ORIGINAL ARTICLES  MICROARRAY MEETING 2003: III CONVEGNO ITALIANO SULLA TECNOLOGIA
Segrate (MI), 9-10 Giugno 2003 

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

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.