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Nicola	
  Ancona	
  
ancona@ba.issia.cnr.it	
  

	
  
	
  

	
  

Bioinformatics	
  	
  and	
  Systems	
  Biology	
  Lab	
  
Institute	
  of	
  Intelligent	
  Systems	
  for	
  Automation,	
  National	
  Research	
  Council	
  -­‐	
  CNR,	
  
Bari,	
  Italy,	
  	
  

05/12/2013	
  
Sommario	
  
—  Laboratorio	
  di	
  Bioinformatics	
  e	
  Systems	
  Biology	
  @	
  

ISSIA	
  –	
  CNR:	
  genesi	
  e	
  costituzione.	
  
—  Infrastrutture	
  di	
  calcolo.	
  
—  Progetti	
  e	
  collaborazioni.	
  
—  Competenze	
  maturate.	
  
—  Ricerca	
  corrente.	
  
—  Conclusioni.	
  

05/12/2013	
  
Laboratorio	
  di	
  Bioinforma/ca	
  e	
  Systems	
  Biology	
  
Genesi	
  
Nei	
  primi	
  anni	
  del	
  2000	
  la	
  comunità	
  scientifica	
  operante	
  
nei	
  settori	
  dell’Intelligenza	
  Artificiale	
  e	
  del	
  Pattern	
  
Recognition	
  scopre	
  che	
  l’interpretazione	
  dei	
  dati	
  
generati	
  da	
  high-­‐throughput	
  technologies	
  costituisce	
  
una	
  formidabile	
  palestra	
  per	
  sperimentare	
  metodi	
  
sviluppati	
  in	
  domini	
  applicativi	
  quali	
  la	
  visione	
  
artificiale	
  e	
  l’apprendimento	
  automatico,	
  caratterizzati	
  
da	
  p	
  >>	
  n,	
  nel	
  settore	
  della	
  scienza	
  della	
  vita.	
  

05/12/2013	
  
Laboratorio	
  di	
  Bioinforma/ca	
  e	
  Systems	
  Biology	
  
Il	
  laboratorio	
  di	
  Bioinformatica	
  e	
  Systems	
  Biology	
  
presso	
  l’ISSIA	
  –	
  CNR	
  di	
  Bari	
  è	
  un	
  laboratorio	
  
multidisciplinare	
  in	
  cui	
  biotecnologi,	
  fisici,	
  ingegneri	
  e	
  
informatici	
  affrontano	
  questioni	
  rilevanti	
  proprie	
  del	
  
settore	
  della	
  scienza	
  della	
  vita	
  con	
  approcci	
  
computazionali.	
  
	
  
Il	
  gruppo	
  è	
  principalmente	
  coinvolto	
  nell’analisi	
  ed	
  
integrazione	
  di	
  dati	
  eterogenei	
  di	
  grandi	
  dimensioni,	
  
generati	
  dalle	
  moderne	
  piattaforme	
  “omiche”,	
  per	
  
mettere	
  in	
  luce	
  marcatori	
  genetici	
  e	
  per	
  svelare	
  
meccanismi	
  molecolari	
  responsabili	
  dell’insorgenza	
  e	
  
progressione	
  di	
  patologie	
  complesse	
  e	
  multifattoriali.	
  
05/12/2013	
  
Infrastru9ura	
  HPC	
  
Il	
  Laboratorio	
  di	
  Bioinformatica	
  e	
  Systems	
  Biology	
  è	
  
dotato	
  di	
  un	
  High	
  Performance	
  Computer	
  Server,	
  
costituito	
  da	
  512	
  cores,	
  1.5	
  TB	
  di	
  RAM	
  e	
  14	
  TB	
  di	
  storage	
  
interconnesso	
  in	
  INFINIBAND.	
  In	
  particolare:	
  
—  64	
  Cluster	
  nodes:	
  2x	
  Intel	
  X5550	
  Quad	
  2.66	
  GHz	
  -­‐	
  24	
  
GB	
  RAM	
  -­‐	
  250GB	
  HD	
  -­‐	
  40	
  Gbit/s	
  Infiniband	
  -­‐	
  2x	
  1	
  
Gbit/s	
  Ethernet	
  
—  NAS:	
  2x	
  2.53	
  GHz	
  -­‐	
  24	
  GB	
  RAM	
  -­‐	
  14	
  TB	
  HD	
  -­‐	
  40	
  Gbit/s	
  
Infiniband	
  -­‐	
  2x	
  1	
  Gbit/s	
  Ethernet	
  
—  Front-­‐end:	
  2x	
  2.53	
  GHz	
  -­‐	
  24	
  GB	
  RAM	
  -­‐	
  2x	
  250GB	
  HD	
  -­‐	
  
40	
  Gbit/s	
  Infiniband	
  -­‐	
  2x	
  1	
  Gbit/s	
  Ethernet	
  
—  MATLAB	
  Parallel	
  and	
  distributed	
  HPC	
  con	
  600	
  
workers.	
  
