Statistical analysis with randomized networks.

<p>Comparison of the classification results by the randomized networks and the true network. The λ parameter was fixed to be 0.1 in all the experiments. The blue star and the red star represent the results with the real network and without network (base EM), respectively. The boxplot shows the results with the randomized networks.</p

Correlation between estimated transcript expressions and ground truth in simulation.

<p>In (A) and (B) x-axis are labeled by the compared methods and different λ parameters of Net-RSTQ. The bar plots show the results of running Net-RSTQ with 100 randomized networks. In (C) and (D), x-axis are the percentage of edges that are removed from the networks. The plots show the results of running Net-RSTQ with the incomplete networks. (A) and (C) report the results of 109 transcripts of the isoforms in the same gene with different domain-domain interactions. (B) and (D) report the results of 712 isoforms in genes with multiple isoforms.</p

An isoform transcript network based on protein domain-domain interactions.

<p>(A) The subnetwork shows the domain-domain interactions among transcripts from four human genes, CD79B, CD79A, LCK and SYK. In the network, the nodes represent isoform transcripts, which are further grouped and annotated by their gene name; and the edges represent domain-domain interactions between two transcripts. Each edge is also annotated by the interacting domains in the two transcripts. (B) RefSeq transcript annotations of CD79A and CD79B are shown with Pfam domain marked in color. The Pfam domains were detected with Pfam-Scan software. Note that no interaction is included between transcripts NM_001039933 and NM_000626 of gene CD79B without assuming self-interactions for modeling simplicity. For better visualization, only the interactions coincide with PPI are shown in the figure.</p

Running time.

<p>The plots show the CPU time (Intel Xeon E5-1620 with 3.70GHZ) for running the Net-RSTQ algorithm one three networks, the small transcript network, the large transcript network, and an artificial huge network of 10000 transcripts.</p

Additional file 1: of Opioid doses required for pain management in lung cancer patients with different cholesterol levels: negative correlation between opioid doses and cholesterol levels

A list of current patients’ information. The records of 282 patients were listed after removing primary information. ID was the reference number provided by the authors for easier accession. “Chol level” represented the serum cholesterol level measured and recorded. “Year” represented when the initial diagnosis of cancer was made. “Initial dose”, “stable dose” and “converted dose” represented the initial dose opioid administration, the final dose of opioids used for analysis and the dose when converted to equivalent oxycodone hydrochloride, respectively. The “increased” column, “1” or “0” were used to represented that “stable dose” was higher than “initial dose”. If the patient has one or multiple additional measurement of cholesterol during the first month after opioid administration, the cholesterol level with largest difference from initial cholesterol level was selected, recorded in “Chol level with largest difference” column, and normalized to the initial cholesterol level. (XLSX 43 kb