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The current study examined the liver transcriptomic profiles of the Large White different in developmental periods. It was performed on pigs of two developmental stages: 70-day fetus (P70) and 70-day piglets (D70). The objective of the study was to identify genes associated with Large White liver lipid metabolism, growth and development. We sequenced eight sRNA libraries of liver samples from four Large White at P70 and D70 respectively. We totally obtained 19,202 genes. 4916 of them were found to be differentially expressed (DEGs) (p < 0.05, fold change ≥ 1), of which 2502 were up-regulated and 2414 were down-regulated. GO enrichment and KEGG pathway analysis indicated that ACACA, ACADM, ACAA2 and HADH were simultaneously enriched in diverse pathways related to lipid metabolism, and so they were considered to be the promising candidate genes which could affect the porcine liver lipid metabolism. Notably, the gene insulin-like growth factor 1 (IGF1) which participated in somatotropic axis signaling was found to be up-regulated in D70 compared with P70. miRWalk and TargetScan softwares were used to screen the miRNAs which bound to the 3' untranslated region (3'UTR) of IGF1. After integration analysis with miRNAs sequencing data, miR-18b and miR-130b-3p were selected for further study. MiR-18b and miR-130b-3p were down-regulated in D70 compared with P70. Dual luciferase assays indicated that miR-18b and miR-130b-3p could obviously decrease (p < 0.05) the fluorescence activity of the group transfected with the wild-type vector of IGF1 3'UTR, while the relative luciferase activity of the group transfected with the mutant vector of IGF1 3'UTR did not change significantly. Taken together, it indicated that miR-18b and miR-130b-3p could target IGF1 directly.
Pubmed ID: 30321659
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Web application to search protein databases using a translated nucleotide query. Translated BLAST services are useful when trying to find homologous proteins to a nucleotide coding region. Blastx compares translational products of the nucleotide query sequence to a protein database. Because blastx translates the query sequence in all six reading frames and provides combined significance statistics for hits to different frames, it is particularly useful when the reading frame of the query sequence is unknown or it contains errors that may lead to frame shifts or other coding errors. Thus blastx is often the first analysis performed with a newly determined nucleotide sequence and is used extensively in analyzing EST sequences. This search is more sensitive than nucleotide blast since the comparison is performed at the protein level.
View all literature mentionsComputable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.
View all literature mentionsCentral online repository for microRNA nomenclature, sequence data, annotation and target prediction.Collection of published miRNA sequences and annotation.
View all literature mentionsCommercial organization for research and development genomics services and technical support to researchers.
View all literature mentionsAn ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Blast2GO (B2G) joins in one universal application similarity search based GO annotation and functional analysis. B2G offers the possibility of direct statistical analysis on gene function information and visualization of relevant functional features on a highlighted GO direct acyclic graph (DAG). Furthermore B2G includes various statistics charts summarizing the results obtained at BLASTing, GO-mapping, annotation and enrichment analysis (Fisher''''s Exact Test). All analysis process steps are configurable and data import and export are supported at any stage. The application also accepts pre-existing BLAST or annotation files and takes them to subsequent steps. The tool offers a very suitable platform for high throughput functional genomics research in non-model species. B2G is a species-independent, intuitive and interactive desktop application which allows monitoring and comprehending the whole annotation and analysis process supported by additional features like GO Slim integration, evidence code (EC) consideration, a Batch-Mode or GO-Multilevel-Pies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
View all literature mentionsWeb tool to predict biological targets of miRNAs by searching for presence of conserved 8mer, 7mer and 6mer sites that match seed region of each miRNA. Nonconserved sites are also predicted and sites with mismatches in seed region that are compensated by conserved 3' pairing. Used to search for predicted microRNA targets in mammals.
View all literature mentionsSoftware tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.
View all literature mentionsSoftware tool to store the predicted and the experimentally validated microRNA (miRNA)-target interaction pairs. Predictions within the complete sequence of genes of human, mouse, and rat genomes. Integrates a comparative platform of miRNA-binding sites resulting from ten different prediction datasets.
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