Interactive, multiscale navigation of large and complicated biological networks

Motivation: Many types of omics data are compiled as lists of connections between elements and visualized as networks or graphs where the nodes and edges correspond to the elements and the connections, respectively. However, these networks often appear as ‘hair-balls’—with a large number of extremely tangled edges—and cannot be visually interpreted

Elm1 kinase activates the spindle position checkpoint kinase Kin4

Elm1 phosphorylates a conserved residue within the Kin4 kinase domain to coordinate spindle position with cell cycle progression

Comparative RNAi screening identifies a conserved core metazoan actinome by phenotype

RNAi Screens in Drosophila and human cells for novel actin regulators revealed conserved roles for proteins involved in nuclear actin export, RNA splicing, and ubiquitination

Analysis of the hybrid proline-rich protein families from seven plant species suggests rapid diversification of their sequences and expression patterns-4

<p><b>Copyright information:</b></p><p>Taken from "Analysis of the hybrid proline-rich protein families from seven plant species suggests rapid diversification of their sequences and expression patterns"</p><p>http://www.biomedcentral.com/1471-2164/8/412</p><p>BMC Genomics 2007;8():412-412.</p><p>Published online 12 Nov 2007</p><p>PMCID:PMC2216038.</p><p></p>BioEdit) suggests a possible mechanism of independent acquisition of Gly-rich N-termini by inversion of a region encoding a part of a conventional Pro-rich domain. Triplets encoding glycine (when read left to right) are shown in red letters, while those encoding proline on the opposite strand are highlighted in gray (dark and bright shades used to distinguish individual triplets). Nucleotides conserved in at least two thirds of the sequences are shown in bold and marked by dots, absolutely conserved positions are marked by asterisks. Note the generally low degree of sequence conservation

Top: multiple alignment of the conserved C-terminal domain sequences from representative HyPRPs of all major phylogenetic branches (see Figure 3)

<p><b>Copyright information:</b></p><p>Taken from "Analysis of the hybrid proline-rich protein families from seven plant species suggests rapid diversification of their sequences and expression patterns"</p><p>http://www.biomedcentral.com/1471-2164/8/412</p><p>BMC Genomics 2007;8():412-412.</p><p>Published online 12 Nov 2007</p><p>PMCID:PMC2216038.</p><p></p> At – , Le – , Mt – , Os – , Pt – , St – , Zm – . Residues conserved between at least 75 % of the depicted sequences are shown on black background, positions with conserved amino acid properties on gray background. Conserved cysteines are shown in red and denoted by numbers, selected substitutions at the conserved cysteine positions are highlighted in blue. Bottom: consensus sequence expressed as a PROSITE – style pattern that detects most HyPRPs and no false positives

Left: an unrooted consensus phylogenetic tree (cladogram) of nucleotide sequences encoding the conserved C-terminal domains of HyPRPs from potato and , constructed by the ML method (see Materials and Methods)

<p><b>Copyright information:</b></p><p>Taken from "Analysis of the hybrid proline-rich protein families from seven plant species suggests rapid diversification of their sequences and expression patterns"</p><p>http://www.biomedcentral.com/1471-2164/8/412</p><p>BMC Genomics 2007;8():412-412.</p><p>Published online 12 Nov 2007</p><p>PMCID:PMC2216038.</p><p></p> Bootstrap values above 50 % (from 500 replicates) are shown above the individual branches, numbers below branches denote bootstrap values of a NJ tree from the same input data. The ML and NJ trees agreed in all clades with bootstrap support over 50 % with exception of (i) swapping St1 and At1g62500 and (ii) swapping At4g15160 and At4g15160, in both cases with NJ bootstrap values below 76 %. loci are denoted by standard AGI locus identifiers. Gene names are color-coded and typographically marked according to the composition of the N-terminal domains of the encoded proteins as in Figure 1; in addition, proline- and glycine-rich N-terminal domains (not fitting into the categories of proline- or glycine-rich, but containing more than 10 % of each of these amino acids) are shown in blue. genes with reliable potato orthologues are denoted by black filled squares, chromosomal clusters and tandem duplications are marked by chromosome cluster numbers to the right of the tree (see Additional file ). Right: expression profiles of selected genes according to the publicly available expression data: top – orthologues of potato genes (with potato expression patterns from Figure 1 for comparison; apical stems shown in the "shoot apex" position), bottom – genes from the four chromosomal clusters. Order of genes within each cluster corresponds to that in the tree