FAQ

1. Data Sources

1.1 What kind of data resources are deposited in IC4R?

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.

1.2 What information can be obtained from Protein-coding Genes?

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.

  • Transcript features and protein information are provided for each gene page.
  • RNA-Seq supported evidence from specific tissue is presented for each gene.
  • Genome browser is built on JBrowse to visualize the annotated gene structure and provide comparison between different annotation systems.
  • Functional annotation information including ‘Functional Categories’, ‘ID’ and ‘Description’ derived from PAFM, GO, PRINTS, PROSITE, PANTHER and SMART database are provided for each gene.
  • Diversified biological ontologies including Gene Ontology, Plant Ontology, Trait Ontology and Environment Ontology are displayed on the ‘Biological Ontologies’ section.
  • Community Curation & Comments provides a platform for users to contribute their knowledge on each gene by submitting the publication title, additional functional annotation, experimental evidence and free comments. For confirmation and feedback, we sincerely ask users for E-mail and institution name.

1.3 What information can be obtained from Long non-coding RNAs?

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.

1.4 What information can be obtained from Circular RNAs?

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.

1.5 IC4R-1.0 Omic Modules

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.

1.6 Can users get the information of RNA-Seq support dataset?

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.

2.1 How to search in IC4R?

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.

2.2 What will users find in the Search Results?

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.

3. Are there some Tools provided by IC4R ?

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.

3.1 BLAST

In IC4R, sequence similarity alignment can be conducted through blastn (nucleotide to nucleotide), blastp (protein to protein), and blastx (translated nucleotide to protein).

3.2 ID Conversion

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.

3.3 Genome Browser

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.

3.4 HK-TS Genes Filter

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.

4. Data Access

4.1 Download

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.

4.2 APIs

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.

5. Support & Feedback

  • If you have any problems or questions using one of the IC4R data or tools;
  • If you are interested in improving our annotation information or website;
  • You would like to send us some suggestions or feedback, please find our contact information here. We are looking forward to receiving worldwide comments, suggestions and guidance from colleagues and peers with common research interests.