Abstract
Motivation
Gene lists are routinely produced from various omic studies. Enrichment analysis can link these gene lists with underlying molecular pathways and functional categories such as ...gene ontology (GO) and other databases.
Results
To complement existing tools, we developed ShinyGO based on a large annotation database derived from Ensembl and STRING-db for 59 plant, 256 animal, 115 archeal and 1678 bacterial species. ShinyGO’s novel features include graphical visualization of enrichment results and gene characteristics, and application program interface access to KEGG and STRING for the retrieval of pathway diagrams and protein–protein interaction networks. ShinyGO is an intuitive, graphical web application that can help researchers gain actionable insights from gene-sets.
Availability and implementation
http://ge-lab.org/go/.
Supplementary information
Supplementary data are available at Bioinformatics online.
RNA-seq is widely used for transcriptomic profiling, but the bioinformatics analysis of resultant data can be time-consuming and challenging, especially for biologists. We aim to streamline the ...bioinformatic analyses of gene-level data by developing a user-friendly, interactive web application for exploratory data analysis, differential expression, and pathway analysis.
iDEP (integrated Differential Expression and Pathway analysis) seamlessly connects 63 R/Bioconductor packages, 2 web services, and comprehensive annotation and pathway databases for 220 plant and animal species. The workflow can be reproduced by downloading customized R code and related pathway files. As an example, we analyzed an RNA-Seq dataset of lung fibroblasts with Hoxa1 knockdown and revealed the possible roles of SP1 and E2F1 and their target genes, including microRNAs, in blocking G1/S transition. In another example, our analysis shows that in mouse B cells without functional p53, ionizing radiation activates the MYC pathway and its downstream genes involved in cell proliferation, ribosome biogenesis, and non-coding RNA metabolism. In wildtype B cells, radiation induces p53-mediated apoptosis and DNA repair while suppressing the target genes of MYC and E2F1, and leads to growth and cell cycle arrest. iDEP helps unveil the multifaceted functions of p53 and the possible involvement of several microRNAs such as miR-92a, miR-504, and miR-30a. In both examples, we validated known molecular pathways and generated novel, testable hypotheses.
Combining comprehensive analytic functionalities with massive annotation databases, iDEP ( http://ge-lab.org/idep/ ) enables biologists to easily translate transcriptomic and proteomic data into actionable insights.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Instead of testing predefined hypotheses, the goal of exploratory data analysis (EDA) is to find what data can tell us. Following this strategy, we re-analyzed a large body of genomic data to study ...the complex gene regulation in mouse pre-implantation development (PD).
Starting with a single-cell RNA-seq dataset consisting of 259 mouse embryonic cells derived from zygote to blastocyst stages, we reconstructed the temporal and spatial gene expression pattern during PD. The dynamics of gene expression can be partially explained by the enrichment of transposable elements in gene promoters and the similarity of expression profiles with those of corresponding transposons. Long Terminal Repeats (LTRs) are associated with transient, strong induction of many nearby genes at the 2-4 cell stages, probably by providing binding sites for Obox and other homeobox factors. B1 and B2 SINEs (Short Interspersed Nuclear Elements) are correlated with the upregulation of thousands of nearby genes during zygotic genome activation. Such enhancer-like effects are also found for human Alu and bovine tRNA SINEs. SINEs also seem to be predictive of gene expression in embryonic stem cells (ESCs), raising the possibility that they may also be involved in regulating pluripotency. We also identified many potential transcription factors underlying PD and discussed the evolutionary necessity of transposons in enhancing genetic diversity, especially for species with longer generation time.
Together with other recent studies, our results provide further evidence that many transposable elements may play a role in establishing the expression landscape in early embryos. It also demonstrates that exploratory bioinformatics investigation can pinpoint developmental pathways for further study, and serve as a strategy to generate novel insights from big genomic data.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The global spreading of the COVID-19 coronavirus is still a serious public health challenge. Although there are a large number of public resources that provide statistics data, tools for ...retrospective historical data and convenient visualization are still valuable. To provide convenient access to data and visualization on the pandemic we developed an R package, nCov2019 (https://github.com/YuLab-SMU/nCov2019).
We collect stable and reliable data of COVID-19 cases from multiple authoritative and up-to-date sources, and aggregate the most recent and historical data for each country or even province. Medical progress information, including global vaccine development and therapeutics candidates, were also collected and can be directly accessed in our package. The nCov2019 package provides an R language interfaces and designed functions for data operation and presentation, a set of interfaces to fetch data subset intuitively, visualization methods, and a dashboard with no extra coding requirement for data exploration and interactive analysis.
As of January 14, 2021, the global health crisis is still serious. The number of confirmed cases worldwide has reached 91,268,983. Following the USA, India has reached 10 million confirmed cases. Multiple peaks are observed in many countries. Under the efforts of researchers, 51 vaccines and 54 drugs are under development and 14 of these vaccines are already in the pre-clinical phase.
The nCov2019 package provides detailed statistics data, visualization functions and the Shiny web application, which allows researchers to keep abreast of the latest epidemic spread overview.
