Guangchuang Yu

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters. The analysis module and visualization module were combined into a reusable workflow. Currently, clusterProfiler supports three species, including humans, mice, and yeast. Methods provided in this package can be easily extended to other species and ontologies. The clusterProfiler package is released under Artistic-2.0 License within Bioconductor project. The source code and vignette are freely available at http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html.

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

SUMMARY The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. Four information content (IC)- and a graph-based methods are implemented in the GOSemSim package, multiple species including human, rat, mouse, fly and yeast are also supported. The functions provided by the GOSemSim offer flexibility for applications, and can be easily integrated into high-throughput analysis pipelines. AVAILABILITY GOSemSim is released under the GNU General Public License within Bioconductor project, and freely available at http://bioconductor.org/packages/2.6/bioc/html/GOSemSim.html.

ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

Summary We present an r package, ggtree, which provides programmable visualization and annotation of phylogenetic trees. ggtree can read more tree file formats than other softwares, including newick, nexus, NHX, phylip and jplace formats, and support visualization of phylo, multiphylo, phylo4, phylo4d, obkdata and phyloseq tree objects defined in other r packages. It can also extract the tree/branch/node-specific and other data from the analysis outputs of beast, epa, hyphy, paml, phylodog, pplacer, r8s, raxml and revbayes software, and allows using these data to annotate the tree. The package allows colouring and annotation of a tree by numerical/categorical node attributes, manipulating a tree by rotating, collapsing and zooming out clades, highlighting user selected clades or operational taxonomic units and exploration of a large tree by zooming into a selected portion. A two-dimensional tree can be drawn by scaling the tree width based on an attribute of the nodes. A tree can be annotated with an associated numerical matrix (as a heat map), multiple sequence alignment, subplots or silhouette images. The package ggtree is released under the artistic-2.0 license. The source code and documents are freely available through bioconductor (http://www.bioconductor.org/packages/ggtree).

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

UNLABELLED ChIPseeker is an R package for annotating ChIP-seq data analysis. It supports annotating ChIP peaks and provides functions to visualize ChIP peaks coverage over chromosomes and profiles of peaks binding to TSS regions. Comparison of ChIP peak profiles and annotation are also supported. Moreover, it supports evaluating significant overlap among ChIP-seq datasets. Currently, ChIPseeker contains 15 000 bed file information from GEO database. These datasets can be downloaded and compare with users own data to explore significant overlap datasets for inferring co-regulation or transcription factor complex for further investigation. AVAILABILITY AND IMPLEMENTATION ChIPseeker is released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http://www.bioconductor.org/packages/release/bioc/html/ChIPseeker.html).

DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis

SUMMARY Disease ontology (DO) annotates human genes in the context of disease. DO is important annotation in translating molecular findings from high-throughput data to clinical relevance. DOSE is an R package providing semantic similarity computations among DO terms and genes which allows biologists to explore the similarities of diseases and of gene functions in disease perspective. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented to support discovering disease associations of high-throughput biological data. This allows biologists to verify disease relevance in a biological experiment and identify unexpected disease associations. Comparison among gene clusters is also supported. AVAILABILITY AND IMPLEMENTATION DOSE is released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http://www.bioconductor.org/packages/release/bioc/html/DOSE.html). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. CONTACT gcyu@connect.hku.hk or tqyhe@jnu.edu.cn.

Cellular microRNA let-7c inhibits M1 protein expression of the H1N1 influenza A virus in infected human lung epithelial cells

The influenza virus (IV) triggers a series of signalling events inside host cells and induces complex cellular responses. Studies have suggested that host factors play an essential role in IV replication. MicroRNAs (miRNAs) represent a class of small non‐coding RNAs that target mRNAs, triggering either translation repression or RNA degradation. Emerging research suggests that host‐derived cellular miRNAs are involved in mediating the host–IV interaction. Using miRNA microarrays, we identified several miRNAs aberrantly expressed in IV‐infected human lung epithelial cells (A549). Specifically, miR‐let‐7c was highly up‐regulated in IV‐infected A549 cells. PITA and miRanda database screening indicated that the let‐7c seed sequence is a perfect complementary sequence match to the 3′ untranslated region (UTR) of viral gene M1 (+) cRNA, but not to PB2 and PA. As detected by a luciferase reporter system, let‐7c directly targeted the 3′‐UTR of M1 (+) cRNA, but not PB2 and PA. To experimentally identify the function of cellular let‐7c, precursor let‐7c was transfected into A549 cells. Let‐7c down‐regulated IV M1 expression at both the (+) cRNA and protein levels. Furthermore, transfection with a let‐7c inhibitor enhanced the expression of M1. Therefore, let‐7c may reduce IV replication by degrading M1 (+) cRNA. This is the first report indicating that cellular miRNA regulates IV replication through the degradation of viral gene (+) cRNA by matching the 3′‐UTR of the viral cRNA. These findings suggest that let‐7c plays a role in protecting host cells from the virus in addition to its known cellular functions.

