Annotation and sequence information of Genes (Protein-coding Genes), and Non-coding Genes, such as LncRNAs (Long non-coding RNAs) or CircRNAs (Circular RNAs) are core data in IC4R. For each gene type, detailed sectional structural and functional information is provided for each gene locus. IC4R also integrates adjunctive metadata data of RNA-Seq data used for genome re-annotation and curated expression data that can be used for measuring expression breadth, expression level and expression constancy. Furthermore, community-contributed modules of multi-level omics data can also be reached by linking to original IC4R gene identifiers. The data resources mentioned above can be obtained directly from the Homepage or by ‘Browse’, ‘Search’ and ‘Download’ functions.
A total of 56,221 protein-coding genes were annotated in IC4R-2.0. The list of protein-coding genes with many gene features are supplied including gene identifier in IC4R-2.0, symbol, location, ID mapping, gene length, functional description and corresponding gene identifier in IC4R-1.0.
Protein-coding gene page: gene summary provides many helpful links for users to get a panorama of the gene of interest.
A total of 6,259 long non-coding RNAs are annotated in IC4R-2.0. The list of long non-coding RNAs is supplied with many basic features, shown as sortable column headings, including lncRNAs identifier in IC4R-2.0, location, gene length, GC content (%), Purine content (%) and exon numbers.
Circular RNA page: For each circular RNA, both basic and detailed information are displayed on each gene page. Basic information is shown below on the accession list.
Detailed information provides the RNA-Seq datasets which the circular is identified, such as SRR Accession, tissue and the accession of back-spliced junction reads.
From IC4R Omic Module, users can obtain annotation information of each gene accession in IC4R-1.0 system, constituted of gene summary, transcripts, methylation profile, expression, homology, variation, literature miner, community annotation, genome browser of genes and QTL of interest.
Yes, users can explore the metadata of each RNA-Seq experiment applied for IC4R-2.0 annotation system. Details of the RNA-Seq datasets containing Run ID’, ‘Layout’, ‘Spots’, ‘Bases’, ‘Tissues’, ‘Description’ and ‘Release Date’ are also listed here for further check and curation. profile, expression, homology, variation, literature miner, community annotation, genome browser of genes and QTL of interest.
In IC4R-2.0, users can exploit the Search function to search gene of interest by keyword (e.g. IC4R, sd1), locus identifier (e.g. IC4R-OSJ07G257400), symbol (e.g. sd1), functional identifier (e.g. PF00447) or functional term (e.g. HSF) either on the homepage or on the specified search page.
The primary search results are listed as follows: IC4R-2.0, Symbol, gene length, location, description and corresponding IC4R-1.0 identifier. Users can further find detailed information by clicking on the IC4R-2.0 or IC4R-1.0 gene identifier.
Yes, IC4R integrates a series of online tools, such as BLAST, ID Conversion, Genome Browser and TS-HK Genes Filter, to facilitate users to retrieve, analyze, visualize and make better use of relevant data.
In IC4R, sequence similarity alignment can be conducted through blastn (nucleotide to nucleotide), blastp (protein to protein), and blastx (translated nucleotide to protein).
ID Conversion is a useful tool to convert gene accession from one to the other among three ID systems of IC4R-2.0, MSU-7.0 and RAP-DB.
As mentioned above, Jbrowse is used for navigation of genome annotations and visualization of various omics data. There are several different annotation tracks and biological features integrated in the Jbrowse of IC4R, which are vertically listed on the left panel.
Once you select the specific check buttons of interest, all checked items will be dynamically shown in JBrowse’s main window.
TS-HK Genes Filter is developed for users to select rice Tissue-Specific and House-keeping Genes based on the τ-value (Tissue Specificity Index) and expression breadth.
IC4R-2.0 provides a specific interface for downloading rice genomic annotation as well as various types of relavent data. All these IC4R data are open access for academic research, however, we sincerely appreciate a citation of this work.
Just like IC4R-1.0, the current IC4R version continuously provides web service Application Programming Interface (APIs), which can help users and software developers to conveniently access data in bulk.