Summary
Rhizodeposits play a key role in shaping rhizosphere microbial communities. In soybean, isoflavonoids are a key rhizodeposit component that aid in plant defense and enable symbiotic ...associations with rhizobia. However, it is uncertain if and how they influence rhizosphere microbial communities. Isoflavonoid biosynthesis was silenced via RNA interference of isoflavone synthase in soybean hairy root composite plants. Rhizosphere soil fractions tightly associated with roots were isolated, and PCR amplicons from 16S rRNA gene variable regions V1–V3 and V3–V5 from these fractions were sequenced using 454. The resulting data was resolved using MOTHUR and vegan to identify bacterial taxa and evaluate changes in rhizosphere bacterial communities. The soybean rhizosphere was enriched in Proteobacteria and Bacteroidetes, and had relatively lower levels of Actinobacteria and Acidobacteria compared with bulk soil. Isoflavonoids had a small effect on bacterial community structure, and in particular on the abundance of Xanthomonads and Comamonads. The effect of hairy root transformation on rhizosphere bacterial communities was largely similar to untransformed plant roots with approximately 74% of the bacterial families displaying similar colonization underscoring the suitability of this technique to evaluate the influence of plant roots on rhizosphere bacterial communities. However, hairy root transformation had notable influence on Sphingomonads and Acidobacteria.
Previously, we found that gene expression in histologically normal breast epithelium (NlEpi) from women at high breast cancer risk can resemble gene expression in NlEpi from cancer-containing ...breasts. Therefore, we hypothesized that gene expression characteristic of a cancer subtype might be seen in NlEpi of breasts containing that subtype.
We examined gene expression in 46 cases of microdissected NlEpi from untreated women undergoing breast cancer surgery. From 30 age-matched cases 15 estrogen receptor (ER)+, 15 ER- we used Affymetryix U133A arrays. From 16 independent cases (9 ER+, 7 ER-), we validated selected genes using quantitative real-time PCR (qPCR). We then compared gene expression between NlEpi and invasive breast cancer using four publicly available data sets.
We identified 198 genes that are differentially expressed between NlEpi from breasts with ER+ (NlEpiER+) compared with ER- cancers (NlEpiER-). These include genes characteristic of ER+ and ER- cancers (e.g., ESR1, GATA3, and CX3CL1, FABP7). qPCR validated the microarray results in both the 30 original cases and the 16 independent cases. Gene expression in NlEpiER+ and NlEpiER- resembled gene expression in ER+ and ER- cancers, respectively: 25% to 53% of the genes or probes examined in four external data sets overlapped between NlEpi and the corresponding cancer subtype.
Gene expression differs in NlEpi of breasts containing ER+ compared with ER- breast cancers. These differences echo differences in ER+ and ER- invasive cancers. NlEpi gene expression may help elucidate subtype-specific risk signatures, identify early genomic events in cancer development, and locate targets for prevention and therapy.
• Recent studies mainly in Arabidopsis have renewed interest and discussion in some of the key issues in hydrotropism of roots, such as the site of water sensing and the involvement of auxin. We ...examined hydrotropism in maize (Zea mays) primary roots.
• We determined the site of water sensing along the root using a nonintrusive method. Kinematic analysis was conducted to investigate spatial root elongation during hydrotropic response. Indole-3-acetic acid (IAA) and other hormones were quantified using LC–MS/MS. The transcriptome was analyzed using RNA sequencing.
• Main results: The very tip of the root is the most sensitive to the hydrostimulant. Hydrotropic bending involves coordinated adjustment of spatial cell elongation and cell flux. IAA redistribution occurred in maize roots, preceding hydrotropic bending. The redistribution is caused by a reduction of IAA content on the side facing a hydrostimulant, resulting in a higher IAA content on the dry side. Transcriptomic analysis of the elongation zone prior to bending identified IAA response and lignin synthesis/wall cross-linking as some of the key processes occurring during the early stages of hydrotropic response.
• We conclude that maize roots differ from Arabidopsis in the location of hydrostimulant sensing and the involvement of IAA redistribution.
AbstractOver two hundred health awareness events take place in the United States in order to educate the public about various diseases. It would be informative and instructive for the organizations ...to know the impact of these events, although such information could be difficult to measure. We investigated whether 46 selected events attract the public attention by increasing the search frequencies of certain keywords. Internet search data from 2004 to 2017 were downloaded from Google Trend (GT). Three statistical methods including Transfer Function Noise modeling, Wilcoxon Rank Sum test, and Binomial inference were conducted. Our study showed that 10 health awareness events resulted in increased search frequencies in the event months, and 28 events did not, with the rest being classified as unclear.
Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide. Several studies have identified signature gene sets that may be useful as potential diagnostic tools by global ...microarray analysis. Here we report the cloning and characterization of a novel gene, lin-28 homolog B (LIN28B), which is overexpressed in hepatocellular carcinoma. The heterochronic gene lin-28 is a key regulator of developmental timing in the nematode
Caenorhabditis elegans. Similar with lin-28 proteins, LIN28B conserves a cold shock domain and a pair of CCHC zinc finger domains. Phylogenetic analysis suggests that they might arise as a result of duplication from an ancestral gene. Overexpression of LIN28B was noted in most HCC cell lines and clinical samples. By western blot analysis using a polyclonal antibody against LIN28B, a short LIN28B isoform was also identified in non-tumor liver tissue and fetal liver. Although predominantly localized in the cytoplasm, we found that LIN28B protein shows cell cycle-dependent nuclear translocation in Huh7 cells. Induced expression of exogenous LIN28B in a tet-off cell line promoted cancer cell proliferation. Interestingly, the segment of the unusually long 3′UTR of LIN28B contains complementary sites to let-7 microRNA of mammals. And our studies provided indirect evidence that LIN28B is a possibly natural target for let-7 mediated regulation. These findings strongly implicate a critical role of LIN28B during development and tumorigenesis and suggest a possible novel mechanism.
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