A subset of the protein sequence compilation containing amphibian, bovine or human sequences was downloaded in GenPept format from http://www.ncbi.nlm.nih.gov/genbank/ (Benson et al. 2008).
This acceptance criterion was subsequently strengthened to a minimum of two peptides per protein for compilation of the final list, as described in Materials and Methods.
Numerous amphibian peptides, which match the tripeptide-consensus (Ile, Leu, Phe, Glu, Lys, Tyr, Trp -Xaa-(Gly, Ala, Asn, Phe), could be idenTrp -Xaa- the NIH protein sequence compilation (Table S1).
Attempts to find common characteristics for protein-protein recognition sites have only been moderately successful, since the average binding epitope of a large compilation of protein-protein interfaces is almost indistinguishable from a regular protein surface [ 51].
Performing a similar analysis on a compilation of protein-protein interactions derived from multiple high-throughput sources (the Interologous Interaction Database - I2D) in with the Edge Weight (K I2D ) is defined as the number of protein-protein interaction databases containing a given revealed a similar distribution.
We also improved performance against the original MS analysis in ROC and precision recall plots, using our compilation of protein reference sets, showing 10 24% increase in ROC-AUC.
There are two recent independent reports on the identification and prioritization of candidate disease genes in general as well as specific to primary immunodeficiencies by integrating functional annotations from gene ontology and compilation of protein interaction network data sets from BIND, BioGRID and HPRD.
In order to be on the more conservative side of the human genome annotation errors, we retrieved from public databases the same compilation of human protein sequences (20,259 unique proteins) that were used in the recent cancer genome sequencing projects [ 48].
We present P2CS (Prokaryotic 2-Component Systems), an integrated and comprehensive database of TCS signal transduction proteins, which contains a compilation of the TCS genes within 755 completely sequenced prokaryotic genomes and 39 metagenomes.
This bioinformatics compilation of proteins containing the AMPK phosphorylation consensus sequence represents a novel database for putative AMPK targets and suggests the involvement of AMPK in cellular functions spanning both top-down (receptor response to stimulus) and bottom-up perspectives (transcriptional regulation for cellular functions).
