UserGuide:RNAi Search

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OVERVIEW: RNAi PHENOTYPE SEARCH

The ability to inactivate C. elegans genes by RNAi has allowed mass screens for diverse phenotypes, induced by mass RNAi-knockout of most of the genes on a chromosome or in a preselected set of functionally interesting clones. Such data is potentially of great value, but is difficult to decipher without automated searches for those RNAi results with particular characteristics. The RNAi Phenotype Search page is meant to allow such searches. It searches data that include both large-scale RNAi experiments and small-scale RNAi experiments, both of which are curated by Wormbase staff as soon as possible after publication.

It is important to note that while mass RNAi screens are highly valuable, the results are -- necessarily -- frequently incomplete, and sometimes just wrong. This is unavoidable given that RNAi does not act with equal efficacy on all tissues or developmental stages in C. elegans, and that a mass RNAi screen can only be done on a predetermined set of well-defined phenotypes. It is thus entirely possible that an RNAi result of 'wild-type' ("WT") is misleading because the gene inactivated by RNAi acts in a tissue insusceptible to RNAi, or because there was a perfectly valid phenotype that was too subtle, specialized, or original to be seen in a mass screen. As always in science, there is no easy substitute for empirically checking the reproducibility of data oneself.

SEARCH OPTIONS

Searches of Wormbase RNAi phenotypes have several different options:

  • Maternal phenotype:

One of the most common RNAi phenotypes in mass screens is maternal sterility. If one is looking for genes with early roles in gametogenesis, it is reasonable to look for partially or completely sterile RNAi phenotypes. Conversely, to select for genes that are specific to a later stage of the life cycle, one can try screening for genes lacking such a phenotype. Sterile RNAi phenotypes are expected to identify those genes where a substantial amount of gene activity is maternal in addition to (or rather than) zygotic.

  • Embryonic phenotype:

Another very common RNAi phenotype in mass screens is embryonic lethality. This phenotype is expected to arise without maternal sterility where an inactivated gene is zygotically active in early development. If one is interested in genes that are primarily active in postembryonic life, it would be reasonable to search for genes that are neither maternally sterile nor embryonically lethal.

  • General postembryonic phenotypes:

A great many postembryonic phenotypes are imaginable (several hundred have been assigned gene class abbreviations as of mid-2003). However, it can sometimes be useful to combine postembryonic phenotypes into broad groups. The current groups used by WormBase are defects in growth, morphology, movement, or reproduction. In general, genes affecting metabolic control or efficiency might be expected to affect growth, those affecting development to affect morphology or reproduction, and those affecting nerve or muscles to affect movement.

  • Specific postembryonic phenotypes:

These are listed individually, and should be reasonably self-explanatory. They are meant to be identical in character to the phenotypes that would be used for a classical genetic screen; if an animal is made hyperactive by RNAi of a given gene, that Hya phenotype should be equivalent to what would be scored as Hya if mutagenesis had been done through ethylmethane sulfonate (EMS) or through transposon mobilization.

  • Combined traits:

It is possible to search for RNAi results that combine two or more characteristics. For instance, one can search for genes that are both Sterile and Uncoordinated when treated with RNAi; in this instance, the syndrome of joint Vul and Unc is a symptom of genes that may control postembryonic cell division, since normal proliferation of postembryonic tissues is required in adult C. elegans for both locomotion and fertility. Many other such combinations can be considered and used in a RNAi search.

  • Large lists of RNAi results:

It can be very useful to have a plain text file of all the RNAi results falling into a very broad group -- wild-type results, non-wild-type results, or any results at all. Buttons are provided on the RNAi Phenotype Search page allowing any of these lists to be displayed. Such lists can then be saved as plain (ASCII) text, and then searched by whatever means may be useful on one's own computer (e.g. through shell or Perl scripts).

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