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Jan. 5, 2007: RNAiDB Version 5 Released

This update of RNAiDB includes all RNAi data from the Piano lab, and all RNAi experiments in WormBase WS150. Reagent to gene mappings are curated at RNAiDB and may differ from those available at WormBase (explain ...).

RNAiDB v5.0 features:

  • Website redesign: the website infrastructure has been completely overhauled and the interface redesigned to improve the user interface and maintainability. Changes to all pages and gene graphs have been implemented.
  • Integration with WormBase WS150: RNAiDB v5 incorporates all RNAi experiments present in WS150, including annotated phenotypes and raw data (images and time-lapse movies). Reagent to gene mappings are annotated independently at RNAiDB using a sliding n-mer window method to evaluate sequence similarity between dsRNA reagents and predicted transcripts. Primary (canonical) and secondary (off-target) RNAi targets identified in this way may differ from targets identified at WormBase using BLAST/BLAT.
  • Sliding window analysis: calculation of potential off-target inhibition has been reimplemented to streamline the analysis with generation of GFF annotations.
  • New PhenoBlast: PhenoBlast has been reimplemented to improve speed, and has been extended to include two new phenotypic signatures: an early embryo signatures from Sönnichsen et al., 2005 (also used in Gunsalus et al., 2005) and a signature for postembryonic phenotypes.
  • Search by chromosomal location or interval has been added, which allows the discovery of all RNAi results within a specified interval on the physical map. This can help users identify potential candidate genes for genetic mutations mapped to a rough physical interval.
  • Links to N-Browse: N-Browse is a web-based interactive graphical browser for molecular interaction data developed by Huey-Ling Kao in the Gunsalus lab. N-Browse allows the integrated analysis of heterogeneous functiona links between genes and proteins, such as protein-protein and genetic interactions, co-expression, phenotypic correlations, and predicted miRNA-target interactions. N-Browse can be used to visualize data in Gunsalus et al., 2005) and is described briefly in Lall et al., 2006.

Other News:

RNAi data from Sönnichsen et al., 2005 included in RNAiDB

This study reports the identification and phenotypic characterization of 661 genes with phenotypes in the early embryo (up to the 2-cell stage) in an RNAi survey of over 95% of C. elegans genes. In RNAiDB, experiment names from this study begin with "Cenix:". A phenotypic signature of 45 characters was generated for each of the 661 genes. The 661 Cenix Early Embryonic phenotypic signatures can now be queried using PhenoBlast.

RNAi data from Fernandez et al., 2005 included in RNAiDB

In this study RNAi was performed using ORFeome clones for over 1,000 genes with transcripts enriched in the ovary with no previously identified embryonic phenotypes. 155 new genes with roles in embryogenesis were identified, raising the total number of known embryonic essential genes to ~1,800. Notably, over two-thirds of the newly identified genes showed partial penetrance lethality, suggesting that most genes with strong embryonic phenotypes have already been identified. Experiment names from this study begin with "PF:ORC_" in RNAiDB.

An article describing RNAiDB and PhenoBlast has been published in NAR: Gunsalus et al., 2004.

RNAi data from Piano et al., 2002 included in RNAiDB

Over 750 ovary-enriched transcripts identified by microarray analysis in Reinke et al., 2000 were evaluated for embryonic lethality and postembryonic phenotypes by RNAi. 161 genes with phenotypes in the early embryo were systematically analyzed using a 47-character "phenotypic signature" developed for this study, encompassing all detectable phenotypes up to the 4-cell stage. The first systematic phenotypic analysis in C. elegans, this study pioneered the concept of a high-resolution phenotypic signature and demonstrated gene clustering based on phenotypic similarity. Experiment names from this study begin with "PF:GL1_" in RNAiDB.

RNAi data from Piano et al., 2000 included in RNAiDB

This study reports the first large-scale RNAi screen in C. elegans. Clones from an ovary cDNA library were screened for embryonic lethality and 81 genes with phenotypes in the early embryo were analyzed and grouped into phenotypic classes. Experiment names from this study begin with "KK:SP" in RNAiDB.


Development of RNAiDB is supported by grants from the National Science Foundation and the National Institutes of Health.