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Minerva Biotecnologica 2003 December;15(4):223-34

Copyright © 2004 EDIZIONI MINERVA MEDICA

lingua: Inglese

Strategies and tools for upgrading the information content of regulated gene lists from microarray experiments

Bicciato S. 1, Mangano E. 2, Frosini A. 2, 3, Luchini A. 1, De Bellis G. 3, 4, Battaglia C. 2, 3

1 Department of Chemical Process Engineering, University of Padua, Padova, Italy; 2 Array Technology Group, Department of Science and Biomedical Technologies, University of Milan, Segrate (MI), Italy; 3 CISI, University of Milan, Segrate (MI), Italy; 4 Institute for Biomedical Technologies (ITB), CNR, Segrate (MI), Italy


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The tran­scrip­tion­al pro­fil­ing of ­whole ­genomes ­using cDNA or oli­go­nu­cleo­tide ­high-den­sity ­arrays is becom­ing increas­ing­ly pop­u­lar ­among the bio­med­i­cal ­research com­mu­nity. Although advanc­es in tech­nol­o­gy and the rap­id ­rise in micro­ar­ray ­data avail­abil­ity are lead­ing to new ­insight ­into fun­da­men­tal bio­log­i­cal prob­lems, inves­ti­ga­tors are ­still con­front­ed ­with the ­major prob­lem of upgrad­ing the infor­ma­tion con­tent of reg­u­lat­ed ­gene ­lists ­obtained ­from micro­ar­ray experi­ments. Indeed, the effi­cient exploi­ta­tion of ­gene expres­sion data­bas­es ­requires not ­only com­pu­ta­tion­al ­tools for man­age­ment and anal­y­sis of pri­mary ­data, but ­also inte­grat­ing ­lists of mod­ulat­ed ­genes ­with of oth­er sourc­es of bio­log­i­cal infor­ma­tion, ­such as bio­chem­i­cal path­ways and bio­med­i­cal lit­er­a­ture. However, ­such inte­gra­tion, essen­tial to func­tion­al­ly inter­pret ­derived ­gene ­lists and to ­relate expres­sion pro­files to molec­u­lar phys­iol­o­gy, ­often ­results in an explo­sion of the infor­ma­tion con­tent ­instead of knowl­edge ­growth. This arti­cle ­reviews sev­er­al pub­lic resourc­es for vis­u­al­iza­tion, anno­ta­tion, and func­tion­al inter­pre­ta­tion of ­gene expres­sion data­sets. The ­focus is on ­tools ­that inte­grate func­tion­al genom­ic infor­ma­tion, bio­chem­i­cal path­ways, and bib­lio­graph­ic ­records ­with intui­tive graph­i­cal sum­mar­ies.

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