05/12/2013	
  
Proge=	
  
—  22/02/2012	
  –	
  FIRB	
  Accordi	
  di	
  Programma	
  2011,	
  Protocollo	
  RBAP11B2SX,	
  dal	
  titolo	
  

— 

— 

— 

— 

“Strategie	
  innovative	
  ad	
  alta	
  tecnologia	
  per	
  lo	
  studio	
  del	
  carcinoma	
  renale.	
  Uso	
  degli	
  
“OMICS”	
  e	
  della	
  Biologia	
  dei	
  Sistemi	
  per	
  lo	
  sviluppo	
  dei	
  nuovi	
  biomarkers	
  
(CAROMICS)”.	
  
01/12/2011	
  –Ricerca	
  Finalizzata	
  artt	
  12	
  e	
  12	
  bis	
  D.Lgs	
  502/92	
  e	
  s.m.i.	
  Esercizio	
  
Finanziario	
  2009.	
  Progetto	
  ordinario	
  RF/2009-­‐1471624	
  dal	
  titolo	
  “Chronic	
  Rejection	
  in	
  
Kidney	
  Transplantation:	
  identification	
  of	
  new	
  diagnostics	
  targets”.	
  
17/07/2009	
  –	
  P.O.	
  Puglia	
  2007	
  –	
  2013	
  Fondo	
  Sociale	
  Europeo	
  2007IT051PO005.	
  Reti	
  di	
  
Laboratori	
  Pubblici	
  di	
  Ricerca,	
  Codice	
  Progetto	
  44,	
  dal	
  titolo	
  “Costituzione	
  di	
  una	
  rete	
  
regionale	
  per	
  gli	
  approcci	
  di	
  biologia	
  sistemica	
  nelle	
  malattie	
  umane	
  (BISIMANE)”.	
  
31/11/2006	
  –	
  POR	
  Puglia	
  2000	
  –	
  2006.	
  Progetto	
  Strategico	
  Regionale	
  PS_012	
  dal	
  titolo	
  
“Ricerca	
  e	
  sviluppo	
  di	
  nuovi	
  strumenti	
  bioinformatici	
  e	
  biotecnologici	
  per	
  l’analisi	
  del	
  
profilo	
  di	
  espressione	
  genica	
  e	
  proteica	
  del	
  cancro	
  e	
  per	
  l’identificazione	
  di	
  marcatori	
  
biologici	
  per	
  la	
  diagnosi	
  precoce	
  delle	
  neoplasie	
  colo-­‐rettali,	
  renali	
  e	
  del	
  cavo	
  orale”.	
  
2/1/2002	
  –	
  02/04/2006	
  MURST	
  -­‐	
  Cluster	
  C03	
  -­‐	
  Calcolo	
  Avanzato,	
  Infrastrutture	
  
Informatiche	
  e	
  di	
  Rete	
  per	
  i	
  Laboratori	
  di	
  Analisi	
  del	
  Gene,	
  finanziato	
  dal	
  MURST.	
  

05/12/2013	
  
Collaborazioni	
  
—  Renal,	
  Dialysis	
  and	
  Transplantation	
  Unit,	
  Department	
  of	
  Emergency	
  
— 
— 
— 
— 
— 
— 

and	
  Organ	
  Transplantation,	
  University	
  of	
  Bari,	
  Bari,	
  Italy.	
  
Laboratory	
  and	
  Division	
  of	
  Gastroenterology,	
  IRCCS	
  ‘Casa	
  Sollievo	
  
della	
  Sofferenza’	
  Hospital,	
  San	
  Giovanni	
  Rotondo	
  –	
  Foggia,	
  Italy.	
  
Hematology	
  Section,	
  Department	
  of	
  Emergency	
  and	
  Organ	
  
Transplantation,	
  University	
  of	
  Bari,	
  Bari,	
  Italy.	
  
Department	
  of	
  Medical	
  and	
  Surgical	
  Sciences,	
  University	
  of	
  Foggia,	
  
Foggia,	
  Italy.	
  
Institute	
  of	
  Sciences	
  of	
  Food	
  Production,	
  National	
  Research	
  Council,	
  
Bari,	
  Italy.	
  
Institute	
  of	
  Molecular	
  Cancer	
  Research,	
  University	
  of	
  Zurich,	
  
Winterthurerstrasse	
  190,	
  8057	
  Zurich,	
  Switzerland.	
  
Institute	
  for	
  Genome	
  Sciences	
  and	
  Policy,	
  Center	
  for	
  Interdisciplinary	
  
Engineering,	
  Medicine	
  and	
  Applied	
  Sciences,	
  Duke	
  University,	
  101	
  
Science	
  Drive,	
  Durham,	
  NC	
  27708,	
  USA.	
  
