scholarly journals MicroScope—an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data

2017 ◽  
Vol 20 (4) ◽  
pp. 1071-1084 ◽  
Author(s):  
Claudine Médigue ◽  
Alexandra Calteau ◽  
Stéphane Cruveiller ◽  
Mathieu Gachet ◽  
Guillaume Gautreau ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Genome Annotation ◽  
Daily Basis ◽  
Original Method ◽  
Graph Representation ◽  
Integrated Analysis ◽  
Sequencing Data ◽  
Bacterial Genomes ◽  
Manual Curation ◽  
Expert Annotation

Abstract The overwhelming list of new bacterial genomes becoming available on a daily basis makes accurate genome annotation an essential step that ultimately determines the relevance of thousands of genomes stored in public databanks. The MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Starting from the results of our syntactic, functional and relational annotation pipelines, MicroScope provides an integrated environment for the expert annotation and comparative analysis of prokaryotic genomes. It combines tools and graphical interfaces to analyze genomes and to perform the manual curation of gene function in a comparative genomics and metabolic context. In this article, we describe the free-of-charge MicroScope services for the annotation and analysis of microbial (meta)genomes, transcriptomic and re-sequencing data. Then, the functionalities of the platform are presented in a way providing practical guidance and help to the nonspecialists in bioinformatics. Newly integrated analysis tools (i.e. prediction of virulence and resistance genes in bacterial genomes) and original method recently developed (the pan-genome graph representation) are also described. Integrated environments such as MicroScope clearly contribute, through the user community, to help maintaining accurate resources.

scholarly journals Integrated Analysis of Long Non-Coding RNA and mRNA Expression Profiles in Testes of Calves and Sexually Mature Wandong Bulls (Bos taurus)

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 2006
Author(s):  
Hongyu Liu ◽  
Ibrar Muhammad Khan ◽  
Huiqun Yin ◽  
Xinqi Zhou ◽  
Muhammad Rizwan ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Profiles ◽  
Age Groups ◽  
Adherens Junction ◽  
Integrated Analysis ◽  
Sequencing Data ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Rna Interaction ◽  
Long Non Coding Rna

The mRNAs and long non-coding RNAs axes are playing a vital role in the regulating of post-transcriptional gene expression. Thereby, elucidating the expression pattern of mRNAs and long non-coding RNAs underlying testis development is crucial. In this study, mRNA and long non-coding RNAs expression profiles were investigated in 3-month-old calves and 3-year-old mature bulls’ testes by total RNA sequencing. Additionally, during the gene level analysis, 21,250 mRNAs and 20,533 long non-coding RNAs were identified. As a result, 7908 long non-coding RNAs (p-adjust < 0.05) and 5122 mRNAs (p-adjust < 0.05) were significantly differentially expressed between the distinct age groups. In addition, gene ontology and biological pathway analyses revealed that the predicted target genes are enriched in the lysine degradation, cell cycle, propanoate metabolism, adherens junction and cell adhesion molecules pathways. Correspondingly, the RT-qPCR validation results showed a strong consistency with the sequencing data. The source genes for the mRNAs (CCDC83, DMRTC2, HSPA2, IQCG, PACRG, SPO11, EHHADH, SPP1, NSD2 and ACTN4) and the long non-coding RNAs (COX7A2, COX6B2, TRIM37, PRM2, INHBA, ERBB4, SDHA, ATP6VOA2, FGF9 and TCF21) were found to be actively associated with bull sexual maturity and spermatogenesis. This study provided a comprehensive catalog of long non-coding RNAs in the bovine testes and also offered useful resources for understanding the differences in sexual development caused by the changes in the mRNA and long non-coding RNA interaction expressions between the immature and mature stages.

scholarly journals MiR-146a Regulates Migration and Invasion by Targeting NRP2 in Circulating-Tumor Cell Mimicking Suspension Cells

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 45
Author(s):  
Yeojin Do ◽  
Jin Gu Cho ◽  
Ji Young Park ◽  
Sumin Oh ◽  
Doyeon Park ◽  
...  
Keyword(s):  
Cancer Metastasis ◽  
Metastatic Cancer ◽  
Molecular Networks ◽  
Migration And Invasion ◽  
Integrated Analysis ◽  
Molecular Characteristics ◽  
Breast Cancer Patients ◽  
Sequencing Data ◽  
Suspension Cells

