Searching the Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
Edwardsiella tarda, the bacterial pathogen that causes ascites disease and red-head disease, poses a serious threat to yellow catfish (Pelteobagrus fulvidraco) aquaculture. In this study, the spleens of E. tarda-infected and non-infected yellow catfish were sequenced to obtain the microRNA (miRNA) and mRNA expression profiles. We obtained 657 differentially expressed (DE) miRNAs and 6867 DE mRNAs between two groups and annotated them using the KEGG database. In addition, the 43 negatively correlated miRNA-mRNA pairs were identified using integrated miRNA-mRNA analysis, which including immune-related miRNAs and target genes such as miR-144, miR-1260, miR-1388, miR-33, miR-338, miR-181b, miR-34c, miR-135 and CLEC4E, LITR, PIKfyve, NCF4, IL-12β, IP6K2, TNFRSF9, IL-4Rα, IRF2, Mx2. We verified 8 DE miRNAs pairs and 10 DE mRNAs by quantitative real-time PCR. Finally, the CLEC4E and Mx2 mRNAs were selected for further verification using in situ hybridization. Together, our results provide valuable information for further analyses of the mechanisms of yellow catfish defense against E. tarda infection.
Pubmed ID: 33476668
Publication data is provided by the National Library of Medicine ® and PubMed ®. Data is retrieved from PubMed ® on a weekly schedule. For terms and conditions see the National Library of Medicine Terms and Conditions.
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 mentionsSoftware platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
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 mentionsA database for phylogenetic classification for proteins encoded in complete genomes. Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. Please be aware that COGs hasn't been updated in many years and will not be.
View all literature mentionsThe Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: Non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion. Rfam is also available via FTP. You can find data in Rfam in various ways... * Analyze your RNA sequence for Rfam matches * View Rfam family annotation and alignments * View Rfam clan details * Query Rfam by keywords * Fetch families or sequences by NCBI taxonomy * Enter any type of accession or ID to jump to the page for a Rfam family, sequence or genome
View all literature mentionsR package to identify differentially expressed genes from RNA-Seq data.
View all literature mentions