IDENTIFICAZIONE DI GENI ESTROGENO RESPONSIVI CON METODI COMPUTAZIONALI. Francesca Cordero Fulvio Lazzarato Raffaele A. Calogero

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1 IDENTIFICAZIONE DI GENI ESTROGENO RESONSIVI CON METODI COMUTAZIONALI Francesca Cordero Fulvio Lazzarato Raffaele A Calogero

2 romoters analysis Identification of common transcriptional elements, within co-regulated genes, might help to unmask hidden regulative mechanisms Identification of transcriptional regulative elements (TRE)( clusters linked to co- regulated genes might help to identify, in the genome, uncharacterized genes regulated by the same mechanism

3 romoters analysis: : limitations Computational tools are quite inefficient in the identification of eukaryotic promoters Our approach: Relay on NCBI genomic annotations Repeating the analysis as annotations are upgraded

4 Hs genome data Rn genome data Mm genome data Automatic download (Curl/Zlib) Non-coding regions Extraction (Gene ID linked) Upstream UTR Introns UTR UTR Downstream ATG Transcription start site TAA

5 romoters analysis Transcriptional signatures might be linked to co-regulated genes Transcriptional signatures might be characterized by the presence of TRE T clusters The identification of TRE clusters (eg CISTER, CREME) relays on availability of a set of potential TREs mapped on promoters

6 TRE clusters in ERE containing genes The first step to search for TRE clusters is the availability of a set of genes sharing some common regulative behaviour(s) Our study: The set we are interested is a set of genes directly controlled by the estrogens in breast cancer

7 Il complesso estrogeno-er, in forma dimerica, riconosce la sequenza ERE: nnaggtcannntgacctnn nntccagtnnnactggann L interazione tra ER-DNA è principalmente guidata dai residui evidenziati in rosso

8 Count matrix 9 G 9 9 C A 9 Frequency matrix C 9 9 A Log Odds matrix T G C A log f i e i

9 T G C A Score: - Score: - C A G G T G A C C T C A C C C T Score:, Score:, T G A Score: - Score: T G C A nnnggtcannntgaccnnn nnnggtcannntgaccnnn nnnccagtnnnactggnnn nnnccagtnnnactggnnn

10 E possibile migliorare la matrice ERE di TRANSFAC?

11 Endocrinology Oct;():- Epub Jul Frasor et al 9 Cicatiello et al J Mol Endocrinol Jun;():9-

12 TFF CG up-modulati geni GGTCACATGGG GGACAGACAGACC LOC ARM EGFL LOC LOC LOC99 LOC9 RDM LOC ARHGEF WDR GGTCACAATGA GC GGTCATTCTGA CT GCTCAGGCTGA GC GATGAGTCTGA CC GGTCAGGGCCA CC GCTCAGAATAACC KIAA DFFB LOC9 RKCZ ERE in geni AGTCACTGTGG CC AGTGATTTTGAC C AGTCACACTGA CC GTGCATTCTGACC GGACACCCAGACC GGACATACTG ATC GGTCACGGTGGC C GCCAAGATGA CC ACCAGCCTGA CC LOC9 Biol harm FLJ Bull Feb;():-9 A 9 C 9 T ERBB G 9 J Biol Chem 99 Nov ;():9- T ERE-M Oncogene Jan ;9():-

13 CONTENUTO INFORMAZIONALE (Ci) Matrice di Ci= ERE-M ln Transfac p b *ln p b ln b = A,T,C,G A C G T, A C G G T T 9 9,

14 ERE-M Hs ChR ln(p-value)~- ATSER (Hertz & Stormo) Frequenza Elementi ERE in geni up-modulati in Frasor o Cicatiello Score è lo score minimo necessario per identificare ERE nelle sequenze -/+ dei geni utilizzati per generare la matrice ERE-M