05/12/2013	
  
Competenze	
  
In	
  questi	
  anni	
  il	
  gruppo	
  ha	
  sviluppato	
  modelli	
  in	
  silico	
  
per	
  l’analisi	
  ed	
  integrazione	
  di	
  dati	
  di	
  trascrittomica,	
  
genomica,	
  proteomica	
  per	
  l’identificazione	
  di	
  segnali	
  
molecolari,	
  processi	
  biologici	
  e	
  pathways	
  deregolati	
  in	
  
patologie	
  complesse	
  e	
  per	
  mettere	
  in	
  luce	
  marcatori	
  
responsabili	
  dell’insorgenza	
  e	
  progressione	
  di	
  neoplasie:	
  
—  statistiche	
  predittive.	
  
—  statistiche	
  associative.	
  

05/12/2013	
  
Classificazione	
  su	
  base	
  molecolare	
  di	
  neoplasie	
  
BMC Bioinformatics

BioMed Central

Open Access

Research article

Regularized Least Squares Cancer Classifiers from DNA
microarray data
Nicola Ancona*1, Rosalia Maglietta1, Annarita D'Addabbo1, Sabino Liuni2
and Graziano Pesole2,3
Address: 1Istituto di Studi sui Sistemi Intelligenti per I'Automazione, CNR, Via Amendola 122/D-I, 70126 Bari, Italy, 2Istituto di Tecnologie
Biomediche-Sezione di Bari, CNR, Via Amendola 122/D, 70126 Bari Italy and 3Dipartimento Scienze Biomolecolari e Biotecnologie, Universitá
di Milano, Via Caloria 26, 20133 Milano, Italy
Email: Nicola Ancona* - ancona@ba.issia.cnr.it; Rosalia Maglietta - maglietta@ba.issia.cnr.it; Annarita D'Addabbo - daddabbo@ba.issia.cnr.it;
Sabino Liuni - sabino.liuni@ba.itb.cnr.it; Graziano Pesole - graziano.pesole@unimi.it
* Corresponding author

from Italian Society of Bioinformatics (BITS): Annual Meeting 2005
Milan, Italy, 17–19 March 2005
Published: 1 December 2005
</supplement>
<supplement> <title> <p>Italian Society of Bioinformatics (BITS): Annual Meeting 2005</p> </title> <editor>Rita Casadio, Alessandro Guffanti, Manuela Helmer-Citterich, Giancarlo Mauri, Luciano Milanesi, Graziano Pesole, Cecilia Saccone and Giorgio Valle</editor> <note>Research articles</note>

BMC Bioinformatics 2005, 6(Suppl 4):S2

Abstract

doi:10.1186/1471-2105-6-S4-S2

05/12/2013	
  

Background: The advent of the technology of DNA microarrays constitutes an epochal change
size is adequate for accurate and significant prediction estimates. The strength of this methodology, in contrast to
classical statistical methods, is that it accounts simultaneously for the effect of several genetics markers and their
possible interactions. The findings of this study show that RLS methodology is able to increase the diagnostic
accuracy of CD prediction by contemporary evaluation of a large number of gene polymorphisms. This approach
may be particularly useful in large-scale population screening programs, and when evaluating large datasets of gene
polymorphisms (i.e. chips, microarrays). Moreover, it could shed more light on possible candidate genes with a weak
genetic contribution, and for evaluating gene-gene and gene-phenotype interactions by analyzing populations with
doi: 10.1111/j.1469-1809.2007.00349.x
a reasonably small sample size.

Predizione	
  del	
  morbo	
  di	
  Crohn	
  

Regularized Least Squares Classifiers may Predict
Keywords: SingleCrohn’s Disease from Profiles of Single Nucleotide
Nucleotide Polymorphisms, Crohn’s disease, CARD15, prediction
Polymorphisms
It has recently been recognized that CD is a complex
genetic disorder where susceptibility alleles and environCrohn’s Disease (CD) is an inflammatory bowel disease
mental exposure are required for disease development.
(IBD) that can affect any part of the gastrointestinal tract,
Association studies have proposed several loci and genes
Summary
with a maximum occurrence in teenagers and young
In this paper we focus on the prediction of Crohn’s disease (CD) susceptibility with CD, with NOD2 (NOD2/CARD15)
correlated by analyzing SNP profiles for a
adults from Western number of definedIt is a life-long diseaseWe assess the correlation between genetic markers and the
countries. or suggested gene polymorphisms.
being the best validated gene
phenotype by using well-founded methods and procedures developed in the field of statistical learning theory. To(reviewed in Gaya et al.
which affects about one million people in the world, composed of 178 CD patients and 127 healthy controls.
this end, we use a sample generated by a case-control study
2006). In particular three mutations in this gene are asThe
profile of
with a chronic, relapsinggeneticleast squares each subject is composed (re- disease with a statistically significant accuracy We62% ( pthat
course and(RLS) classifiers predict Crohn’s genetic variants distributed over 11 genes. of find =
complications of 16
regularized
sociated with CD (R702W, G908R, and L1007fsinsC),
viewed in Shanahan, 0.018), significantly increasing the diagnostic accuracy by at least 10% compared to that obtained with the more
2002).
largely confirmed gene involved in CD predisposition, namely and are This also frequentthat our sample ileal disease, young ageCARD15. more demonstrates in cases of
size is adequate for accurate and significant prediction estimates. The strength of this methodology, in contrast to
of-onset, and complications (reviewed in Economou
classical statistical methods, is that it accounts simultaneously for the effect of several genetics markers and their
possible interactions. The findings of this study show that RLS methodology is able to increase theof other candidate genes based
et al. 2004). A number diagnostic
accuracy of CD prediction by contemporary evaluation
∗ Corresponding Author: Ancona Nicola, Istituto di Studi sui of a large number of gene polymorphisms. This approach
on positional or functional plausibility, have been tested,
may be particularly useful in large-scale population screening programs, and when evaluating large datasets of gene
Sistemi Intelligenti per polymorphisms (i.e. chips, microarrays). Moreover, it could shed more light on possible candidate genes with a weak
l’Automazione, CNR, Via Amendola
with interactions by analyzing populations can
genetic contribution, and for evaluating Fax: +39122/D-I, 70126 Bari, Italy. Tel: +39-080-5929428; gene-gene and gene-phenotype conflicting results that with be explained by differa reasonably small sample size.
ent genetic backgrounds and insufficient power of the
080-5929460. E-mail: ancona@ba.issia.cnr.it

