Recent high-throughput techniques have generated a flood of biological data in all aspects. The transformation and visualization of multi-dimensional and numerical gene or protein expression data in a single heatmap can provide a concise but comprehensive presentation of molecular dynamics under different conditions. In this work, we developed an easy-to-use tool named HemI (Heat map Illustrator), which can visualize either gene or protein expression data in heatmaps. Additionally, the heatmaps can be recolored, rescaled or rotated in a customized manner. In addition, HemI provides multiple clustering strategies for analyzing the data. Publication-quality figures can be exported directly. We propose that HemI can be a useful toolkit for conveniently visualizing and manipulating heatmaps. The stand-alone packages of HemI were implemented in Java and can be accessed at http://hemi.biocuckoo.org/down.php.
In eukaryotes, protein phosphorylation is specifically catalyzed by numerous protein kinases (PKs), faithfully orchestrates various biological processes, and reversibly determines cellular dynamics and plasticity. Here we report an updated algorithm of Group-based Prediction System (GPS) 5.0 to improve the performance for predicting kinase-specific phosphorylation sites (p-sites). Two novel methods, position weight determination (PWD) and scoring matrix optimization (SMO), were developed. Compared with other existing tools, GPS 5.0 exhibits a highly competitive accuracy. Besides serine/threonine or tyrosine kinases, GPS 5.0 also supports the prediction of dual-specificity kinase -specific p-sites. In the classical module of GPS 5.0, 617 individual predictors were constructed for predicting p-sites of 479 human PKs. To extend the application of GPS 5.0, a species-specific module was implemented to predict kinase-specific p-sites for 44,795 PKs in 161 eukaryotes. The online service and local packages of GPS 5.0 are freely available for academic research at http://gps.biocuckoo.cn .
Various posttranslational modifications (PTMs) participate in nearly all aspects of biological processes by regulating protein functions, and aberrant states of PTMs are frequently implicated in human diseases. Therefore, an integral resource of PTM–disease associations (PDAs) would be a great help for both academic research and clinical use. In this work, we reported PTMD, a well-curated database containing PTMs that are associated with human diseases. We manually collected 1950 known PDAs in 749 proteins for 23 types of PTMs and 275 types of diseases from the literature. Database analyses show that phosphorylation has the largest number of disease associations, whereas neurologic diseases have the largest number of PTM associations. We classified all known PDAs into six classes according to the PTM status in diseases and demonstrated that the upregulation and presence of PTM events account for a predominant proportion of disease-associated PTM events. By reconstructing a disease–gene network, we observed that breast cancers have the largest number of associated PTMs and AKT1 has the largest number of PTMs connected to diseases. Finally, the PTMD database was developed with detailed annotations and can be a useful resource for further analyzing the relations between PTMs and human diseases. PTMD is freely accessible at http://ptmd.biocuckoo.org.
Endocytic recycling of internalized transmembrane proteins is essential for many important physiological processes. Recent studies have revealed that retromer-related Sorting Nexin family (SNX)-Bin/Amphiphysin/Rvs (BAR) proteins can directly recognize cargoes like cation-independent mannose 6-phosphate receptor (CI-MPR) and Insulin-like growth factor 1 receptor (IGF1R); however, it remains poorly understood how SNX-BARs select specific cargo proteins and whether they recognize additional ligands. Here, we discovered that the binding between SNX-BARs and CI-MPR or IGF1R is mediated by the phox-homology (PX) domain of SNX5 or SNX6 and a bipartite motif, termed SNX-BAR-binding motif (SBM), in the cargoes. Using this motif, we identified over 70 putative SNX-BAR ligands, many of which play critical roles in apoptosis, cell adhesion, signal transduction, or metabolite homeostasis. Remarkably, SNX-BARs could cooperate with both SNX27 and retromer in the recycling of ligands encompassing the SBM, PDZ-binding motif, or both motifs. Overall, our studies establish that SNX-BARs function as a direct cargo-selecting module for a large set of transmembrane proteins transiting the endosome, in addition to their roles in phospholipid recognition and biogenesis of tubular structures.have been linked with a variety of human diseases including Alzheimer's disease, Parkinson's disease, cancer, and diabetes [4,5].Key protein machineries important for the sequence-dependent recycling include the evolutionarily conserved retromer complex (vacuolar protein sorting 35 [VPS35]/VPS26/VPS29 in higher eukaryotes) [6][7][8], the recently discovered retriever [9], the WASH complex [10][11][12], and members of the Sorting Nexin family (SNX) [13][14][15]. A subset of SNX proteins possessing a Bin/Amphiphysin/Rvs (BAR) domain, in addition to the phox-homology (PX) domain, have been linked with the retromer complex. The retromer-related SNX-BAR proteins (referred as SNX-BARs herein) SNX1, SNX2, SNX5, SNX6, and SNX32 form heterodimeric complexes and are critical for both endosome-to-plasma membrane recycling and endosome-to-TGN retrieval [16,17]. Current models suggest that SNX-BARs promote the endosome-to-plasma membrane recycling via associating with SNX27 and retromer, with the PDZ domain of SNX27 as the predominant cargo-recognition module [14]. For endosome-to-TGN trafficking, one of the best-characterized cargoes is cation-independent mannose 6-phosphate receptor (CI-MPR), which is necessary to deliver newly synthesized lysosomal hydrolases to the endosomal lumen and thus critical for lysosomal function [18]. However, previous studies have provided contradictory models regarding the role of retromer and SNX-BARs in the endosome-to-TGN retrieval of CI-MPR. Work from many different labs has initially supported the idea that retromer is necessary for the retrieval of CI-MPR, likely through a direct association with its cytoplasmic tail, in particular, the hydrophobic WLM motif [19][20][21]. However, recent work by Cullen and Steinberg has provi...
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