC (3’ UTR shortening) and UCEC (lengthening). (a-d) Inside each left-hand panel, each group of bars represents the frequency of a specific CS in normal (blue) and tumor (red) samples. Bar groups are ordered by corresponding CS genomic coordinates. The text box shows the number of normal (N) and tumor (T) samples that were used for frequency calculation. The label box color indicates the trend of 3’ UTR length modulation in cancer. At the top, we indicate the number of cancer types with recurrent tumor-specific APA regulations. For example, “4 cancers” means that besides LUAD, tumor-specific APA regulation of FGF2 is also observed in three other cancer types with consistent patterns (see text and Additional file 3: Figure S4 for details). Inside each right-hand panel, the diagram represents a depiction of the 3′ end region of each gene with 3’ UTR models directly below the genome axis. The axis direction (right/left) indicates the relative DNA strand (plus/minus); the axis coordinates are offset by that of the gene’s first stop codon. On the axis, arcs show the relationship between CSs and stop codons based solely on annotation. Below the axis, vertical arrows indicate the positions of predicted CSs. Annotated and predicted CSs match well, but they are not expected to overlap exactly. An arrow pointing upwards (downwards) represents an increase (decrease) in frequency from normal to tumor. Arrow height represents the difference (Δ) of the increase/decrease. Bars and arrows of insignificant difference are colored gray. For clarity, CSs with frequencies lower than 5% in both normal and tumor samples, and that do not undergo any significant change in any cancer type considered herein are not shown. For a comprehensive view of all CSs with distribution of gene expression levels, see Additional file 3: Figure S4. A high-resolution version of this figure is available for download in Additional file 5