Genistein-induced mitotic arrest of gastric cancer cells by downregulating KIF20A, a proteomics study

Genistein exerts its anticarcinogenic effects by inducing G2/M arrest and apoptosis of cancer cells. However, the precise molecular mechanism of action of genistein has not been completely elucidated. In this study, we used quantitative proteomics to identify the genistein‐induced protein alterations in gastric cancer cells and investigate the molecular mechanism responsible for the anti‐cancer actions of genistein. Total 86 proteins were identified to be regulated by genistein, most of which were clustered into the regulation of cell division and G2/M transition, consistent with the anti‐cancer effect of genistein. Many proteins including kinesin family proteins, TPX2, CDCA8, and CIT were identified for the first time to be regulated by genistein. Interestingly, five kinesin family proteins including KIF11, KIF20A, KIF22, KIF23, and CENPF were found to be simultaneously downregulated by genistein. Significantly decreased KIF20A was selected for further functional studies. The silencing of KIF20A inhibited cell viability and induced G2/M arrest, similar to the effects of genistein treatment in gastric cancer. And the silencing of KIF20A also increased cancer cell sensitivity to genistein inhibition, whereas overexpression of KIF20A markedly attenuated genistein‐induced cell viability inhibition and G2/M arrest. These observations suggested that KIF20A played an important role in anti‐cancer actions of genistein, and thus may be a potential molecular target for drug intervention of gastric cancer.

ACK1 promotes gastric cancer epithelial–mesenchymal transition and metastasis through AKT–POU2F1–ECD signalling

Amplification of the activated Cdc42‐associated kinase 1 (ACK1) gene is frequent in gastric cancer (GC). However, little is known about the clinical roles and molecular mechanisms of ACK1 abnormalities in GC. Here, we found that the ACK1 protein level and ACK1 phosphorylation at Tyr 284 were frequently elevated in GC and associated with poor patient survival. Ectopic ACK1 expression in GC cells induced epithelial–mesenchymal transition (EMT) and promoted migration and invasion in vitro, and metastasis in vivo; the depletion of ACK1 induced the opposite effects. We utilized SILAC quantitative proteomics to discover that the level of the cell cycle‐related protein ecdysoneless homologue (ECD) was markedly altered by ACK1. Overexpression of ECD promoted EMT, migration, and invasion in GC, similar to the effects of ACK1 overexpression. Silencing of ECD completely blocked the augmentation of ACK1 overexpression‐induced EMT, migration, and invasion. Mechanistically, ACK1 phosphorylated AKT at Thr 308 and Ser 473 and activated the AKT pathway to up‐regulate the transcription factor POU2F1, which directly bound to the promoter region of its novel target gene ECD and thus regulated ECD expression in GC cells. Furthermore, the phosphorylation levels of AKT at Thr 308 and Ser 473 and POU2F1 and ECD levels were positively associated with ACK1 levels in clinical GC specimens. Collectively, we have demonstrated that ACK1 promotes EMT, migration, and invasion by activating AKT–POU2F1–ECD signalling in GC cells. ACK1 may be employed as a new prognostic factor and therapeutic target for GC. Copyright

Putative cobalt- and nickel-binding proteins and motifs in Streptococcus pneumoniae

Cobalt and nickel play important roles in various biological processes. The present work focuses on the enrichment and identification of Co- and Ni-binding motifs and proteins in Gram-positive bacteria. Immobilized metal affinity column (IMAC) was used to partially enrich putative metal-binding proteins and peptides from Streptococcus pneumoniae, and then LTQ-Orbitrap mass spectrometry (MS) was applied to identify and characterize the metal-binding motifs and proteins. In total, 208 and 223 proteins were isolated by Co- and Ni-IMAC columns respectively, in which 129 proteins were present in both preparations. Based on the gene ontology (GO) analysis, the putative metal-binding proteins were found to be mainly involved in protein metabolism, gene expression regulation and carbohydrate metabolism. These putative metal-binding proteins form a highly connected network, indicating that they may synergistically work together to achieve specific biological functions. Putative Co- and Ni-binding motifs were identified with H(X)nH, M(X)nH and H(X)nM derived from the identified 51 Co-binding peptides and 66 Ni-binding peptides. Statistics of frequency of amino acids in the metal-binding motifs showed that cobalt and nickel prefer to bind histidine and methionine, but not cysteine. These results obtained by a systematic metalloproteomic approach provide important clues for the further investigation of metal homeostasis and metal-related virulence of bacteria.

A novel andrographolide derivative AL-1 exerts its cytotoxicity on K562 cells through a ROS-dependent mechanism.

Andrographolide‐lipoic acid conjugate (AL‐1) is a new in‐house synthesized chemical entity, which was derived by covalently linking andrographolide with lipoic acid. However, its anti‐cancer effect and cytotoxic mechanism remains unknown. In this study, we found that AL‐1 could significantly inhibit cell viability of human leukemia K562 cells by inducing G2/M arrest and apoptosis in a dose‐dependent manner. Thirty‐one AL‐1‐regulated protein alterations were identified by proteomics analysis. Gene ontology and ingenuity pathway analysis revealed that a cluster of proteins of oxidative redox state and apoptotic cell death‐related proteins, such as PRDX2, PRDX3, PRDX6, TXNRD1, and GLRX3, were regulated by AL‐1. Functional studies confirmed that AL‐1 induced apoptosis of K562 cells through a ROS‐dependent mechanism, and anti‐oxidant, N‐acetyl‐l‐cysteine, could completely block AL‐1‐induced cytotoxicity, implicating that ROS generation played a vital role in AL‐1 cytotoxicity. Accumulated ROS resulted in oxidative DNA damage and subsequent G2/M arrest and mitochondrial‐mediated apoptosis. The current work reveals that a novel andrographolide derivative AL‐1 exerts its anticancer cytotoxicity through a ROS‐dependent DNA damage and mitochondrial‐mediated apoptosis mechanism.