Cancer metastasis is the primary cause of cancer-related death and metastatic cancer has circulating-tumor cells (CTCs), which circulate in the bloodstream before invading other organs. Thus, understanding the precise role of CTCs may provide new insights into the metastasis process and reduce cancer mortality. However, the molecular characteristics of CTCs are not well understood due to a lack of number of CTCs. Therefore, suspension cells were generated from MDA-MB-468 cells to mimic CTCs, and we investigate the microRNA (miRNA)-dependent molecular networks and their role in suspension cells. Here, we present an integrated analysis of mRNA and miRNA sequencing data for suspension cell lines, through comparison with adherent cells. Among the differentially regulated miRNA–mRNAs axes, we focus on the miR-146a-Neuropilin2 (NRP2) axis, which is known to influence tumor aggressiveness. We show that miR-146a directly regulates NRP2 expression and inhibits Semaphorin3C (SEMA3C) signaling. Functional studies reveal that miR-146a represses SEMA3C-induced invasion and proliferation by targeting NRP2. Finally, high-NRP2 is shown to be associated with poor outcomes in breast cancer patients. This study identifies the key role of the miR-146a–NRP2 signaling axis that is critical for the regulation of migration and invasion in CTC-mimicking cells.

scholarly journals Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA

2014 ◽  
Vol 2014 ◽  
pp. 1-8
Author(s):  
Momchilo Vuyisich ◽  
Ayesha Arefin ◽  
Karen Davenport ◽  
Shihai Feng ◽  
Cheryl Gleasner ◽  
...  
Keyword(s):  
Genomic Dna ◽  
De Novo ◽  
Gc Content ◽  
Library Preparation ◽  
Sequencing Data ◽  
Bacterial Genomes ◽  
Dna Amount ◽  
High Quality ◽  
Preparation Methods

Sequencing bacterial genomes has traditionally required large amounts of genomic DNA (~1 μg). There have been few studies to determine the effects of the input DNA amount or library preparation method on the quality of sequencing data. Several new commercially available library preparation methods enable shotgun sequencing from as little as 1 ng of input DNA. In this study, we evaluated the NEBNext Ultra library preparation reagents for sequencing bacterial genomes. We have evaluated the utility of NEBNext Ultra for resequencing andde novoassembly of four bacterial genomes and compared its performance with the TruSeq library preparation kit. The NEBNext Ultra reagents enable high quality resequencing andde novoassembly of a variety of bacterial genomes when using 100 ng of input genomic DNA. For the two most challenging genomes (Burkholderiaspp.), which have the highest GC content and are the longest, we also show that the quality of both resequencing andde novoassembly is not decreased when only 10 ng of input genomic DNA is used.

scholarly journals rCASC: reproducible classification analysis of single-cell sequencing data

GigaScience ◽  
2019 ◽  
Vol 8 (9) ◽  
Author(s):  
Luca Alessandrì ◽  
Francesca Cordero ◽  
Marco Beccuti ◽  
Maddalena Arigoni ◽  
Martina Olivero ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Cellular Heterogeneity ◽  
Cell Subpopulation ◽  
Integrated Analysis ◽  
Specific Gene ◽  
Sequencing Data ◽  
Single Cell Sequencing ◽  
Cell Stability ◽  
Reproducible Analysis

Abstract Background Single-cell RNA sequencing is essential for investigating cellular heterogeneity and highlighting cell subpopulation-specific signatures. Single-cell sequencing applications have spread from conventional RNA sequencing to epigenomics, e.g., ATAC-seq. Many related algorithms and tools have been developed, but few computational workflows provide analysis flexibility while also achieving functional (i.e., information about the data and the tools used are saved as metadata) and computational reproducibility (i.e., a real image of the computational environment used to generate the data is stored) through a user-friendly environment. Findings rCASC is a modular workflow providing an integrated analysis environment (from count generation to cell subpopulation identification) exploiting Docker containerization to achieve both functional and computational reproducibility in data analysis. Hence, rCASC provides preprocessing tools to remove low-quality cells and/or specific bias, e.g., cell cycle. Subpopulation discovery can instead be achieved using different clustering techniques based on different distance metrics. Cluster quality is then estimated through the new metric "cell stability score" (CSS), which describes the stability of a cell in a cluster as a consequence of a perturbation induced by removing a random set of cells from the cell population. CSS provides better cluster robustness information than the silhouette metric. Moreover, rCASC's tools can identify cluster-specific gene signatures. Conclusions rCASC is a modular workflow with new features that could help researchers define cell subpopulations and detect subpopulation-specific markers. It uses Docker for ease of installation and to achieve a computation-reproducible analysis. A Java GUI is provided to welcome users without computational skills in R.

