Supplementary Figure 1 Supplementary Figure 1. Kaplan–Meier estimates of recurrence-free survival (RFS) according to the expression of every ten mRNA/lncRNA incorporated in the integrated signature in the training set (n=165). RNA expression level was coded as high or low according to the median expression level.

Supplementary Figure 2 Supplementary Figure 2. Validation of the expression of each mRNA/lncRNA incorporated in the integrated signature in the 33 paired tumor and normal breast tissues from the training set using quantitative real-time polymerase chain reaction (qRT-PCR). Expression of these mRNAs and lncRNAs measured by qRT-PCR was notably different between tumor and non-cancerous breast tissues and were significantly correlated with their microarray data.

Supplementary Figure 3 Supplementary Figure 3. Flowchart of the study design, patient selection and analytical strategy.

Supplementary Figure 4 Supplementary Figure 4. Details of the filtration procedures. For lncRNAs, either lncRNAs with fold change >1.5 and P 2 and P<0.1 were included.

PI Annexin v FITC PI Annexin v FITC MDA-MB-231 BT549 ControlHIST2H2BC siRNASNRPEP4 siRNA Supplementary Figure 5 Supplementary Figure 5. Down regulations of the HIST2H2BC and SNRPEP4 enhanced apoptosis induced by paclitaxel. A. Flow cytometric results of different status cells distribution in control and siRNAs knockdown breast cancer cells (left upper quadrant: necrotic cells; right upper quadrant: late apoptotic cells; left lower quadrant: live cells; right lower quadrant: early apoptotic cells). B. average proportions of apoptotic cells (including early and late apoptotic cells) from three independent experiment (two- sided Student’s t-test, *P<0.05, **P<0.01). A B

MDA-MB-231 BT549 ControlHIST2H2BC siRNASNRPEP4 siRNA MDA-MD-231BT549 Control (%) HIST2H2BC siRNA (%) SNRPEP4 siRNA (%) Control (%) HIST2H2BC siRNA (%) SNRPEP4 siRNA (%) G S G P*-0.021< Supplementary Figure 6 Supplementary Figure 6. Flow cytometric analyses of cell cycle distribution in control and siRNA knockdown breast cancer cells. Down regulations of the HIST2H2BC and SNRPEP4 enhanced G2-M arrest induced by pacxitaxel. The lower table shows the average proportions of G1, S, G2 cells from three independent experiment. For paclitaxel mainly induced G2-M arrest, the proportions of G2 cells were compared between control and siRNA transfected group (two-sided Student’s t-test). G1 S G2 G1 S G2 G1 S G2 G1 S G2 G1 S G2 G1 S G2