About this supplement

Installation

Widget Catalog

D. discoideum example

S. cerevisiae example

Spotlight

Our widgets for functional genomics use Orange, a data mining and machine learning suite. Orange can be accessed through scripting in Python, or by visual programming in Orange Canvas.

In functional genomics, we have also designed a web-based tool for mutant data analysis called GenePath (also featured in Science's NetWatch).


FRI > Biolab > Supplements > Microarray Data Mining with Visual Programming

This set of web pages provides a supplemental material (installation and two examples) to the following paper submitted to Bioinformatics:

Microarray Data Mining with Visual Programming
Tomaz Curk, Janez Demsar, Qikai Xu, Gregor Leban, Uros Petrovic, Ivan Bratko, Gad Shaulsky and Blaz Zupan

Abstract: Visual programming offers an intuitive means of combining known analysis and visualization methods into powerful applications. The system presented here enables users who are not programmers to manage microarray and genomic data flow and to customize their analysis by combining common data analysis tools to fit their needs.

Supplemental information on the following topics is available:

  • Installation, where you can download a program that installs Orange, Orange Canvas with widgets, and all the data sets needed to replicate the examples from the paper and these web pages.
  • Orange Widgets for Functional Genomics, which is a 16-page widget catalog and reference guide that describes the implemented widgets and their data interfaces in detail.
  • D. discoideum example, which describes the schema used in the analysis of Dictyostelium discoideum development. We show the overall layout of the schema and comment on each of the widgets used.
  • S. cerevisiae example, similar as above, but showing a different schema for the analysis of Saccharomyces cerevisiae cell cycle data.

References

Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T. and others. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet, 25, 25-9.

Cho R.J., Campbell M.J., Winzeler E.A., Steinmetz L., Conway A., Wodicka L., Wolfsberg T.G., Gabrielian A.E., Landsman D., Lockhart D.J. and others. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell, 2, 65-73.

Dolinski K., Balakrishnan R., Christie K.R., Costanzo M.C., Dwight S.S., Engel S.R., Fisk D.G., Hirschman J.E., Hong E.L., Nash R. and others. (2003) Saccharomyces Genome Database (http://www.yeastgenome.org/).

Katoh M., Shaw C., Xu Q., Van Driessche N., Morio T., Kuwayama H., Obara S., Urushihara H., Tanaka Y., Shaulsky G. (2004) An Orderly  Retreat: Dedifferentiation is a Regulated Process. Under revision, Proc. Natl. Acad. Sci.

Spellman P.T., Sherlock G., Zhang M.Q., Iyer V.R., Anders K., Eisen M.B., Brown P.O., Botstein D., Futcher B. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell, 9, 3273-97.

Van Driessche N., Shaw C., Katoh M., Morio T., Sucgang R., Ibarra M., Kuwayama H., Saito T., Urushihara H., Maeda M. and others. (2002) A transcriptional profile of multicellular development in Dictyostelium discoideum. Development, 129, 1543-52.