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
With the popularity of photovoltaic based green energy in smart grid systems, accurate information gathering becomes a critical issue in predicting microgrid power input. In this paper, we propose a ...new quality-optimized multimedia information gathering scheme, in the energy harvesting wireless sensor networks based Internet of things system, to provide the best-effort sky camera information accuracy for further predicting available photovoltaic power. In the proposed approach, the power control and relay node selection strategies are jointly optimized to achieve maximum sky camera image quality subject to the harvestable energy neutrality constraint. Simulation results show that the proposed scheme can improve multimedia data transmission quality by exploring adaptive transmission power and relay selection strategy.
Multimedia applications based on cloud services for mobile devices have recently gained considerable popularity. However, the increasing density of devices leads to a high level of interference, ...which reduces the performance of wireless communication between devices and cloud. In this paper, we propose a new approach which allows the network to adaptively find a transmission opportunity scheduling strategy by choosing the most valuable transmission request opportunity. In this approach, the transmission request selection strategy is optimized by considering multimedia distortion reduction, hidden node problem, transmission interference, and signal coverage. Simulation results show that the proposed request selecting strategy significantly improves the systems overall data transmission quality by exploring the tradeoff between communication node pair and their neighbor nodes.
Embryo survival and pregnancy success is increased among animals that exhibit estrus prior to fixed time-artificial insemination, but there are no differences in conceptus survival to d16. The ...objective of this study was to determine effects of preovulatory estradiol on uterine transcriptomes, select trophectoderm (TE) transcripts, and uterine luminal fluid proteins. Beef cows/heifers were synchronized, artificially inseminated (d0), and grouped into either high (highE2) or low (lowE2) preovulatory estradiol. Uteri were flushed (d16); conceptuses and endometrial biopsies (n = 29) were collected. RNA sequencing was performed on endometrium. Real-time polymerase chain reaction (RT-PCR) was performed on TE (n = 21) RNA to measure relative abundance of IFNT, PTGS2, TM4SF1, C3, FGFR2, and GAPDH. Uterine fluid was analyzed using 2D Liquid Chromatography with tandem mass spectrometry-based Isobaric tags for relative and absolute quantitation (iTRAQ) method. RT-PCR data were analyzed using the MIXED procedure in SAS. There were no differences in messenger RNA (mRNA) abundances in TE, but there were 432 differentially expressed genes (253 downregulated, 179 upregulated) in highE2/conceptus versus lowE2/conceptus groups. There were also 48 differentially expressed proteins (19 upregulated, 29 downregulated); 6 of these were differentially expressed (FDR < 0.10) at the mRNA level. Similar pathways for mRNA and proteins included: calcium signaling, protein kinase A signaling, and corticotropin-releasing hormone signaling. These differences in uterine function may be preparing the conceptus for improved likelihood of survival after d16 among highE2 animals. Summary sentence Preovulatory estradiol did not impact conceptus survival to d16; however, it did influence uterine gene/protein expressions related to adhesion, endometrial remodeling, metabolism, and immune regulation, which may explain improved pregnancy success.
The uterine environment must provide sufficient endocrine conditions and nutrients for pregnancy maintenance and conceptus survival. The objective of this study was to determine the effects of ...preovulatory estradiol and conceptus presence on uterine transcripts and uterine luminal fluid (ULF) proteins. Beef cows/heifers were synchronized and artificially inseminated (d 0). Uteri were flushed (d 16); conceptuses and endometrial biopsies were collected. Total cellular RNA was extracted from endometrium for RNA sequencing and RT-PCR validation. There were two independent ULF pools made for each of the following groups: highE2/conceptus, highE2/noconceptus, lowE2/conceptus, and lowE2/noconceptus that were analyzed using the 2D LC-MS/MS based iTRAQ method. There were 64 differentially expressed genes (DEGs) and 77 differentially expressed proteins (DEPs) in common among the highE2/conceptus vs highE2/noconceptus and lowE2/conceptus vs lowE2/noconceptus groups. In summary, the interaction between preovulatory estradiol and the conceptus induces the expression of genes, proteins, and pathways necessary for pregnancy.
