MOESM6 of Improving chemical similarity ensemble approach in target prediction

Additional file 6.  Kinase test data set

Parallel evolution of <i>Pcdh15</i> in bats and dolphins.

<p>(A) Gene tree of <i>Pcdh15</i> based on nucleotide sequences. Numbers above the branches are the ML and NJ bootstrap values, respectively. Numbers below the branches are Bayesian posterior probabilities. * indicates all values equal 100. (B) Gene tree of <i>Pcdh15</i> based on nonsynonymous changes and amino acid sequences. Numbers along the branches are NJ bootstrap values. (C) Species tree based on the previous studies <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002788#pgen.1002788-Teeling1" target="_blank">[26]</a>–<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002788#pgen.1002788-Murphy2" target="_blank">[28]</a>. Symbols above the branches correspond to amino acid replacements. ★ indicates parallel amino acid replacements presenting on branches <i>b</i>, <i>d</i>, and <i>g</i>: M946I and D1278E. ▴ indicates parallel amino acid replacements presenting on branches <i>b</i> and <i>g</i>: N218D, Q310E, E393V, T427S, A433V, I438V, T490I, V546F, I643V, N666K, K820R, I853V, K856T, M946I, V952A, R999L, T1139R, F1160L, A1173S, K1275R, D1278E, and I1404V. • indicates parallel amino acid replacements presenting on branches <i>d</i> and <i>g</i>: A726D, M946I, and D1278E. ▪ indicates parallel amino acid replacements presenting on branches <i>b</i> and <i>d</i>: L423V, Q468P, H765Y, F876L, M946I, F984S, V1019I, and D1278E.</p

Summary of selective pressure analysis for the hearing genes <i>Cdh23</i>, <i>Pcdh15</i>, and <i>Otof</i>.

<p>Summary of selective pressure analysis for the hearing genes <i>Cdh23</i>, <i>Pcdh15</i>, and <i>Otof</i>.</p

Parallel evolution of <i>Otof</i> in bats and dolphins.

<p>(A) Gene tree of <i>Otof</i> based on nucleotide sequences. Numbers above the branches are the ML and NJ bootstrap values, respectively. Numbers below the branches are Bayesian posterior probabilities. * indicates all values equal 100. (B) Gene tree of <i>Otof</i> based on the nonsynonymous changes and corresponding amino acid sequences. Numbers on the branches are NJ bootstrap values. (C) Species tree based on the previous studies <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002788#pgen.1002788-Teeling1" target="_blank">[26]</a>–<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002788#pgen.1002788-Murphy2" target="_blank">[28]</a>. Symbols above the branches correspond to amino acid replacements. ★ indicates a parallel amino acid replacement presenting on branches <i>b</i>, <i>d</i>, and <i>g</i>: D396E. ▴ indicates parallel amino acid replacements presenting on branches <i>b</i> and <i>g</i>: P191H, G213A, D396E, and V440M. • indicates parallel amino acid replacements presenting on branches <i>d</i> and <i>g</i>: D396E and R1238H. ▪ indicates a parallel amino acid replacement presenting on branches <i>b</i> and <i>d</i>: D396E.</p

Parallel evolution of <i>Cdh23</i> in bats and dolphins.

<p>(A) Gene tree of <i>Cdh23</i> based on nucleotide sequences that is consistent with the species tree. Numbers above the branches are the ML and NJ bootstrap values, respectively. Numbers below the branches are Bayesian posterior probabilities. * indicates all values equal 100. (B) Gene tree of <i>Cdh23</i> based on nonsynonymous mutations and the amino acid sequences. Numbers along the branches are NJ bootstrap values. (C) Species tree based on previous studies <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002788#pgen.1002788-Teeling1" target="_blank">[26]</a>–<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002788#pgen.1002788-Murphy2" target="_blank">[28]</a>. Symbols above the branches correspond to amino acid replacements. ★ indicates a parallel amino acid replacement presenting on branches <i>b</i>, <i>d</i>, and <i>g</i>: R204Q. ▴ indicates parallel amino acid replacements presenting on branches <i>b</i> and <i>g</i>: R204Q, D517N, P518A, S639N, N737S, S747T, A1080S, K1141T, S1314T, A1382S, I1673V, N1697D, L1960F, L1974I, A2146V, G2229S, V2427I, T2439R, R2639K, Q2725L, and N3180S. • indicates a parallel amino acid replacement presenting on branches <i>d</i> and <i>g</i>: R204Q. ▪ indicates parallel amino acid replacements presenting on branches <i>b</i> and <i>d</i>: R204Q, R535K, T904I, and V1691I.</p

Primers for hIPI3 qRT-PCR.

<p>Primers for hIPI3 qRT-PCR.</p

Expression patterns of the gene <i>Otof</i> in different cerebral cortexes of bats.

<p>The * indicates baseline value.</p

hIPI3 interacts with hMCM7 in co-IP from total cell extracts.

<p>(A) The HA-hIPI3 stable HeLa cells were arrested at the G1/S boundary by Mimosine, and whole-cell extracts (WCE) were immunoprecipated with an anti-HA antibody or the control mouse IgG. Co-IP assay results showed that the hIPI3 interacts with hMcm7. (B) An anti-Mcm7 antibody was used to perform a reverse co-IP experiment. hMCM7 was found to interact with HA-hIPI3 in the reciprocal co-IP.</p

Cell proliferation was largely inhibited after hIPI3 silencing.

<p>HeLa cells were treated with the transfection reagent, negative control siRNA or two different hIPI3 siRNAs and grown for 3 weeks for the colony formation assay. The numbers of colonies were normalized to that of the transfection agent-treated cells. The data show that after siRNA silencing, the number of colonies was significantly lower that the two controls.</p

The hMCM7 and hCDC6 total protein levels were not reduced after hIPI3 silencing.

<p>HeLa cells were treated with hIPI3 siRNA, and the protein levels of hIPI3, hMCM7 and hCDC6 were analyzed by immunoblotting (A), and relative signal intensities were quantified (B). The results demonstrate that even though the hIPI3 protein has been knocked down by ~90%, the hMCM7 and hORC6 protein levels were not reduced.</p