Introduction

A. D’Addabbo1 , A. Latiano2 , O. Palmieri2 , R. Maglietta1 , V. Annese2 and N. Ancona1, ∗
1
Istituto di Studi sui Sistemi Intelligenti per l’Automazione, CNR, Via Amendola 122/D-I, 70126 Bari, Italy.
2
U.O. Gastroenterologia, Ospedale CSS-IRCCS, San Giovanni Rotondo, Italy.

Keywords: Single Nucleotide Polymorphisms, Crohn’s disease, CARD15, prediction
C 2007 The Authors
Introduction
Journal compilation C 2007 University College London

05/12/2013	
  

Crohn’s Disease (CD) is an inflammatory bowel disease
(IBD) that can affect any part of the gastrointestinal tract,
with a maximum occurrence in teenagers and young

Annals of Human Genetics (2007) 71,537–549

It has recently been recognized that CD is a complex
genetic disorder where susceptibility alleles and environmental exposure are required for disease development.
Association studies have proposed several loci and genes

537
Pathways	
  deregola/	
  in	
  neoplasie	
  
BIOINFORMATICS

ORIGINAL PAPER

Vol. 23 no. 16 2007, pages 2063–2072
doi:10.1093/bioinformatics/btm289

Gene expression

Statistical assessment of functional categories of genes
deregulated in pathological conditions by using microarray data
R. Maglietta1, A. Piepoli2, D. Catalano3, F. Licciulli3, M. Carella4, S. Liuni3, G. Pesole3,5,
F. Perri2 and N. Ancona1,*
1

`
Istituto di Studi sui Sistemi Intelligenti per l’Automazione, CNR, Via Amendola 122/D-I, 70126 Bari, 2Unita Operativa di
Gastroenterologia, IRCCS, ‘Casa Sollievo della Sofferenza’-Ospedale, Viale Cappuccini, 71013 San Giovanni Rotondo
(FG), 3Istituto di Tecnologie Biomediche-Sezione di Bari, CNR, Via Amendola 122/D, 70126 Bari, 4Servizio di Genetica
Medica, IRCCS, ‘Casa Sollievo della Sofferenza’-Ospedale, Viale Cappuccini, 71013 San Giovanni Rotondo (FG) and
5
`
Dipartimento di Biochimica e Biologia Molecolare - Universita di Bari, Via E. Orabona 4, 70126 Bari, Italy
Received on April 5, 2007; revised on May 14, 2007; accepted on May 21, 2007
Advance Access publication May 31, 2007
Associate Editor: Trey Ideker
ABSTRACT
Motivation: A major challenge in current biomedical research is the
identification of cellular processes deregulated in a given pathology
through the analysis of gene expression profiles. To this end,
05/12/2013	
  
predefined lists of genes, coding specific functions, are compared
with a list of genes ordered according to their values of differential

belonging to two distinct categories (e.g. diseased patients versus
healthy controls, or patients in two different stages of the same
pathology) are collected (Alon et al., 1999; Barrier et al., 2006).
Successively, suitable univariate statistics are used for finding
those genes which are differentially expressed in the experimental conditions analyzed (Golub et al., 1999; Guyon et al.,
Gene	
  set	
  enrichment	
  analysis	
  