•There were 64 DEGs in common among the highE2/conceptus vs highE2/noconceptus groups and lowE2/conceptus vs lowE2/noconceptus groups.•There were 77 DEPs in common among highE2/conceptus vs highE2/noconceptus and lowE2/conceptus vs lowE2/noconceptus.•The interaction between preovulatory estradiol and conceptus presence influences uterine gene and protein expression.
With the improvement of hardware, more and more multimedia applications are allowed to run in the mobile device. However, due to the limited radio bandwidth, wireless network performance becomes a ...critical issue. Common mobile solutions are based on the centralized structure, which require an access point to handle all the communication requirement in the work area. The transmission performance of centralized framework relies on the density of access points. But increasing the number of access points will cost lot of money and the interference between access point will reduce the transmission quality. Thanks to the wireless sensor network implementations, the distributed wireless network solution has been well studied. Now, many mobile network studies introduce the device to device idea which is a distributed structure of mobile network. Unlike wireless sensor networks, mobile networks have more movability and higher transmission speed requirement. In order to be used in mobile networks, a distributed network management algorithm needs to perform faster and more accurate. In this thesis, a new pairing algorithm is proposed to provide a better transmission quality for multimedia data. In the proposed approach, the multimedia data is quantized by distortion reduction. Then, the source-relay pairing solution is optimized by a history tracing system using game theory to improve the expected overall distortion reduction of the entire network. Several parameters are introduced in the proposed solution, so the optimization would fit for different situations. Simulation results show that the proposed algorithm achieves higher overall distortion reduction by avoiding the competition between nodes. Simulation results also show the parameters would affect the system performance, such as optimization speed, system stability and system overall transmit speed.
Resource constrained secure deep space Inter-Planetary Multimedia Networks (IPMNs) gathering various planetary sensor information have high requirements for energy-efficient transmission, ...error-resilient multimedia coding and robust content authentication. However, the joint exploration of Intra-Inter video coding versatility in signal processing domain, Signature-Hash diversity in information security domain and Forward Channel Correction (FEC) channel coding application in network protocol domain has largely been ignored in literature. In this paper, we propose a new Source-Authentication-Protocol (SAP) framework to provide multimedia service quality, communication overhead efficiency and multimedia content integrity simultaneously. To provide robust video authentication while keeping bandwidth resource constraints, a novel SAP based network resource allocation scheme is proposed to improve energy efficiency and communication resource utilization in IPMN by jointly exploring the diversities in the source, the authentication and the protocol categories. Results based on simulation studies demonstrate the effectiveness of the proposed SAP scheme in achieving resource efficiency, video quality and authentication robustness, simultaneously.
Using harvestable energy in Wireless Sensor Networks (WSNs) has gained considerable popularity recently. However, how to utilize the unstable power supply to achieve quality performance is still a ...challenge. In this paper, we propose a Weight-Optimized Source Rate Optimization (WOSRO) approach which allows the WSN system to adaptively control source coding rates by choosing the most valuable data packets to transmit. In this approach, the packet selection strategy is optimized by considering multimedia distortion reduction, energy cost, energy neutrality constraint and power saving efficiency. Simulation results show that the proposed data packet selecting strategy significantly improves data transmission quality by exploring harvesting-storage energy neutrality and multimedia data packet importance.
Abstract
Array signal processing technology has been widely used in signal detection and underwater target radiation noise measurement. A design and realization method of an ultra-wideband and ...high-robustness constant beamwidth beamformer based on a vertical nested array is proposed. Using the nested array multiplexing, the ultra-wideband constant beamwidth beamforming was realized by using fewer array elements; the main lobe of each sub-band beam in the designed band was made to approach the desired constraint value based on the convex optimization method; the beamforming robustness and array gain were improved through the constraint of the weight vector two-norm. In the paper, the influence on beamforming due to inconsistent array element amplitude-phases in a measured waveguide environment is analyzed. The computer simulation was used to realize the measurement of constant beamwidth beamforming within a 100-octave band range in the measured waveguide environment and verify the effectiveness of the proposed method.
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