PMC:1481596 / 24382-27023
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1481596","sourcedb":"PMC","sourceid":"1481596","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1481596","text":"Pheromone signaling pathway\nThe yeast Saccharomyces cerevisiae may be present in one of two haploid cell types, which are able to mate. Pheromones released by one type of cell bind to a specific receptor of the other type. This triggers the activation of a scaffold protein-bound mitogen-activated protein kinase (MAPK) cascade and subsequent activation of nuclear proteins that control subsequent cellular events. In a recent paper, Spirin et al. [13] identified a subnetwork of proteins involved in this process within a yeast protein interaction network [21]. We analyzed this subnetwork using the COD to see if our method can extract elements of temporal ordering. The subnetwork identified by Spirin et al. and its Tree of Complexes representation is given in Figure 4. In this case, the protein network is not chordal. First, the COD method identifies and connects a pair of weak siblings, MKKl and MKK2 .Then, to transform the network to a chordal graph, three additional edges are added: (SPH1, SPA2), (FUS3, KSS1), and (STE11, STE7). In this case, some functional groups will contain more than one protein complex.\nFigure 4 Pheromone Signaling Pathway. The pheromone signaling pathway. (a) The network. (b) The Tree of Complexes representation. For the description of the elements of the tree see the text. This network admits six different Tree of Complexes representations: (i) functional group H can be connected to either B or C; (ii) any interconnection pattern that spans groups E, F, and G can be chosen. If we ask for a tree with maximum number of leaves, the number of tree variants is reduced to two (option (i)).\nThe MAPK cascade module consists of three sequentially acting protein kinases: MAP kinase kinase kinase (STE11) MAP kinase kinase (STE7) and MAP kinase (KSS1, FUS3) [22]. MKKl and MKK2 are two redundant protein kinase kinases (most similar to STE7) [23]. Their redundancy is properly captured by the ∨ (OR) in their functional group (H). The MAP kinases KSS1 and FUS3 are two separate kinases both activated by STE7 each of which is essential for a different program: FUS3 – for mating; KSS1 – for the filamentous growth [24]. Once again this is correctly captured by ∨ (OR) in groups F and G. STE5 is a scaffold protein of the MAPK module. It recruits MAPK module kinases (STE11, STE7, FUS3). This is consistent with the central position of a functional group containing STE5 in the tree and relative to the paths of STE7, STE11 and FUS3. Finally, nuclear proteins DIG1 and DIG2 (necessary for transcription inhibition, which are regulated by both FUS3 and KSS1) enter at the endpoint (node F) in the tree.","divisions":[{"label":"title","span":{"begin":0,"end":27}},{"label":"p","span":{"begin":28,"end":1123}},{"label":"figure","span":{"begin":1124,"end":1316}},{"label":"label","span":{"begin":1124,"end":1132}},{"label":"caption","span":{"begin":1134,"end":1316}},{"label":"p","span":{"begin":1134,"end":1316}},{"label":"p","span":{"begin":1317,"end":1633}}],"tracks":[{"project":"2_test","denotations":[{"id":"16722537-14517352-1694491","span":{"begin":449,"end":451},"obj":"14517352"},{"id":"16722537-11752246-1694492","span":{"begin":558,"end":560},"obj":"11752246"},{"id":"16722537-15567849-1694493","span":{"begin":1800,"end":1802},"obj":"15567849"},{"id":"16722537-8386320-1694494","span":{"begin":1884,"end":1886},"obj":"8386320"},{"id":"16722537-15692041-1694495","span":{"begin":2156,"end":2158},"obj":"15692041"}],"attributes":[{"subj":"16722537-14517352-1694491","pred":"source","obj":"2_test"},{"subj":"16722537-11752246-1694492","pred":"source","obj":"2_test"},{"subj":"16722537-15567849-1694493","pred":"source","obj":"2_test"},{"subj":"16722537-8386320-1694494","pred":"source","obj":"2_test"},{"subj":"16722537-15692041-1694495","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93ecac","default":true}]}]}}