BMC Bioinformatics

BioMed Central

Open Access

Research article

Comparative study of gene set enrichment methods
Luca Abatangelo1, Rosalia Maglietta1, Angela Distaso1, Annarita D'Addabbo1,
Teresa Maria Creanza1, Sayan Mukherjee2 and Nicola Ancona*1
Address: 1Istituto di Studi sui Sistemi Intelligenti per l'Automazione, CNR, Via Amendola 122/D-I, Bari, Italy and 2Institute for Genome Science
and Policy, Duke University, Durham, NC, USA
Email: Luca Abatangelo - abatangelo@ba.issia.cnr.it; Rosalia Maglietta - maglietta@ba.issia.cnr.it; Angela Distaso - distaso@ba.issia.cnr.it;
Annarita D'Addabbo - daddabbo@ba.issia.cnr.it; Teresa Maria Creanza - creanza@ba.issia.cnr.it; Sayan Mukherjee - sayan@stat.duke.edu;
Nicola Ancona* - ancona@ba.issia.cnr.it
* Corresponding author

Published: 2 September 2009
BMC Bioinformatics 2009, 10:275

doi:10.1186/1471-2105-10-275

Received: 11 November 2008
Accepted: 2 September 2009

This article is available from: http://www.biomedcentral.com/1471-2105/10/275
© 2009 Abatangelo et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

05/12/2013	
  

Background: The analysis of high-throughput gene expression data with respect to sets of genes
rather than individual genes has many advantages. A variety of methods have been developed for
Pathway	
  anaysis	
  in	
  colon	
  cancer	
  progression	
  
Maglietta et al. BMC Cancer 2012, 12:608
http://www.biomedcentral.com/1471-2407/12/608

RESEARCH ARTICLE

Open Access

Molecular pathways undergoing dramatic
transcriptomic changes during tumor
development in the human colon
Rosalia Maglietta1, Vania Cosma Liuzzi1, Elisa Cattaneo2, Endre Laczko3, Ada Piepoli4, Anna Panza4,
Massimo Carella5, Orazio Palumbo5, Teresa Staiano6, Federico Buffoli6, Angelo Andriulli4, Giancarlo Marra2†
and Nicola Ancona1*†
Abstract
Background: The malignant transformation of precancerous colorectal lesions involves progressive alterations at
05/12/2013	
  

both the molecular and morphologic levels, the latter consisting of increases in size and in the degree of cellular
Riproducibilità	
  dei	
  risulta/	
  
Journal of Biomedical Informatics 43 (2010) 397–406

Contents lists available at ScienceDirect

Journal of Biomedical Informatics
journal homepage: www.elsevier.com/locate/yjbin

On the reproducibility of results of pathway analysis in genome-wide
expression studies of colorectal cancers
Rosalia Maglietta a, Angela Distaso a, Ada Piepoli b, Orazio Palumbo c, Massimo Carella c,
Annarita D’Addabbo a, Sayan Mukherjee d, Nicola Ancona a,*
a

Istituto di Studi sui Sistemi Intelligenti per l’Automazione, CNR, Via Amendola 122/D-I, Bari, Italy
Unità Operativa di Gastroenterologia, IRCCS, ‘‘Casa Sollievo della Sofferenza”-Ospedale, 71013 San Giovanni Rotondo (FG), Italy
c
Servizio di Genetica Medica, IRCCS, ‘‘Casa Sollievo della Sofferenza”-Ospedale, 71013 San Giovanni Rotondo (FG), Italy
d
Institute for Genome Science and Policy, Duke University, Durham, NC, USA
b

a r t i c l e

i n f o

a b s t r a c t

Article history:
Received 26 June 2009
Available online 29 September 2009
Keywords:
Bioinformatics
Microarray data
Pathway
Colorectal cancer

One of the major problems in genomics and medicine is the identification of gene networks and pathways
deregulated in complex and polygenic diseases, like cancer. In this paper, we address the problem of
assessing the variability of results of pathways analysis identified in different and independent genome
wide expression studies, in which the same phenotypic conditions are assayed. To this end, we assessed
the deregulation of 1891 curated gene sets in four independent gene expression data sets of subjects
affected by colorectal cancer (CRC). In this comparison we used two well-founded statistical models
for evaluating deregulation of gene networks. We found that the results of pathway analysis in expression studies are highly reproducible. Our study revealed 53 pathways identified by the two methods in
all the four data sets analyzed with high statistical significance and strong biological relevance with
the pathology examined. This set of pathways associated to single markers as well as to whole biological
processes altered constitutes a signature of the disease which sheds light on the genetics bases of CRC.
Ó 2009 Elsevier Inc. All rights reserved.

