Case study of eve1 in D. rerio

An example workflow illustrates some (though not all) of IMP’s capabilities. Eve1 is a Danio rerio transcription factor implicated in a conserved role in body patterning in a variety of species [1]. However, little is known about the biological mechanism of eve1 beyond its global role in patterning. A researcher may be interested in identifying the specific processes that eve1 participates in.

Search for eve1

To generate testable hypotheses for the functional role of eve1, a biologist can query IMP for the gene. They can search IMP using a variety of identifiers for eve1 (Entrez, Ensembl and Zfin), in addition to its standard name.

Analysis of eve1

The result page for this query contains a list of biological processes predicted for eve1 and a network with genes predicted to be functionally related. Consistent with prior functional knowledge, the top prediction for eve1 is pattern specification process (GO:0007389), which reflects our understanding of eve1 in patterning. To identify a more specific functional role of eve1, the biologist can filter the prediction list by term size directly from the result page. The only process that is both specific (122 known genes) and predicted with high confidence (85% probability) is the biological process of anterior-posterior pattern formation (GO:0009952).

Eve1 experimental results

In a recent publication, with experimental results not included in IMP, authors show that eve1 is an important regulator in posteriorisation and neural induction through a series of loss and gain of function experiments [2]. Thus, in this case, IMP predicts a functional role (anterior-posterior pattern formation) for eve1 that was independently confirmed. Additionally, although the role of eve1 in neural induction was not directly predicted, a higher level but related process was predicted with high confidence (central nervous system development with 78% probability).

References

1. Ahringer,J. (1996) Posterior patterning by the Caenorhabditis elegans even-skipped homolog vab-7. Genes Dev., 10, 1120–1130.

2. Cruz,C., Maegawa,S., Weinberg,E.S., Wilson,S.W., Dawid,I.B. and Kudoh,T. (2010) Induction and patterning of trunk and tail neural ectoderm by the homeobox gene eve1 in zebrafish embryos. Proc. Natl. Acad. Sci. U.S.A., 107, 3564–3569.