Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina-3

<p><b>Copyright information:</b></p><p>Taken from "Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina"</p><p>http://www.biomedcentral.com/1471-2164/8/325</p><p>BMC Genomics 2007;8():325-325.</p><p>Published online 17 Sep 2007</p><p>PMCID:PMC2045113.</p><p></p

Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina-0

<p><b>Copyright information:</b></p><p>Taken from "Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina"</p><p>http://www.biomedcentral.com/1471-2164/8/325</p><p>BMC Genomics 2007;8():325-325.</p><p>Published online 17 Sep 2007</p><p>PMCID:PMC2045113.</p><p></p>lusters i.e. clusters with only a single member ORF (right y-axis) for clusterings made with different inflation values (x-axis)

Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina-1

<p><b>Copyright information:</b></p><p>Taken from "Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina"</p><p>http://www.biomedcentral.com/1471-2164/8/325</p><p>BMC Genomics 2007;8():325-325.</p><p>Published online 17 Sep 2007</p><p>PMCID:PMC2045113.</p><p></p>ro (x-axis) for species which were analysed with InterProScan. Species are coloured by phyla. Names of the species, plotted as abbreviations beside the data points, are explained in Table 1

Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina-10

<p><b>Copyright information:</b></p><p>Taken from "Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina"</p><p>http://www.biomedcentral.com/1471-2164/8/325</p><p>BMC Genomics 2007;8():325-325.</p><p>Published online 17 Sep 2007</p><p>PMCID:PMC2045113.</p><p></p>ditionally two example screenshots are shown. See text for further details

Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina-13

<p><b>Copyright information:</b></p><p>Taken from "Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina"</p><p>http://www.biomedcentral.com/1471-2164/8/325</p><p>BMC Genomics 2007;8():325-325.</p><p>Published online 17 Sep 2007</p><p>PMCID:PMC2045113.</p><p></p>c ORF redundancy (y-axis) versus the size of the genome in ORFs (x-axis) for each species. See Figure 2 for further details

Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina-7

<p><b>Copyright information:</b></p><p>Taken from "Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina"</p><p>http://www.biomedcentral.com/1471-2164/8/325</p><p>BMC Genomics 2007;8():325-325.</p><p>Published online 17 Sep 2007</p><p>PMCID:PMC2045113.</p><p></p>he largest amount of variation in the counts of ORFs with an InterPro entry. The PCA for InterPro entries (a) is shown in picture 11, for InterPro entry structures (b) data not shown. 100 InterPro entries or InterPro entry structures having the most extreme PCA loadings on the two PCs shown are coloured with orange (TOP 100), while the rest are 4373 InterPro entries and 16319 InterPro structures are in blue. InterPro entries identifiers are shown for 20 most extreme PCA loadings

Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina-11

<p><b>Copyright information:</b></p><p>Taken from "Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina"</p><p>http://www.biomedcentral.com/1471-2164/8/325</p><p>BMC Genomics 2007;8():325-325.</p><p>Published online 17 Sep 2007</p><p>PMCID:PMC2045113.</p><p></p>usters i.e. clusters with only a single member ORF (right y-axis) for clusterings made with different inflation values (x-axis)

Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina-8

<p><b>Copyright information:</b></p><p>Taken from "Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina"</p><p>http://www.biomedcentral.com/1471-2164/8/325</p><p>BMC Genomics 2007;8():325-325.</p><p>Published online 17 Sep 2007</p><p>PMCID:PMC2045113.</p><p></p

Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina-4

<p><b>Copyright information:</b></p><p>Taken from "Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina"</p><p>http://www.biomedcentral.com/1471-2164/8/325</p><p>BMC Genomics 2007;8():325-325.</p><p>Published online 17 Sep 2007</p><p>PMCID:PMC2045113.</p><p></p>the number of ORFs shown by clusters (rows) and by species (columns). Both rows and columns are ordered by hierarchical clustering to group similar rows or columns together. The dendrogram from hierarchical clustering is shown for columns and the phylum of species is indicated by a column colour bar between the heatmap and the dendrogram. Under the heatmap each species is specified by an abbreviation explained in Table 1. On the left side of the main heatmap a black and white side heatmap shows the percentage of ORFs in a cluster that have an InterPro entry of all cluster's ORFs analysed with InterProScan ("wIPR"), cluster's stability and cluster's Saccharomycotina to Pezizomycotina ratio in a clustering where inflation value () was 1.1 ("S/P r 1.1"). Stability reflects the ratio of cluster size between a clustering where = 3.1 to that where = 1.1. As Figure 1 shows, when is set to its minimum value (1.1), TRIBE-MCL clustering produces a minimum amount of clusters and orphan clusters. In consequence the clusters are on average larger when = 1.1. The ratio between cluster size = 3.1 and = 1.1 is shown as a percentage. "S/P 1.1" reflects the ratio of count of Saccharomycotina ORFs to Pezizomycotina ORFs in a cluster when = 1.1. By comparing "S/P 1.1" to the species distribution of a cluster shown on the main heatmap one can see if a cluster retains the Saccharomycotina to Pezizomycotina ratio when = 1.1. On the right side of the main heatmap, a side heatmap shows various functional classifications for the clusters. Whether or not the cluster has a Funcat classification ("Funcat") or has an ORF found in metabolic model iMH805 is shown ("iMH805"). Whether the proteins in the cluster are predicted by Protfun to have a signal sequence directing them into either mitochondrion or secretion pathway ("TargetP"), have transmembrane domains ("TMHMM") or are predicted to be enzymes is shown ("Enz."). Clusters belonging to regions A: "Pezizomycotina abundant", B: "Pezizomycotina specific", C: "Saccharomycotina absent" and D: "Saccharomycotina unique" are specified by a vertical bar between main and right heatmap

Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina-2

<p><b>Copyright information:</b></p><p>Taken from "Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina"</p><p>http://www.biomedcentral.com/1471-2164/8/325</p><p>BMC Genomics 2007;8():325-325.</p><p>Published online 17 Sep 2007</p><p>PMCID:PMC2045113.</p><p></p>ic ORF redundancy (y-axis) versus the size of the genome in ORFs (x-axis) for each species. See Figure 2 for further details