05/12/2013	
  
1. Introduction

two distinct statistical methods: Statistical Analysis of Microarray
(SAM) [7] and Mixed Model Analysis (MMA) [8]. Both methods
RS-­‐SNP:	
  GWAS	
  in	
  morbo	
  di	
  Crohn	
  
D’Addabbo et al. BMC Genomics 2011, 12:166
http://www.biomedcentral.com/1471-2164/12/166

SOFTWARE

Open Access

RS-SNP: a random-set method for genome-wide
association studies
Annarita D’Addabbo1, Orazio Palmieri2, Anna Latiano2, Vito Annese2, Sayan Mukherjee3 and Nicola Ancona1*
Abstract
Background: The typical objective of Genome-wide association (GWA) studies is to identify single-nucleotide
polymorphisms (SNPs) and corresponding genes with the strongest evidence of association (the ‘most-significant
SNPs/genes’ approach). Borrowing ideas from micro-array data analysis, we propose a new method, named RS-SNP,
for detecting sets of genes enriched in SNPs moderately associated to the phenotype. RS-SNP assesses whether
the number of significant SNPs, with p-value P ≤ a, belonging to a given SNP set S is statistically significant. The
rationale of proposed method is that two kinds of null hypotheses are taken into account simultaneously. In the
first null model the genotype and the phenotype are assumed to be independent random variables and the null
distribution is the probability of the number of significant SNPs in S greater than observed by chance. The second
null model assumes the number of significant SNPs in S depends on the size of S and not on the identity of the
SNPs in S . Statistical significance is assessed using non-parametric permutation tests.
Results: We applied RS-SNP to the Crohn’s disease (CD) data set collected by the Wellcome Trust Case Control
Consortium (WTCCC) and compared the results with GENGEN, an approach recently proposed in literature. The
enrichment analysis using RS-SNP and the set of pathways contained in the MSigDB C2 CP pathway collection
highlighted 86 pathways rich in SNPs weakly associated to CD. Of these, 47 were also indicated to be significant
by GENGEN. Similar results were obtained using the MSigDB C5 pathway collection. Many of the pathways found
to be enriched by RS-SNP have a well-known connection to CD and often with inflammatory diseases.
Conclusions: The proposed method is a valuable alternative to other techniques for enrichment analysis of SNP
sets. It is well founded from a theoretical and statistical perspective. Moreover, the experimental comparison with
GENGEN highlights that it is more robust with respect to false positive findings.

Background
The objective of genome-wide association studies
05/12/2013	
  
(GWAS) is to identify genetic variants, a subset of single
nucleotide polymorphisms (SNPs), associated with the
onset and progression of complex disease phenotypes at

For polygenic diseases focusing the analysis on only the
most significant SNPs is particularly problematic as no
particular gene may have a large effect [1] but genic
regions weakly associated to the phenotype are important when susceptibility is conferred by a large number
Inferring	
  gene	
  regulatory	
  networks	
  from	
  
expression	
  profiles	
  

05/12/2013	
  
 

The	
  Gaussian	
  concentration	
  graph	
  models	
  
to	
   describe	
   interac/ons	
   between	
   genes	
   in	
   a	
   Gene	
  
Regulatory	
  Network	
  (GRN).	
  
	
  
	
  
G	
  =	
  (V,E)	
  
GRAPH	
  
VERTICES	
  
EDGES	
  

Genes	
  
Condi0onal	
  dependencies	
  

ABSENCE	
  OF	
  EDGE	
  

The	
  covariance	
  selec0on	
  models:	
  a	
  zero	
  entry	
  in	
  the	
  concentra0on	
  matrix	
  indicates	
  the	
  
condi0onal	
  independence	
  between	
  the	
  two	
  random	
  normal	
  variables.	
  
Dempster,	
  1972	
  
Cox	
  &	
  Wermuth,	
  1996.	
  
APPLICATIONS	
  OF	
  	
  L2C	
  ON	
  REAL	
  DATA	
  
The	
  isoprenoid	
  biosynthesis	
  	
  
pathways	
  in	
  A.	
  thaliana	
  

	
  
Evidence	
  of	
  two	
  modules	
  (plastidial	
  and	
  cytosolic	
  pathways)	
  
with	
  strongly	
  	
  interconnected	
  and	
  positively	
  correlated	
  genes	
  
within	
  them.	
  
	
  
Identification	
  of	
  negative	
  correlated	
  	
  nodes	
  	
  as	
  candidates	
  	
  
for	
  the	
  cross-­‐talk	
  	
  between	
  	
  the	
  two	
  pathways:	
  	
  
HMGS	
  and	
  HDS.	
  

A	
  signature	
  of	
  HRAS	
  oncogene	
  in	
  human	
  	
  
cell	
  cultures	
  (Bild	
  et	
  al.,	
  2006)	
  	
  
	
  

Identification	
  of	
  a	
  common	
  transcriptional	
  regulator	
  
of	
  the	
  direct	
  interactors	
  of	
  Ras:	
  RREB1	
  
Ruolo	
  di	
  elemen/	
  non	
  codifican/	
  nello	
  
studio	
  delle	
  patologie	
  complesse	
  
Utilizzo	
  di	
  miRNA	
  circolanti	
  come	
  potenziali	
  
biomarcatori	
  per	
  la	
  diagnostica	
  precoce	
  del	
  cancro	
  
colorettale.	
  
