clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

Functional enrichment analysis is pivotal for interpreting high-throughput omics data in life science. It is crucial for this type of tool to use the latest annotation databases for as many organisms as possible. To meet these requirements, we present here an updated version of our popular Bioconductor package, clusterProfiler 4.0. This package has been enhanced considerably compared with its original version published 9 years ago. The new version provides a universal interface for functional enrichment analysis in thousands of organisms based on internally supported ontologies and pathways as well as annotation data provided by users or derived from online databases. It also extends the dplyr and ggplot2 packages to offer tidy interfaces for data operation and visualization. Other new features include gene set enrichment analysis and comparison of enrichment results from multiple gene lists. We anticipate that clusterProfiler 4.0 will be applied to a wide range of scenarios across diverse organisms.

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clusterProfiler supports exploring functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation

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It provides a universal interface for gene functional annotation from a variety of sources and thus can be applied in diverse scenarios

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It provides a tidy interface to access, manipulate, and visualize enrichment results to help users achieve efficient data interpretation

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Datasets obtained from multiple treatments and time points can be analyzed and compared in a single run, easily revealing functional consensus and differences among distinct conditions

The functions of self-injurious behavior: an experimental-epidemiological analysis

Data are summarized from 152 single-subject analyses of the reinforcing functions of self-injurious behavior (SIB). Individuals with developmental disabilities referred for assessment and/or treatment over an 11-year period were exposed to a series of conditions in which the effects of antecedent and consequent events on SIB were examined systematically by way of multielement, reversal, or combined designs. Data were collected during approximately 4,000 experimental sessions (1,000 hr), with the length of assessment for individuals ranging from 8 to 66 sessions (M = 26.2) conducted over 2 to 16.5 hr (M = 6.5). Differential or uniformly high responding was observed in 145 (95.4%) of the cases. Social-negative reinforcement (escape from task demands or other sources of aversive stimulation) accounted for 58 cases, which was the largest proportion of the sample (38.1%). Social-positive reinforcement (either attention or access to food or materials) accounted for 40 (26.3%) of the cases, automatic (sensory) reinforcement accounted for 39 (25.7%), and multiple controlling variables accounted for 8 (5.3%). Seven sets of data (4.6%) showed either cyclical or inconsistent patterns of responding that were uninterpretable. Overall results indicated that functional analysis methodologies are extremely effective in identifying the environmental determinants of SIB on an individual basis and, subsequently, in guiding the process of treatment selection. Furthermore, an accumulation of assessment data from such analyses across a large number of individuals provides perhaps the most rigorous approach to an epidemiological study of behavioral function.

Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity

Glioblastoma (GBM) is a cancer comprised of morphologically, genetically, and phenotypically diverse cells. However, an understanding of the functional significance of intratumoral heterogeneity is lacking. We devised a method to isolate and functionally profile tumorigenic clones from patient glioblastoma samples. Individual clones demonstrated unique proliferation and differentiation abilities. Importantly, naïve patient tumors included clones that were temozolomide resistant, indicating that resistance to conventional GBM therapy can preexist in untreated tumors at a clonal level. Further, candidate therapies for resistant clones were detected with clone-specific drug screening. Genomic analyses revealed genes and pathways that associate with specific functional behavior of single clones. Our results suggest that functional clonal profiling used to identify tumorigenic and drug-resistant tumor clones will lead to the discovery of new GBM clone-specific treatment strategies.

Thirty years of research on the functional analysis of problem behavior

Hanley, Iwata, and McCord (2003) reviewed studies published through 2000 on the functional analysis (FA) of problem behavior. We update that review for 2001 through 2012, including 158 more recent studies that reported data from 445 FAs. Combined with data obtained from Hanley et al., 435 FA studies, with line graphs for 981 FAs, have been published since 1961. We comment on recent trends in FA research and introduce the studies in the 2013 special issue of the Journal of Applied Behavior Analysis.

