Influence of the gene structure and number of expressed transcripts in a comparative splicing analysis between different genes (synthetic data)

Estimation of the relative transcript concentrations for different genes. The -axis shows the MAE (%) between simulated and estimated relative concentration of transcripts. The -axis shows the different genes used in the simulation (CASP2, HNRPA2B1, BCL2L1, BIRC5, TERT, VEGF, BAX and WT1). The structure of the different transcripts of these genes and the location of probes is shown in Additional file 1 (Figures S1-S8). Prediction of the splicing structure for different genes. The -axis shows the Hamming distance error rate between real and predicted pre-mRNA splicing structures. Sensitivity of SPACE for different genes. Specificity of SPACE for different genes.<p><b>Copyright information:</b></p><p>Taken from "SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays"</p><p>http://genomebiology.com/2008/9/2/R46</p><p>Genome Biology 2008;9(2):R46-R46.</p><p>Published online 29 Feb 2008</p><p>PMCID:PMC2374713.</p><p></p

Predicted structure and estimated concentrations for the BIRC5 (apoptosis inhibitor survivin) gene in the 'central point' (synthetic data)

Structure of the different transcripts of the BIRC5 gene and location of probes used in the simulation. Representation of the real and predicted splicing structures for the BIRC5 gene given by the probes used. In the graphic representing the real splicing structure the probes that match perfectly with the transcripts are represented by a white box (100% matching) and no hybridization is shown by a black box (0% matching). Gray levels show intermediate matching values. We have assumed that junction probes which include one side of the junction hybridize partially (20%). Estimated relative concentrations of the three isoforms of BIRC5 gene. In each of the three graphics simulated and estimated relative concentration of each isoform is represented.<p><b>Copyright information:</b></p><p>Taken from "SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays"</p><p>http://genomebiology.com/2008/9/2/R46</p><p>Genome Biology 2008;9(2):R46-R46.</p><p>Published online 29 Feb 2008</p><p>PMCID:PMC2374713.</p><p></p

Influence of noise on the estimation of relative transcript concentrations of BIRC5 gene (synthetic data)

BIRC5 gene structure is shown in Figure 6a and in Additional file 1 (Figure S4). Additive noise effect on estimation of relative transcript concentrations. The -axis shows the MAE between the relative concentration of transcripts without noise and that estimated by the algorithm under the effect of different degrees of additive noise (MAE %). Additive noise is in the form of + with ~(0, ). The units of the -axis are the variances of the additive error added to the simulated concentrations (10, 100, 1,000, 10,000, 100,000). These variances represent roughly 0.5%, 2%, 5%, 15% and 50% of the energy of the signal, respectively. Multiplicative noise effect on estimation of relative transcript concentrations. The -axis shows the MAE between simulated and estimated relative concentrations under the effect of different degrees of multiplicative noise (MAE %). Multiplicative noise is in the form of ·with ~(0, ). The units of the -axis represent the variances of the multiplicative error (5 × 10, 0.0005, 0.005, 0.05, 0.5). These variances represent roughly 0.7%, 2%, 7%, 25% and 100% of the energy of the signal, respectively. The different degrees of additive and multiplicative noise are tested while the other parameters are in the 'central point' condition (40 arrays and probes at exons and junctions). This means that there is always a component of additive and multiplicative noise in the form of ·+ . Errors are represented by boxplots. A boxplot is a graphical representation of the variability of a random signal. They are composed by a box and a whisker. The box extends from the lower quartile to the upper quartile values and there is an additional horizontal line that shows the median. The whiskers are vertical lines extending from each end of the boxes to show the extent of the rest of the data. Outliers are data with values beyond the ends of the whiskers and are represented by crosses.<p><b>Copyright information:</b></p><p>Taken from "SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays"</p><p>http://genomebiology.com/2008/9/2/R46</p><p>Genome Biology 2008;9(2):R46-R46.</p><p>Published online 29 Feb 2008</p><p>PMCID:PMC2374713.</p><p></p

Experiment done with the CASP2 gene, transcripts Casp2L and Casp2S (synthetic data)

Three arrays were performed with a concentration ratio between the two isoforms of CASP2 gene equal to 5:1 and another three with the opposite ratio 1:5. Structure of the two transcripts of CASP2 gene and location of probes in the microarray. Real structure of CASP2 gene indicated by probes. Probes that match perfectly are represented in white (100%), no hybridization in black (0%) and partial hybridization by different shades of gray (20%). Predicted splicing structure for CASP2 gene with the alternating concentration ratio 5:1. If compared with the real structure of CASP2 transcripts (b), a strong similarity is noticed. Real and estimated relative concentrations of the two isoforms of CASP2 gene in the experiment.<p><b>Copyright information:</b></p><p>Taken from "SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays"</p><p>http://genomebiology.com/2008/9/2/R46</p><p>Genome Biology 2008;9(2):R46-R46.</p><p>Published online 29 Feb 2008</p><p>PMCID:PMC2374713.</p><p></p

Proportion of predicted number of transcripts for the simulation performed with 100 genes (synthetic data)

The 100 genes used have been randomly selected from the human genome with two to five transcripts. Each of the genes have been simulated 200 times for different noise, concentrations and affinities. The area of each circle represents the proportion of times the corresponding predicted number is chosen by the algorithm for a given number of transcripts. The algorithm tends to underestimate the number of transcripts as the real number of transcripts increases.<p><b>Copyright information:</b></p><p>Taken from "SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays"</p><p>http://genomebiology.com/2008/9/2/R46</p><p>Genome Biology 2008;9(2):R46-R46.</p><p>Published online 29 Feb 2008</p><p>PMCID:PMC2374713.</p><p></p