Figure S1: Clustering analysis of the expression ratio of the sense and antisense pair of transcripts A B C D E F A B C D E F dT Random Sense : Antisense.

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Figure S1: Clustering analysis of the expression ratio of the sense and antisense pair of transcripts A B C D E F A B C D E F dT Random Sense : Antisense = 3:1 Sense : Antisense = 1:1 Sense : Antisense = 1:3 Flag (Protein-Coding / Protein-Coding) (Protein-Coding / Non-Coding) (Non-Coding / Non-Coding) Normal Cancer

(a) Plots of (protein-coding, protein-coding) pairs Figure S2: Changes in expression for sense-antisense gene pairs in cancer tissues, compared with surrounding normal tissues.

(b) Plots of (protein-coding, non-coding) pairs Figure S2: Changes in expression for sense-antisense gene pairs in cancer tissues, compared with surrounding normal tissues.

(c) Plots of (non-coding, non-coding) pairs Figure S2: Changes in expression for sense-antisense gene pairs in cancer tissues, compared with surrounding normal tissues.

Figure S3: Changes in expression for sense-AFAS gene pairs in cancer tissues, compared with surrounding normal tissues.

A B C D A B CD E E Flag dTRandom Normal Cancer Sense : AFAS = 3:1 Sense : AFAS = 1:1 Sense : AFAS = 1:3 Figure S4: Clustering analysis of the expression ratio of well- known genes (sense transcripts) and their putative antisense transcripts.

Truncated N C N C Expressional intensity of sense gene Expressional intensity of AFAS gene Figure S5: Expression intensities detected by probes designed for the sense gene U69611 and its corresponding AFAS transcript.

500 bp Sense transcript Probe Position Average Intensity Normal Cancer Figure S6: Average Expression levels detected by AFAS probes within every 500 bases with respect to the both termini of sense transcripts.