Functional analysis of transcription factors in Arabidopsis

Transcription factors (TFs) regulate the expression of genes at the transcriptional level. Modification of TF activity dynamically alters the transcriptome, which leads to metabolic and phenotypic changes. Thus, functional analysis of TFs using 'omics-based' methodologies is one of the most important areas of the post-genome era. In this mini-review, we present an overview of Arabidopsis TFs and introduce strategies for the functional analysis of plant TFs, which include both traditional and recently developed technologies. These strategies can be assigned to five categories: bioinformatic analysis; analysis of molecular function; expression analysis; phenotype analysis; and network analysis for the description of entire transcriptional regulatory networks.

Functional and molecular biological evidence for a possible beta3-adrenoceptor in the human detrusor muscle

The possible existence of a beta3-adrenergic receptor (beta3-AR) in the human detrusor muscle was investigated by in vitro functional studies and analysis of mRNA expression. Isoprenaline, noradrenaline and adrenaline each produced a concentration-dependent relaxation of the human detrusor. The rank order for their relaxing potencies was isoprenaline (pD2 6.37+/-0.07) > or = noradrenaline (pD2 6.07+/-0.12) > or = adrenaline (pD2 5.88< or =0.11). Neither dobutamine (beta1- and beta2-AR agonist) nor procaterol (beta2-AR agonist) produced any significant relaxation at concentrations up to 10(-5) M. BRL37344A, CL316243 and CGP-12177A (beta3-AR agonists), relaxed the preparations significantly at concentrations higher than 10(-6) M. The pD2 values for BRL37344A, CL316243 and CGP-12177A were 6.42+/-0.25, 5.53+/-0.09 and 5.74+/-0.14, respectively. CGP-20712A (10(-7) - 10(-5) M), a beta1-AR antagonist, did not affect the isoprenaline-induced relaxation. On the other hand, ICI-118,551, a beta2-AR antagonist, produced a rightward parallel shift of the concentration-relaxation curve for isoprenaline only at the highest concentration used (10(-5) > M) and its pKB value was 5.71+/-0.19. Moreover, SR58894A (10(-7) - 10(-5) M), a beta3-AR antagonist, caused a rightward shift of the concentration-relaxation curve for isoprenaline in a concentration-dependent manner. The pA2 value and slope obtained from Schild plots were 6.24+/-0.20 and 0.68+/-0.31. The beta1-, beta2- and beta3-AR mRNAs were all positively expressed in detrusor smooth muscle preparations in a reverse transcription polymerase chain reaction assay. In conclusion, the present results provide the first evidence for the existence of the beta3-AR subtype in the human detrusor. They also suggest that the relaxation induced by adrenergic stimulation of the human detrusor is mediated mainly through beta3-AR activation.

Functional assessment of problem behavior: dispelling myths, overcoming implementation obstacles, and developing new lore

Hundreds of studies have shown the efficacy of treatments for problem behavior based on an understanding of its function. Assertions regarding the legitimacy of different types of functional assessment vary substantially across published articles, and best practices regarding the functional assessment process are sometimes difficult to cull from the empirical literature or from published discussions of the behavioral assessment process. A number of myths regarding the functional assessment process, which appear to be pervasive within different behavior-analytic research and practice communities, will be reviewed in the context of an attempt to develop new lore regarding the functional assessment process. Frequently described obstacles to implementing a critical aspect of the functional assessment process, the functional analysis, will be reviewed in the context of solutions for overcoming them. Finally, the aspects of the functional assessment process that should be exported to others versus those features that should remain the sole technological property of behavior analysts will be discussed.

RNA sequencing and functional analysis implicate the regulatory role of long non-coding RNAs in tomato fruit ripening