	
  
Studio	
  del	
  ruolo	
  dei	
  long	
  non-­‐coding	
  RNA	
  come	
  
modulatori	
  dell’attività	
  dei	
  miRNA	
  nel	
  controllo	
  
dell’insorgenza	
  di	
  neoplasie.	
  

05/12/2013	
  
Systems	
  medicine	
  
Il	
  principale	
  obiettivo	
  è	
  affrontare	
  e	
  risolvere	
  questioni	
  
clinicamente	
  rilevanti.	
  In	
  particolare,	
  si	
  occupa	
  di:	
  
	
  
—  Fornire	
  spiegazioni	
  dei	
  meccanismi	
  patologici;	
  
—  Utilizzare	
  il	
  sangue	
  come	
  una	
  finestra	
  diagnostica	
  per	
  
monitorare	
  lo	
  stato	
  di	
  salute	
  di	
  un	
  individuo;	
  
—  Catalogare	
  e	
  distinguere	
  sottotipi	
  di	
  patologie	
  
complesse	
  al	
  fine	
  di	
  a)	
  studiare	
  i	
  meccanismi	
  biologici	
  
responsabili	
  della	
  loro	
  insorgenza	
  e	
  progressione,	
  b)	
  
individuare	
  appropriati	
  farmaci;	
  
05/12/2013	
  
Systems	
  medicine	
  
—  Fornire	
  nuovi	
  approcci	
  per	
  la	
  scoperta	
  di	
  target	
  

farmaceutici;	
  
—  Generare	
  metriche	
  per	
  valutare	
  lo	
  stato	
  di	
  salute	
  di	
  un	
  
individuo.	
  
Interessante	
  il	
  consorzio	
  
Coordinating	
  Action	
  Systems	
  Medicine	
  www.casym.eu	
  
sviluppato	
  nell’ambito	
  del	
  FP7-­‐Directorate-­‐General	
  for	
  
Research	
  and	
  Innovation	
  of	
  the	
  European	
  Commission.	
  
05/12/2013	
  
Conclusioni	
  
Siamo	
  disponibili	
  a:	
  
—  nuove	
  collaborazioni	
  con	
  gruppi	
  di	
  ricerca	
  operanti	
  
sul	
  territorio;	
  
—  affrontare	
  nuove	
  problematiche;	
  
—  partecipare	
  a	
  nuove	
  iniziative	
  di	
  ricerca	
  in	
  ambito	
  
nazionale	
  ed	
  internazionale.	
  

05/12/2013	
  

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Nicola Ancona – Dall’Intelligenza Artificiale alla Systems Medicine

