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A short overview of the Bioinformatics Core

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 )

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A short overview of the Bioinformatics Core

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  1. A short overview of the Bioinformatics Core

  2. 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&DiegoC&Margherita) • Next Generation Sequencing (Margherita & Veer) • Maintainance and development of bioinformatics databases and software (Diego C&Gennaro) Veer Anna Marghe Diego C Gennaro Luisa

  3. http://bioinformatics.tigem.it

  4. 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: MANTRA2 (SQUARED) SERVICE DESK

  5. 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

  6. Statistical Analysis Please make replicates. Clustering and network analysis Timeseriesanalysis

  7. Image Analysis and processing Cell number : 522 Wt M631 -/- untreated M631 -/- phenylbutyrate treated

  8. Bioinformatics and Genomics analyses

  9. 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 • ChIPseq • Exome / Targeted seq

  10. Hardware resources: a new Computer Cluster Nodes • ProLiant DL380 G7 • CPU: 2 x Intel Xeon E5649 2.53GHz • 2 x 8 CORE, 16 Thread, 64 bit • Memory: 24GB • Disk: 146GB • 8 x ProLiant BL280c G6 • CPU: 2 x Intel Xeon X5675 3.07GHz • 2 x 8 CORE, 16 Thread, 64 bit • Memory: 48GB • Disk: 500GB Storage • 2 x Proliant DL360 G7 • CPU: 2 x Intel Xeon E5645 2.40GHz • 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

  11. 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):e43799. Epub 2012 Aug 29. • Cutillo L, Carissimo A, Figini S (2012) Network Selection: A Method for Ranked Lists Selection. PLoS ONE 7(8): e43678. doi:10.1371/journal.pone.0043678 • GennarinoVA, D’Angelo G, Dharmalingam G, Fernandez S, Russolillo G, Sanges R, Mutarelli M, Belcastro V, Ballabio A, Verde P, Sardiello M, BanfiS (2012) Identification of microRNA-regulated gene networks by expression analysis of target genes. Genome Res., 22: 1163-1172. • GennarinoVA, 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, D’Apice 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 ONE6(4):e18493. • 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. PLoSONE, 4:1932-6203. • 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.,19:481-90. • 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., 118:1955-64. • 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., 283:8736-45.

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

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