Recently, long non-coding RNAs (lncRNAs) have been shown to play critical regulatory roles in model plants, such as Arabidopsis, rice, and maize. However, the presence of lncRNAs and how they function in fleshy fruit ripening are still largely unknown because fleshy fruit ripening is not present in the above model plants. Tomato is the model system for fruit ripening studies due to its dramatic ripening process. To investigate further the role of lncRNAs in fruit ripening, it is necessary and urgent to discover and identify novel lncRNAs and understand the function of lncRNAs in tomato fruit ripening. Here it is reported that 3679 lncRNAs were discovered from wild-type tomato and ripening mutant fruit. The lncRNAs are transcribed from all tomato chromosomes, 85.1% of which came from intergenic regions. Tomato lncRNAs are shorter and have fewer exons than protein-coding genes, a situation reminiscent of lncRNAs from other model plants. It was also observed that 490 lncRNAs were significantly up-regulated in ripening mutant fruits, and 187 lncRNAs were down-regulated, indicating that lncRNAs could be involved in the regulation of fruit ripening. In line with this, silencing of two novel tomato intergenic lncRNAs, lncRNA1459 and lncRNA1840, resulted in an obvious delay of ripening of wild-type fruit. Overall, the results indicated that lncRNAs might be essential regulators of tomato fruit ripening, which sheds new light on the regulation of fruit ripening.

Microbial community analysis using MEGAN

Metagenomics, the study of microbes in the environment using DNA sequencing, depends upon dedicated software tools for processing and analyzing very large sequencing datasets. One such tool is MEGAN (MEtaGenome ANalyzer), which can be used to interactively analyze and compare metagenomic and metatranscriptomic data, both taxonomically and functionally. To perform a taxonomic analysis, the program places the reads onto the NCBI taxonomy, while functional analysis is performed by mapping reads to the SEED, COG, and KEGG classifications. Samples can be compared taxonomically and functionally, using a wide range of different charting and visualization techniques. PCoA analysis and clustering methods allow high-level comparison of large numbers of samples. Different attributes of the samples can be captured and used within analysis. The program supports various input formats for loading data and can export analysis results in different text-based and graphical formats. The program is designed to work with very large samples containing many millions of reads. It is written in Java and installers for the three major computer operating systems are available from http://www-ab.informatik.uni-tuebingen.de.

Unipept 4.0: Functional Analysis of Metaproteome Data

Unipept ( https://unipept.ugent.be ) is a web application for metaproteome data analysis, with an initial focus on tryptic-peptide-based biodiversity analysis of MS/MS samples. Because the true potential of metaproteomics lies in gaining insight into the expressed functions of complex environmental samples, the 4.0 release of Unipept introduces complementary functional analysis based on GO terms and EC numbers. Integration of this new functional analysis with the existing biodiversity analysis is an important asset of the extended pipeline. As a proof of concept, a human faecal metaproteome data set from 15 healthy subjects was reanalyzed with Unipept 4.0, yielding fast, detailed, and straightforward characterization of taxon-specific catalytic functions that is shown to be consistent with previous results from a BLAST-based functional analysis of the same data.

Functional analysis screening for problem behavior maintained by automatic reinforcement

A common finding in previous research is that problem behavior maintained by automatic reinforcement continues to occur in the alone condition of a functional analysis (FA), whereas behavior maintained by social reinforcement typically is extinguished. Thus, the alone condition may represent an efficient screening procedure when maintenance by automatic reinforcement is suspected. We conducted a series of 5-min alone (or no-interaction) probes for 30 cases of problem behavior and compared initial predictions of maintenance or extinction to outcomes obtained in subsequent FAs. Results indicated that data from the screening procedure accurately predicted that problem behavior was maintained by automatic reinforcement in 21 of 22 cases and by social reinforcement in 7 of 8 cases. Thus, results of the screening accurately predicted the function of problem behavior (social vs. automatic reinforcement) in 28 of 30 cases.

A virtual world of paleontology

Computer-aided visualization and analysis of fossils has revolutionized the study of extinct organisms. Novel techniques allow fossils to be characterized in three dimensions and in unprecedented detail. This has enabled paleontologists to gain important insights into their anatomy, development, and preservation. New protocols allow more objective reconstructions of fossil organisms, including soft tissues, from incomplete remains. The resulting digital reconstructions can be used in functional analyses, rigorously testing long-standing hypotheses regarding the paleobiology of extinct organisms. These approaches are transforming our understanding of long-studied fossil groups, and of the narratives of organismal and ecological evolution that have been built upon them.

