IgorRodchenkov
commented
8 years ago Not a bug. The user's task simply required a custom made pattern SIF (to exclude long-range via intermediate complex and small molecules KRAS-MTOR, etc. interaction types).
User (colm.ryan at ucd dot ie) reported to pc-info:
"I have downloaded the file "Pathway Commons.7.All.EXTENDED_BINARY_SIF" and found a number of direct connections not visible through the web interface [Igor: via PCViz or using a PATHSBETWEEN PC2 graph query]. For example in the SIF file KRAS is reported to 'controls-state-change-of' AKT3 and MTOR. However searching the web interface for paths between these two genes draws a blank. The data source for both interactions is pid, with the following PUBMED IDs :'10383446;10570282;10648629;10669418;11029009;11136732;11438544;11546794;12077227;12421919;12431978;12682230;12750173;12951049;15994292;16033886;16456542;1652056;16787925;16798838;18033240;18662984;20153221;7982920;8052307;9029085;9307042;9512493;9593664;9722546', and the following Pathway Names: 'BCR signaling pathway;CXCR3-mediated signaling events;CXCR4-mediated signaling events;Class I PI3K signaling events;Class I PI3K signaling events mediated by Akt;E-cadherin signaling in the nascent adherens junction;EPHA2 forward signaling;ErbB1 downstream signaling;ErbB2/ErbB3 signaling events;FAS (CD95) signaling pathway;IFN-gamma pathway;IL2 signaling events mediated by PI3K;IL4-mediated signaling events;IL8- and CXCR1-mediated signaling events;IL8- and CXCR2-mediated signaling events;Insulin Pathway;Nephrin/Neph1 signaling in the kidney podocyte;PDGFR-beta signaling pathway;Plasma membrane estrogen receptor signaling;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met);Signaling events mediated by VEGFR1 and VEGFR2;TCR signaling in na\xc3\xafve CD4+ T cells;TCR signaling in na\xc3\xafve CD8+ T cells;Trk receptor signaling mediated by PI3K and PLC-gamma;VEGFR1 specific signals'. Doing a connected molecule search on PID does not reveal the reported connections either (no direct link between KRAS and AKT3). Any ideas what is going wrong or how I am misinterpreting the data?"
I confirm, that's the case both in PC2 v7 and v8 (pre-release). I.e., records: KRAS\tcontrols-state-change-of\tAKT3\t... KRAS\tcontrols-state-change-of\tMTOR\t... are indeed present in the Pathway Commons_All.__SIF.hgnc.sif.gz but PCViz or PC2 graph (PATHSBETWEEN, PATHSFROMTO) queries using KRAS,AKT3 or KRAS,MTOR pairs won't return any connection, result.