p53FamTaG: a database resource of human p53, p63 and p73 direct target genes combining in silico prediction and microarray data.
BACKGROUND
The p53 gene family consists of the three genes p53, p63 and p73, which have polyhedral non-overlapping functions in pivotal cellular processes such as DNA synthesis and repair, growth arrest, apoptosis, genome stability, angiogenesis, development and differentiation. These genes encode sequence-specific nuclear transcription factors that recognise the same responsive element (RE) in their target genes. Their inactivation or aberrant expression may determine tumour progression or developmental disease. The discovery of several protein isoforms with antagonistic roles, which are produced by the expression of different promoters and alternative splicing, widened the complexity of the scenario of the transcriptional network of the p53 family members. Therefore, the identification of the genes transactivated by p53 family members is crucial to understand the specific role for each gene in cell cycle regulation. We have combined a genome-wide computational search of p53 family REs and microarray analysis to identify new direct target genes. The huge amount of biological data produced has generated a critical need for bioinformatic tools able to manage and integrate such data and facilitate their retrieval and analysis.


METHODS
We have developed the p53FamTaG database (p53 FAMily TArget Genes), a modular relational database, which contains p53 family direct target genes selected in the human genome searching for the presence of the REs and the expression profile of these target genes obtained by microarray experiments. p53FamTaG database also contains annotations of publicly available databases and links to other experimental data. The genome-wide computational search of the REs was performed using PatSearch, a pattern-matching program implemented in the DNAfan tool. These data were integrated with the microarray results we produced from the overexpression of different isoforms of p53, p63 and p73 stably transfected in isogenic cell lines, allowing the comparative study of the transcriptional activity of all the proteins in the same cellular background.p53FamTaG database is available free at http://www2.ba.itb.cnr.it/p53FamTaG/ CONCLUSION: p53FamTaG represents a unique integrated resource of human direct p53 family target genes that is extensively annotated and provides the users with an efficient query/retrieval system which displays the results of our microarray experiments and allows the export of RE sequences. The database was developed for supporting and integrating high-throughput in silico and experimental analyses and represents an important reference source of knowledge for research groups involved in the field of oncogenesis, apoptosis and cell cycle regulation.
Sbisà
Elisabetta
E
Istituto di Tecnologie Biomediche-Sede di Bari, CNR, Via Amendola, 122/D 70126 Bari, Italy. elisabetta.sbisa@ba.itb.cnr.it
Catalano
Domenico
D
Grillo
Giorgio
G
Licciulli
Flavio
F
Turi
Antonio
A
Liuni
Sabino
S
Pesole
Graziano
G
De Grassi
Anna
A
Caratozzolo
Mariano Francesco
MF
D'Erchia
Anna Maria
AM
Navarro
Beatriz
B
Tullo
Apollonia
A
Saccone
Cecilia
C
Gisel
Andreas
A
D000465:Algorithms; D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000235:genetics*; D030541:Databases, Genetic; D018390:Gene Targeting / Q000379:methods*; D006801:Humans; D005810:Multigene Family / Q000235:genetics; D009687:Nuclear Proteins / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D012984:Software; D015534:Trans-Activators / Q000235:genetics*; D014157:Transcription Factors; D016159:Tumor Suppressor Protein p53 / Q000235:genetics*; D025521:Tumor Suppressor Proteins / Q000235:genetics*
D004268:DNA-Binding Proteins; D009687:Nuclear Proteins; C495901:TP53 protein, human; C115051:TP63 protein, human; D015534:Trans-Activators; D014157:Transcription Factors; D016159:Tumor Suppressor Protein p53; D025521:Tumor Suppressor Proteins