Functional assays for analysis of variants of uncertain significance in BRCA2

Missense variants in the BRCA2 gene are routinely detected during clinical screening for pathogenic mutations in patients with a family history of breast and ovarian cancer. These subtle changes frequently remain of unknown clinical significance because of the lack of genetic information that may help establish a direct correlation with cancer predisposition. Therefore, alternative ways of predicting the pathogenicity of these variants are urgently needed. Since BRCA2 is a protein involved in important cellular mechanisms such as DNA repair, replication, and cell cycle control, functional assays have been developed that exploit these cellular activities to explore the impact of the variants on protein function. In this review, we summarize assays developed and currently utilized for studying missense variants in BRCA2. We specifically depict details of each assay, including variants of uncertain significance analyzed, and describe a validation set of (genetically) proven pathogenic and neutral missense variants to serve as a golden standard for the validation of each assay. Guidelines are proposed to enable implementation of laboratory-based methods to assess the impact of the variant on cancer risk.

Conducting functional analyses of problem behavior via telehealth

Behavior consultants conducted functional analyses (FAs) via telehealth with 20 young children with autism spectrum disorders between the ages of 29 and 80 months who displayed problem behavior and lived an average of 222 miles from the tertiary hospital that housed the behavior consultants. Participants' parents conducted all procedures during weekly telehealth consultations in regional clinics located an average of 15 miles from the participants' homes. Behavior consultants briefly trained parent assistants to provide on-site support for families during consultations. FAs completed within a multielement design identified environmental variables that maintained problem behavior for 18 of the 20 cases, and interrater agreement averaged over 90%. Results suggested that behavior analysts can conduct FAs effectively and efficiently via telehealth.

Using modified visual-inspection criteria to interpret functional analysis outcomes

The development of functional analysis (FA) methodologies allows the identification of the reinforcers that maintain problem behavior and improved intervention efficacy in the form of function-based treatments. Despite the profound impact of FA on clinical practice and research, questions still remain about the methods by which clinicians and researchers interpret FA graphs. In the current study, 141 FA data sets were evaluated using the structured visual-inspection criteria developed by Hagopian et al. (1997). However, the criteria were modified for FAs of varying lengths. Interobserver agreement assessments revealed high agreement coefficients across expert judges, postdoctoral reviewers, master's-level reviewers, and postbaccalaureate reviewers. Once the validity of the modified visual-inspection procedures was established, the utility of those procedures was examined by using them to categorize the maintaining reinforcement contingency related to problem behavior for all 141 data sets and for the 101 participants who contributed to the 141 data sets.

Towards the identification of the loci of adaptive evolution

1. Establishing the genetic and molecular basis underlying adaptive traits is one of the major goals of evolutionary geneticists in order to understand the connection between genotype and phenotype and elucidate the mechanisms of evolutionary change. Despite considerable effort to address this question, there remain relatively few systems in which the genes shaping adaptations have been identified. 2. Here, we review the experimental tools that have been applied to document the molecular basis underlying evolution in several natural systems, in order to highlight their benefits, limitations and suitability. In most cases, a combination of DNA, RNA and functional methodologies with field experiments will be needed to uncover the genes and mechanisms shaping adaptation in nature.

Comparative Analysis of the Gut Microbiota Composition between Captive and Wild Forest Musk Deer

The large and complex gut microbiota in animals has profound effects on feed utilization and metabolism. Currently, gastrointestinal diseases due to dysregulated gut microbiota are considered important factors that limit growth of the captive forest musk deer population. Compared with captive forest musk deer, wild forest musk deer have a wider feeding range with no dietary limitations, and their gut microbiota are in a relatively natural state. However, no reports have compared the gut microbiota between wild and captive forest musk deer. To gain insight into the composition of gut microbiota in forest musk deer under different food-source conditions, we employed high-throughput 16S rRNA sequencing technology to investigate differences in the gut microbiota occurring between captive and wild forest musk deer. Both captive and wild forest musk deer showed similar microbiota at the phylum level, which consisted mainly of Firmicutes and Bacteroidetes, although significant differences were found in their relative abundances between both groups. α-Diversity results showed that no significant differences occurred in the microbiota between both groups, while β-diversity results showed that significant differences did occur in their microbiota compositions. In summary, our results provide important information for improving feed preparation for captive forest musk deer and implementing projects where captive forest musk deer are released into the wild.

