A SHORT OVERVIEW OF THE BIOINFORMATICS CORE

Bioinformatics core expertises Training in bioinformatics and statistics (all of us) Statistical data analysis (Annamaria&Luisa) Image analysis and processing (Annamaria) Gemonics and proteomics analysis (Veer&Diego C&Margherita) Next Generation Sequencing (Margherita & Veer) Maintainance and development of bioinformatics databases and software (Diego C&Gennaro) Veer Gennaro Marghe Luisa Anna Diego C

Databases and software development and maintenance Tools available on the BC website: Microarray Analysis Pipeline Mode of Action by NeTwoRk Analysis (MANTRA) Local UCSC genome browser Local CLUSTALW NetView Cometa Coming Soon: MANTRA 2 (SQUARED)SERVICE DESK

Training in Bioinformatics and Statistics TIGEM Statistics and Bioinformatics Internal Seminars Basic Statistics course Bioinformatics tools overview Seminars for the TIGEM PhD courses Statistical Analysis of Microarray data Next generation sequencing Bioinformatics Awareness Day Presentations A presentation periodically held to demonstrate new tools and services offered by the BC to TIGEM community European Bioinformatics Institute (EBI) - TIGEM joint Bioinformatics Course An overview on EBI biological databases relevant to the areas of genomics, transcriptomics and proteomics, held on 1st-2nd July 2010.

Training: Internal courses calendar 07 November Basic Statistic: summary statistics (mean, standard error, histograms etc.) and hypothesis testing in excel (T-test, Anova, Chisquare etc.) Deadline: 04 November 21 November Microarray analysis: Microarray Pipeline, Gene ontology annotation with David and Array Express Deadline: 16 November 05 December Gene List functional annotation: transcription factor binding sites with Transfac, gene set enrichment analysis with GSEA tool and basic usage of Ingenuity pathway analysis tool 17 December Image Analysis: Image Analysis with ImageJ and CellProfiler Register at bioinformatics.tigem.it

Statistical Analysis Clustering and network analysisTime series analysis Please make replicates.

Image Analysis and processing Cell number : 522 M631 -/- untreatedM631 -/- phenylbutyrate treatedWt

Bioinformatics and Genomics analyses

Next Generation Sequencing support in planning NGS experiments keep up-to-date with literature and analysis tools development of ad-hoc analysis pipelines support in visualization and interpretation of results NGS Applications: -RNA seq -small RNA seq -ChIP seq -Exome / Targeted seq

Hardware resources: a new Computer Cluster Nodes ProLiant DL380 G7 CPU: 2 x Intel Xeon E GHz –2 x 8 CORE, 16 Thread, 64 bit Memory: 24GB Disk: 146GB 8 x ProLiant BL280c G6 CPU: 2 x Intel Xeon X GHz –2 x 8 CORE, 16 Thread, 64 bit Memory: 48GB Disk: 500GB Storage 2 x Proliant DL360 G7 CPU: 2 x Intel Xeon E GHz –2 x 8 CORE, 16 Thread, 64 bit Memory: 36GB Disk: 146GB OS: LINUX CentOS 6 Storage Area Network Disk: 5TB SAS + 20 TB SATA Interconnect: 8Gbs Fibre Channel

Publications Licastro D, Mutarelli M, Peluso I, Neveling K, Wieskamp N, Rispoli R, Vozzi D, Athanasakis E, D'Eustacchio A, Pizzo M, D'Amico F, Ziviello C, Simonelli F, Fabretto A, Scheffer H, Gasparini P, Banfi S, Nigro V (2012) Molecular diagnosis of usher syndrome: application of two different next generation sequencing-based procedures. PLoS One, 2012;7(8):e Epub 2012 Aug 29. Cutillo L, Carissimo A, Figini S (2012) Network Selection: A Method for Ranked Lists Selection. PLoS ONE 7(8): e doi: /journal.pone Gennarino VA, DAngelo G, Dharmalingam G, Fernandez S, Russolillo G, Sanges R, Mutarelli M, Belcastro V, Ballabio A, Verde P, Sardiello M, Banfi S (2012) Identification of microRNA-regulated gene networks by expression analysis of target genes. Genome Res., 22: Gennarino VA, Sardiello M, Mutarelli M, Dharmalingam G, Maselli V, Lago G, Banfi S. (2011) HOCTARdb: a unique resource for microRNA target prediction. Gene, Jul 1;480(1-2):51-8. Costa V, Angelini C, DApice L, Mutarelli M, Casamassimi A, Rienzo M, Sommese L, Gallo MA, Aprile M, Esposito R, Leone L, Donizetti A, Crispi S, Sarubbi B, Calabrò R, Picardi M, Salvatore P, De Berardinis P, Napoli C, Ciccodicola A (2011) Massive-Scale RNA-Seq Analysis of Non Ribosomal Transcriptome in Human Trisomy 21. PLoS ONE 6(4):e Cutillo L, Carissimo A, Di Bernardo D (2010) Optimal length choice in top k ordered lists aggregation. GFKL – CLADAG 2010 proceedings. Vitiello C, Faraso S, Sorrentino N.C, Di Salvo G, Nusco E, Nigro G, Cutillo L, Calabrò R, Auricchio A, Nigro V (2009) Disease Rescue and Increased Lifespan in a Model of Cardiomyopathy and Muscular Dystrophy by Combined AAV Treatments. PLoS ONE, 4: Gennarino VA, Sardiello M, Avellino R, Meola N, Maselli V, Anand S, Cutillo L, Ballabio A, Banfi S (2009) MicroRNA target prediction by expression analysis of host genes. Genome Res., 19: Allocca M, Doria M, Petrillo M, Colella P, Garcia-Hoyos M, Gibbs D, Kim SR, Maguire A, Rex TS, Di Vicino U, Cutillo L, Sparrow JR, Williams DS, Bennett J, Auricchio A (2008) Serotype-dependent packaging of large genes in adeno-associated viral vectors results in effective gene delivery in mice. J Clin Invest., 118: Angelini C, Cutillo L, De Canditiis D, Mutarelli M, Pensky M (2008) BATS: a Bayesian user-friendly software for Analyzing Time Series microarray experiments. BMC Bioinformatics, 9:415. Lanza A, Cirillo N, Rossiello R, Rienzo M, Cutillo L, Casamassimi A, de Nigris F, Schiano C, Rossiello L, Femiano F, Gombos F, Napoli C (2008) Evidence of key role of Cdk2 overexpression in pemphigus vulgaris. J Biol Chem., 283:

Bioinformatics Core Team Annamaria Carissimo Diego Carrella Luisa Cutillo Veer Singh Marwah Margherita Mutarelli Gennaro Oliva Supervisor: Diego di Bernardo