15 ERE-M Hs Chrs Mm Chrs Rn Chrs ATSER Score > (Hertz & Stormo) Genome Res May;():-9 Geni contenenti ERE

16 roc Natl Acad Sci U S A Sep ;():9- Epub Aug Nature Jan ;():-

17 Sotiriou (9) van t Veer () 99 value <= Wilcoxon s Test Hs Mm Rn Contenenti ERE Freq uenza Frequenza,,,,,, W ilcoxon's p- values 9 value <= W ilcoxon's p- value Hs Mm Rn,,,,,, Contenenti ERE Identificazione di geni differenzialmente espressi tra tessuti tumorali ER+/ER-

18 GO category cell death GENE ONTOLOGY p-value in regulation of cell proliferation Non significativo apoptosis programmed cell death positive regulation of programmed cell death positive regulation of apoptosis induction of programmed cell death induction of apoptosis regulation of programmed cell death cell growth and/or maintenance regulation of apoptosis Non significativo Non significativo p-value in p-value in Non significativo E un vocabolario death dinamico, Non significativo che permette l associazione Non significativo dei geni differenzialmente espressi a specifiche classi funzionali

19 Contenenti elementi ERE localizzati intorno al primo nucleotide trascritto Frequenza Classe - -

20 Set Geni Estrogeno Responsivi : Geni con ERE in Hs Mm Rn wwwbioinformaticaunitoit/bioinformatics/rre/rrehtml Differenzialmente espressi tra tumori ER+ ed ER- Arricchiti in classi di gene ontology associate al ciclo cellulare Contenenti elementi ERE localizzati intorno al primo nucleotide trascritto Bioinformatics -, : resenza di ERE raggruppati in cluster

21 wwwbioinformaticaunitoit/bioinformatics/rre/rrehtml Bioinformatics Apr 9

22 RRE database RRE allows the extraction of non-coding regions surrounding a coding sequence [ie gene upstream region, -untranslated region (-UTR), introns, -UTR, downstream region] from annotated genomic datasets available at NCBI RRE parser and web-based interface are accessible at s/rre/rrehtml

23 RRE database Available genomes data: Arabidopsis thaliana Caenorhabditis elegans Drosophila Melanogaster Homo Sapiens Mus Musculus lasmodium falciparum Rattus Norvegicus Schizosaccharomyces pombe

24 RRE database Available retrieval options: Upstream, -/+, UTR, Introns, Exons, UTR, Downstream Available quieries: By gene symbols list By gene ID (Locus Link) list By orthologs gene ID list By genomic contig(s) list By chromosome

25 Other features: RRE database Searching for a specific feature (eg 'UTR) genes located within a certain distance from a list of genes This query is interesting for users guessing the presence of some regulative common mechanism associate to a specific chromosomal locus

26 RRE database (Genes containing ERE elements)

27 RRE database (Genes containing ERE elements) Available retrieval options: Homo S genes containing at least a predicted ERE in the -/+ region AND/OR -value associated to ER-responsive breast cancer (Sotiriou/LJ van 't Veer) -value associated to early onset of metastasis (LJ van 't Veer)

28 roc Natl Acad Sci U S A Sep ;():9- Epub Aug Nature Jan ;():-

29 Sotiriou (9) van t Veer () 99 value <= Wilcoxon s Test Hs Mm Rn Contenenti ERE Freq uenza Frequenza,,,,,, W ilcoxon's p- values 9 value <= W ilcoxon's p- value Hs Mm Rn,,,,,, Contenenti ERE Identificazione di geni differenzialmente espressi tra tessuti tumorali ER+/ER-

30 RRE database (Genes containing ERE elements) Available retrieval options: AND/OR Genes found modulated by estrogen in microarray analysis in MCF cell line (Frasor et al /) AND/OR Genes found modulated by estrogen in microarray analysis in ZR cell line (Cicatiello et al ) AND/OR Homo S genes containing at least a predicted ERE also conserved in Mus musculus AND/OR Homo S genes containing at least a predicted ERE also conserved in Rattus norvegicus