OsTTG1, a WD40 repeat gene, regulates anthocyanin biosynthesis in rice

Anthocyanins play an important role in the growth of plants, and are beneficial to human health. In plants, the MYB-bHLH-WD40 (MBW) complex activates the genes for anthocyanin biosynthesis. However, in rice, the WD40 regulators remain to be conclusively identified. Here, a crucial anthocyanin biosynthesis gene was fine mapped to a 43.4-kb genomic region on chromosome 2, and a WD40 gene OsTTG1 (Oryza sativa TRANSPARENT TESTA GLABRA1) was identified as ideal candidate gene. Subsequently, a homozygous mutant (osttg1) generated by CRISPR/Cas9 showed significantly decreased anthocyanin accumulation in various rice organs. OsTTG1 was highly expressed in various rice tissues after germination, and it was affected by light and temperature. OsTTG1 protein was localized to the nucleus, and can physically interact with Kala4, OsC1, OsDFR and Rc. Furthermore, a total of 59 hub transcription factor genes might affect rice anthocyanin biosynthesis, and LOC_Os01g28680 and LOC_Os02g32430 could have functional redundancy with OsTTG1. Phylogenetic analysis indicated that directional selection has driven the evolutionary divergence of the indica and japonica OsTTG1 alleles. Our results suggest that OsTTG1 is a vital regulator of anthocyanin biosynthesis, and an important gene resource for the genetic engineering of anthocyanin biosynthesis in rice and other plants.

Functional analysis of flavonoid 3',5'-hydroxylase from tea plant (Camellia sinensis): critical role in the accumulation of catechins

BACKGROUND

Flavonoid 3',5'-hydroxylase (F3'5'H), an important branch point enzyme in tea plant flavan-3-ol synthesis, belongs to the CYP75A subfamily and catalyzes the conversion of flavones, flavanones, dihydroflavonols and flavonols into 3',4',5'-hydroxylated derivatives. However, whether B-ring hydroxylation occurs at the level of flavanones and/or dihydroflavonols, in vivo remains unknown.

RESULTS

The Camellia sinensis F3'5'H (CsF3'5'H) gene was isolated from tea cDNA library. Expression pattern analysis revealed that CsF3'5'H expression was tissue specific, very high in the buds and extremely low in the roots. CsF3'5'H expression was enhanced by light and sucrose. Over-expression of CsF3'5'H produced new-delphinidin derivatives, and increased the cyanidin derivative content of corollas of transgenic tobacco plants, resulting in the deeper transgenic plant flower color. Heterologous expressions of CsF3'5'H in yeast were carried out to demonstrate the function of CsF3'5'H enzyme in vitro. Heterologous expression of the modified CsF3'5'H (CsF3'5'H gene fused with Vitis vinifera signal peptide, FSI) revealed that 4'-hydroxylated flavanone (naringenin, N) is the optimum substrate for CsF3'5'H, and was efficiently converted into both 3'4'- and 3'4'5'-forms. The ratio of 3'4'5'- to 3'4'-hydroxylated products in FSI transgenic cells was significantly higher than VvF3'5'H cells.

CONCLUSIONS

CsF3'5'H is a key controller of tri-hydroxyl flavan-3-ol synthesis in tea plants, which can effectively convert 4'-hydroxylated flavanone into 3'4'5'- and/or 3'4'-hydroxylated products. These findings provide animportant basis for further studies of flavonoid biosynthesis in tea plants. Such studies would help accelerate flavonoid metabolic engineering in order to increase B-ring tri-hydroxyl product yields.

Response latency as an index of response strength during functional analyses of problem behavior

Dependent variables in research on problem behavior typically are based on measures of response repetition, but these measures may be problematic when behavior poses high risk or when its occurrence terminates a session. We examined response latency as the index of behavior during assessment. In Experiment 1, we compared response rate and latency to the first response under acquisition and maintenance conditions. In Experiment 2, we compared data from existing functional analyses when graphed as rate versus latency. In Experiment 3, we compared results from pairs of independent functional analyses. Sessions in the first analysis were terminated following the first occurrence of behavior, whereas sessions in the second analysis lasted for 10 min. Results of all three studies showed an inverse relation between rate and latency, indicating that latency might be a useful measure of responding when repeated occurrences of behavior are undesirable or impractical to arrange.

