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Supplemental Table S1-C contains instances where no interacting proteins were found or instances where the TAP-tagged PKs was not recovered in sufficient amounts to be identified by MS/MS analysis but possible interacting proteins were found.
The genes coding for the interacting proteins were found using Biomart [ 48] to mine Ensembl cross-references.
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Such characteristic spectral periodicities have been previously identified for a number of protein families, including interacting proteins such as certain growth factors and their receptor proteins [30] [33], although the phases corresponding to the common characteristic frequencies of interacting proteins are found to be opposite [27].
After statistical analysis, 33 Oct4-interacting proteins were found to be significantly less expressed in differentiated cells compared to ESCs, in correlation with Oct4's expression pattern.
Ssx2ip (Synovial sarcoma, X breakpoint 2 interacting protein) was found over-expressed in some AML patients and is expressed by K562 erythroid cells [ 45].
At alkaline pH, DtxR-repressed genes like cg0925-28, encoding a siderophore ABC transporter, or cg0767, encoding a siderophore interacting protein, are found to be repressed, while the mRNA levels respectively peptide numbers of DtxR-activated genes like ftn (encoding a ferritin-like protein involved in iron storage) and dps (cg3327) are increased.
Interestingly, 27 interfacing proteins were found interacting with partners from different dynamic co-expression clusters, which contain both highly-connected proteins and lowly connected proteins.
Proteins involved in PM internalisation and endosome trafficking, such as a clathrin heavy chain isoform 5, the clathrin interacting protein epsin and two dynamin-like proteins, were found in pollen tube DIMs.
Internal interactions were tested by co-IP using 74 interactions for which the pair of PDZ/interacting proteins was found multiple times through the screening process of the AD-wrmcDNA library but that had no C-terminal consensus PDZ binding motif.
The STITCH database (37) goes one step further by providing interacting proteins that were found experimentally besides proteins that co-occur in the literature.
This cluster of interacting proteins is also found in a third species, the Epstein-Barr virus EBV, which is of the same viral family as KSHV.
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