Identification of diagnostic and prognostic lncRNA biomarkers in oral squamous carcinoma by integrated analysis and machine learning

2020 ◽  
Vol 29 (2) ◽  
pp. 265-275
Author(s):  
Sen Yang ◽  
Yingshu Wang ◽  
Jun Ren ◽  
Xueqin Zhou ◽  
Kaizhi Cai ◽  
...  
Keyword(s):  
Machine Learning ◽  
Clinical Data ◽  
Expression Profiles ◽  
Squamous Carcinoma ◽  
Prognostic Indicators ◽  
Receptor Interaction ◽  
Integrated Analysis ◽  
Sequencing Data ◽  
Oral Squamous Carcinoma ◽  
Precise Diagnosis

BACKGROUND: Patients with oral squamous carcinoma (OSCC) present difficulty in precise diagnosis and poor prognosis. OBJECTIVE: We aimed to identify the diagnostic and prognostic indicators in OSCC and provide basis for molecular mechanism investigation of OSCC. METHODS: We collected sequencing data and clinical data from TCGA database and screened the differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) in OSCC. Machine learning and modeling were performed to identify the optimal diagnostic markers. In order to determine lncRNAs with prognostic value, survival analysis was performed through combing the expression profiles with the clinical data. Finally, co-expressed DEmRNAs of lncRNAs were identified by interacted network construction and functional annotated by GO and KEGG analysis. RESULTS: A total of 1114 (345 up- and 769 down-regulated) DEmRNAs and 156 (86 up- and 70 down-regulated) DElncRNAs were obtained in OSCC. Following the machine learning and modeling, 15 lncRNAs were identified to be the optimal diagnostic indicators of OSCC. Among them, FOXD2.AS1 was significantly associated with survival rate of patients with OSCC. In addition, Focal adhesion and ECM-receptor interaction pathways were found to be involved in OSCC. CONCLUSIONS : FOXD2.AS1 might be a prognostic marker for OSCC and our study may provide more information to the further study in OSCC.

Results of application of a new method for the treatment of hallux valgus of the first toe

2016 ◽  
Vol 94 (6) ◽  
pp. 458-462
Author(s):  
L. K. Brizhan’ ◽  
A. V. Boichenko ◽  
D. V. Davydov ◽  
L. N. Solomin ◽  
A. A. Kerimov ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Hallux Valgus ◽  
Original Method ◽  
Surgical Correction ◽  
Aofas Score ◽  
Intermetatarsal Angle ◽  
Standard Methods ◽  
X Ray ◽  
Significant Difference ◽  
Better Than

Background. The aim of the present article was to report our experience with the treatment ofpatients with hallux valgus and to perform comparative analysis of the results of the newly proposed and standard methods for its surgical correction. Methods. The data on 70patients (101 feet) with hallux valgus that were operated on between 2011 and 2015 in St. Petersburg Hospital No 2 using the new and standard methods were analysed. The functional assessment (AOFAS score) and X-ray examination were performed preoperatively, 3 and 12 months after the procedure. Comparative analysis between patients undergoing surgical correction by the new and standard methods has been undertaken. Results. We did not find any significant difference between the two groups in mean AOFAS score 12 months after surgery. Nevertheless, the function score of the patients treated by the newly proposed method (79.4±6.5 in 3 months) was significantly better than in those given the standard treatment (72.2±7.6 in 3 months). Mean intermetatarsal angle 12 months after surgery by standard and new methods was 9,7±0,7° and 8,6±0,7° (p<0.05), mean metatarsophalangeal angle 13,6±0,9° and 13,0±1,1° (p<0,05) respectively. Conclusion. According to the data obtained, the original method of hallux valgus surgical correction allows to improve its functional and x-ray results.

scholarly journals BG7: A New Approach for Bacterial Genome Annotation Designed for Next Generation Sequencing Data

PLoS ONE ◽  
2012 ◽  
Vol 7 (11) ◽  
pp. e49239 ◽  
Author(s):  
Pablo Pareja-Tobes ◽  
Marina Manrique ◽  
Eduardo Pareja-Tobes ◽  
Eduardo Pareja ◽  
Raquel Tobes
Keyword(s):  
Next Generation Sequencing ◽  
Genome Annotation ◽  
Bacterial Genome ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
New Approach ◽  
Generation Sequencing
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