Structural genomics: computational methods for structure analysis

The success of structural genomics initiatives requires the development and application of tools for structure analysis, prediction, and annotation. In this paper we review recent developments in these areas; specifically structure alignment, the detection of remote homologs and analogs, homology modeling and the use of structures to predict function. We also discuss various rationales for structural genomics initiatives. These include the structure-based clustering of sequence space and genome-wide function assignment. It is also argued that structural genomics can be integrated into more traditional biological research if specific biological questions are included in target selection strategies.

Classroom application of a trial-based functional analysis

We evaluated a trial-based approach to conducting functional analyses in classroom settings. Ten students referred for problem behavior were exposed to a series of assessment trials, which were interspersed among classroom activities throughout the day. Results of these trial-based functional analyses were compared to those of more traditional functional analyses. Outcomes of both assessments showed correspondence in 6 of the 10 cases and partial correspondence in a 7th case. Results of the standard functional analysis suggested reasons for obtained differences in 2 cases of noncorrespondence, which were verified when portions of the trial-based functional analyses were modified and repeated. These results indicate that a trial-based functional analysis may be a viable assessment method when resources needed to conduct a standard functional analysis are unavailable. Implications for classroom-based assessment methodologies and future directions for research are discussed.

Initial functional analysis outcomes and modifications in pursuit of differentiation: a summary of 176 inpatient cases

The functional analysis (FA) described by Iwata, Dorsey, Slifer, Bauman, and Richman (1982/1994) delineated not only a set a specific procedures, but also a model that involves the use of analogue conditions wherein antecedent and consequent variables are systematically manipulated. This consecutive case-series analysis describes FAs of 176 individuals with intellectual disabilities who had been admitted to an inpatient unit for severe problem behavior. Following an initial standardized FA, additional modifications were performed in pursuit of differentiation. Ultimately, a function was identified in 86.9% of the 176 cases and in 93.3% of the 161 cases for which the FA, if necessary, was modified up to 2 times. All modifications were documented and classified as involving changes to antecedents, consequences, or design (or some combination of these). Outcomes for each type of modification are reported. The results support the utility of ongoing hypothesis testing through individualized modifications to FA procedures, and provide information regarding how each type of modification affected results.

Reliability and validity of the functional analysis screening tool

The Functional Analysis Screening Tool (FAST) is a 16-item questionnaire about antecedent and consequent events that might be correlated with the occurrence of problem behavior. Items are organized into 4 functional categories based on contingencies that maintain problem behavior. We assessed interrater reliability of the FAST with 196 problem behaviors through independent administration to pairs of raters (Study 1). Mean item-by-item agreement between pairs of raters was 71.5%. Agreement for individual items ranged from 53.3% to 84.5%. Agreement on FAST outcomes, based on comparison of informants' highest totals, was 64.8%. We assessed the validity of the FAST by comparing its outcomes with results of 69 functional analyses (Study 2). The FAST score predicted the condition of the functional analysis in which the highest rate of problem behavior occurred in 44 cases (63.8%). Potential uses of the FAST in the context of a clinical interview, as well as limitations, are discussed.

Delineating subtypes of self-injurious behavior maintained by automatic reinforcement

Self-injurious behavior (SIB) is maintained by automatic reinforcement in roughly 25% of cases. Automatically reinforced SIB typically has been considered a single functional category, and is less understood than socially reinforced SIB. Subtyping automatically reinforced SIB into functional categories has the potential to guide the development of more targeted interventions and increase our understanding of its biological underpinnings. The current study involved an analysis of 39 individuals with automatically reinforced SIB and a comparison group of 13 individuals with socially reinforced SIB. Automatically reinforced SIB was categorized into 3 subtypes based on patterns of responding in the functional analysis and the presence of self-restraint. These response features were selected as the basis for subtyping on the premise that they could reflect functional properties of SIB unique to each subtype. Analysis of treatment data revealed important differences across subtypes and provides preliminary support to warrant additional research on this proposed subtyping model.