Selected examples of the detected SREs.

<p># Occ. is abbreviation for number of occurrences.</p

Illustration of equation (12).

<p>Two possible SREs are considered in this example, one for SF1, and the other one for SF2. Four different conditions are shown. Binding of either SF can affect the probability of spliceosome assembly. The arrow connecting two SFs indicates the interaction between two SFs. The contribution to spliceosome assembly from SFs is represented by , and .</p

Illustration of Proposition 1.

<p>The dashed curve is for and the dashed lines with arrows define the region where or . The dash-dot curve is for and the dash-dot lines with arrows define the region where or . The solid lines define the decision region of described in Proposition 1.</p

Percentage of different types of SRE pairs.

<p>Two hundred and forty-one SRE pairs are detected in different or same regions. This figure shows breakdown of the SRE pairs in different regions.</p

Summary of the final selected models in each tissue.

<p>The second column is the number of ASEs used in model inference. The third and fourth columns list the number of SREs and SRE pairs in the final model. The last column gives the percentage of the variance explained () by the final model.</p

Five regions around ASEs used to extract SREs and the model inference framework.

<p>(<b>A</b>) All hexamers in the five regions around ASEs are considered as candidate SREs. UU (upstream/upstream) stands for the 5′ end of the upstream intron. UD (upstream/downstream) denotes the 3′ end of the upstream intron. DU and DD are defined in a similar way. EXON stands for the ASE region. (<b>B</b>) The inference framework for detecting active SREs and SRE pairs. RCV: refitted cross-validation; OLS: ordinary least squares regression.</p

Expression level of several splicing factors in 9 tissues.

<p>The expression levels are calculated from the RNA-Seq data <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054885#pone.0054885-Wang1" target="_blank">[1]</a> as reads per kilobases per million mapped reads (RPKM).</p

Additional file 5 of Longitudinal multi-omics study of palbociclib resistance in HR-positive/HER2-negative metastatic breast cancer

Additional file 5. Table S5. Summary of oncogenic events in paired PDtumors. Endocrine therapy: endocrine therapy in combination with Palbo treatment

Additional file 2 of Longitudinal multi-omics study of palbociclib resistance in HR-positive/HER2-negative metastatic breast cancer

Additional file 2. Table S2. PFS association statistics for clinical variables and molecular features e.g. p-value, HR ratio, median PFS

Additional file 3 of Longitudinal multi-omics study of palbociclib resistance in HR-positive/HER2-negative metastatic breast cancer

Additional file 3. Table S3. PFS associationstatistics for gene signatures (GSVA scores)