Abstract:The InParanoid database (http://InParanoid.sbc.su.se) provides a user interface to orthologs inferred by the InParanoid algorithm. As there are now international efforts to curate and standardize complete proteomes, we have switched to using these resources rather than gathering and curating the proteomes ourselves. InParanoid release 8 is based on the 66 reference proteomes that the ‘Quest for Orthologs’ community has agreed on using, plus 207 additional proteomes from the UniProt complete proteomes—in total … Show more
“…The total PTM sites are 101,844 for house mice and 16,567 for brown rats. The 1-to-1 orthologs of mouse and rat genes to the 77 human genes were obtained from InParanoid database v8 (37). Only the 1-to-1 orthologs with Inparanoid confidence scores greater than 0.9 were considered.…”
Post-translational modification (PTM) 1 plays an important role in regulating the functions of proteins. PTMs of multiple residues on one protein may work together to determine a functional outcome, which is known as PTM crosstalk. Identification of PTM cross-talks is an emerging theme in proteomics and has elicited great interest, but their properties remain to be systematically characterized. To this end, we collected 193 PTM cross-talk pairs in 77 human proteins from the literature and then tested location preference and co-evolution at the residue and modification levels. We found that cross-talk events preferentially occurred among nearby PTM sites, especially in disordered protein regions, and cross-talk pairs tended to co-evolve. Given the properties of PTM cross-talk pairs, a naïve Bayes classifier integrating different features was built to predict cross-talks for pairwise combination of PTM sites. By using a 10-fold cross-validation, the integrated prediction model showed an area under the receiver operating characteristic (ROC) curve of 0.833, superior to using any individual feature alone. The prediction performance was also demonstrated to be robust to the biases in the collected PTM cross-talk pairs. The integrated approach has the potential for large-scale prioritization of PTM cross-talk candidates for functional validation and was implemented as a web server available at
“…The total PTM sites are 101,844 for house mice and 16,567 for brown rats. The 1-to-1 orthologs of mouse and rat genes to the 77 human genes were obtained from InParanoid database v8 (37). Only the 1-to-1 orthologs with Inparanoid confidence scores greater than 0.9 were considered.…”
Post-translational modification (PTM) 1 plays an important role in regulating the functions of proteins. PTMs of multiple residues on one protein may work together to determine a functional outcome, which is known as PTM crosstalk. Identification of PTM cross-talks is an emerging theme in proteomics and has elicited great interest, but their properties remain to be systematically characterized. To this end, we collected 193 PTM cross-talk pairs in 77 human proteins from the literature and then tested location preference and co-evolution at the residue and modification levels. We found that cross-talk events preferentially occurred among nearby PTM sites, especially in disordered protein regions, and cross-talk pairs tended to co-evolve. Given the properties of PTM cross-talk pairs, a naïve Bayes classifier integrating different features was built to predict cross-talks for pairwise combination of PTM sites. By using a 10-fold cross-validation, the integrated prediction model showed an area under the receiver operating characteristic (ROC) curve of 0.833, superior to using any individual feature alone. The prediction performance was also demonstrated to be robust to the biases in the collected PTM cross-talk pairs. The integrated approach has the potential for large-scale prioritization of PTM cross-talk candidates for functional validation and was implemented as a web server available at
“…The post-processing was done by UCSC Kent utilities. InParanoid [35] was used to generate the orthologs mapping between carp and zebrafish.Fig. 2Correlation plot using the Spearman correlation test on the RPKM rank-normalized data ( n = 87) after mixed/outlier samples were removed.…”
BackgroundThe common carp (Cyprinus carpio) is the oldest, most domesticated and one of the most cultured fish species for food consumption. Besides its economic importance, the common carp is also highly suitable for comparative physiological and disease studies in combination with the animal model zebrafish (Danio rerio). They are genetically closely related but offer complementary benefits for fundamental research, with the large body mass of common carp presenting possibilities for obtaining sufficient cell material for advanced transcriptome and proteome studies.ResultsHere we have used 19 different tissues from an F1 hybrid strain of the common carp to perform transcriptome analyses using RNA-Seq. For a subset of the tissues we also have performed deep proteomic studies. As a reference, we updated the European common carp genome assembly using low coverage Pacific Biosciences sequencing to permit high-quality gene annotation. These annotated gene lists were linked to zebrafish homologs, enabling direct comparisons with published datasets. Using clustering, we have identified sets of genes that are potential selective markers for various types of tissues. In addition, we provide a script for a schematic anatomical viewer for visualizing organ-specific expression data.ConclusionsThe identified transcriptome and proteome data for carp tissues represent a useful resource for further translational studies of tissue-specific markers for this economically important fish species that can lead to new markers for organ development. The similarity to zebrafish expression patterns confirms the value of common carp as a resource for studying tissue-specific expression in cyprinid fish. The availability of the annotated gene set of common carp will enable further research with both applied and fundamental purposes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3038-y) contains supplementary material, which is available to authorized users.
“…I(i, j) is an indicator tells if there is a homologous interaction pair in a certain species. l(A, i) or l(B, j) is an indicator reflects how much is the homology between two proteins(genes), and in this study, there are two different methods were used to generate this indicator: one is the e-Value from the BLAST, and the other one is the ortholog mapping score in the InParanoid database [31].…”
Abstract-The Predicted Arabidopsis Interactome Resource (PAIR) is an online database of the functional interactions between Arabidopsis genes. PAIR is inferred by integrating six types of evidence each of which suggests a different aspect of functional associations between Arabidopsis genes and therefore enables extended analysis on the potential functional impacts of the observed omics changes at the physiological level.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