  • 1. Nicola  Ancona   ancona@ba.issia.cnr.it         Bioinformatics    and  Systems  Biology  Lab   Institute  of  Intelligent  Systems  for  Automation,  National  Research  Council  -­‐  CNR,   Bari,  Italy,     05/12/2013  
  • 2. Sommario   —  Laboratorio  di  Bioinformatics  e  Systems  Biology  @   ISSIA  –  CNR:  genesi  e  costituzione.   —  Infrastrutture  di  calcolo.   —  Progetti  e  collaborazioni.   —  Competenze  maturate.   —  Ricerca  corrente.   —  Conclusioni.   05/12/2013  
  • 3. Laboratorio  di  Bioinforma/ca  e  Systems  Biology   Genesi   Nei  primi  anni  del  2000  la  comunità  scientifica  operante   nei  settori  dell’Intelligenza  Artificiale  e  del  Pattern   Recognition  scopre  che  l’interpretazione  dei  dati   generati  da  high-­‐throughput  technologies  costituisce   una  formidabile  palestra  per  sperimentare  metodi   sviluppati  in  domini  applicativi  quali  la  visione   artificiale  e  l’apprendimento  automatico,  caratterizzati   da  p  >>  n,  nel  settore  della  scienza  della  vita.   05/12/2013  
  • 4. Laboratorio  di  Bioinforma/ca  e  Systems  Biology   Il  laboratorio  di  Bioinformatica  e  Systems  Biology   presso  l’ISSIA  –  CNR  di  Bari  è  un  laboratorio   multidisciplinare  in  cui  biotecnologi,  fisici,  ingegneri  e   informatici  affrontano  questioni  rilevanti  proprie  del   settore  della  scienza  della  vita  con  approcci   computazionali.     Il  gruppo  è  principalmente  coinvolto  nell’analisi  ed   integrazione  di  dati  eterogenei  di  grandi  dimensioni,   generati  dalle  moderne  piattaforme  “omiche”,  per   mettere  in  luce  marcatori  genetici  e  per  svelare   meccanismi  molecolari  responsabili  dell’insorgenza  e   progressione  di  patologie  complesse  e  multifattoriali.   05/12/2013  
  • 5. Infrastru9ura  HPC   Il  Laboratorio  di  Bioinformatica  e  Systems  Biology  è   dotato  di  un  High  Performance  Computer  Server,   costituito  da  512  cores,  1.5  TB  di  RAM  e  14  TB  di  storage   interconnesso  in  INFINIBAND.  In  particolare:   —  64  Cluster  nodes:  2x  Intel  X5550  Quad  2.66  GHz  -­‐  24   GB  RAM  -­‐  250GB  HD  -­‐  40  Gbit/s  Infiniband  -­‐  2x  1   Gbit/s  Ethernet   —  NAS:  2x  2.53  GHz  -­‐  24  GB  RAM  -­‐  14  TB  HD  -­‐  40  Gbit/s   Infiniband  -­‐  2x  1  Gbit/s  Ethernet   —  Front-­‐end:  2x  2.53  GHz  -­‐  24  GB  RAM  -­‐  2x  250GB  HD  -­‐   40  Gbit/s  Infiniband  -­‐  2x  1  Gbit/s  Ethernet   —  MATLAB  Parallel  and  distributed  HPC  con  600   workers.   05/12/2013  
  • 6. Proge=   —  22/02/2012  –  FIRB  Accordi  di  Programma  2011,  Protocollo  RBAP11B2SX,  dal  titolo   —  —  —  —  “Strategie  innovative  ad  alta  tecnologia  per  lo  studio  del  carcinoma  renale.  Uso  degli   “OMICS”  e  della  Biologia  dei  Sistemi  per  lo  sviluppo  dei  nuovi  biomarkers   (CAROMICS)”.   01/12/2011  –Ricerca  Finalizzata  artt  12  e  12  bis  D.Lgs  502/92  e  s.m.i.  Esercizio   Finanziario  2009.  Progetto  ordinario  RF/2009-­‐1471624  dal  titolo  “Chronic  Rejection  in   Kidney  Transplantation:  identification  of  new  diagnostics  targets”.   17/07/2009  –  P.O.  Puglia  2007  –  2013  Fondo  Sociale  Europeo  2007IT051PO005.  Reti  di   Laboratori  Pubblici  di  Ricerca,  Codice  Progetto  44,  dal  titolo  “Costituzione  di  una  rete   regionale  per  gli  approcci  di  biologia  sistemica  nelle  malattie  umane  (BISIMANE)”.   31/11/2006  –  POR  Puglia  2000  –  2006.  Progetto  Strategico  Regionale  PS_012  dal  titolo   “Ricerca  e  sviluppo  di  nuovi  strumenti  bioinformatici  e  biotecnologici  per  l’analisi  del   profilo  di  espressione  genica  e  proteica  del  cancro  e  per  l’identificazione  di  marcatori   biologici  per  la  diagnosi  precoce  delle  neoplasie  colo-­‐rettali,  renali  e  del  cavo  orale”.   2/1/2002  –  02/04/2006  MURST  -­‐  Cluster  C03  -­‐  Calcolo  Avanzato,  Infrastrutture   Informatiche  e  di  Rete  per  i  Laboratori  di  Analisi  del  Gene,  finanziato  dal  MURST.   05/12/2013  
  • 7. Collaborazioni   —  Renal,  Dialysis  and  Transplantation  Unit,  Department  of  Emergency   —  —  —  —  —  —  and  Organ  Transplantation,  University  of  Bari,  Bari,  Italy.   Laboratory  and  Division  of  Gastroenterology,  IRCCS  ‘Casa  Sollievo   della  Sofferenza’  Hospital,  San  Giovanni  Rotondo  –  Foggia,  Italy.   Hematology  Section,  Department  of  Emergency  and  Organ   Transplantation,  University  of  Bari,  Bari,  Italy.   Department  of  Medical  and  Surgical  Sciences,  University  of  Foggia,   Foggia,  Italy.   Institute  of  Sciences  of  Food  Production,  National  Research  Council,   Bari,  Italy.   Institute  of  Molecular  Cancer  Research,  University  of  Zurich,   Winterthurerstrasse  190,  8057  Zurich,  Switzerland.   Institute  for  Genome  Sciences  and  Policy,  Center  for  Interdisciplinary   Engineering,  Medicine  and  Applied  Sciences,  Duke  University,  101   Science  Drive,  Durham,  NC  27708,  USA.   05/12/2013  
  • 8. Competenze   In  questi  anni  il  gruppo  ha  sviluppato  modelli  in  silico   per  l’analisi  ed  integrazione  di  dati  di  trascrittomica,   genomica,  proteomica  per  l’identificazione  di  segnali   molecolari,  processi  biologici  e  pathways  deregolati  in   patologie  complesse  e  per  mettere  in  luce  marcatori   responsabili  dell’insorgenza  e  progressione  di  neoplasie:   —  statistiche  predittive.   —  statistiche  associative.   05/12/2013  
  • 9. Classificazione  su  base  molecolare  di  neoplasie   BMC Bioinformatics BioMed Central Open Access Research article Regularized Least Squares Cancer Classifiers from DNA microarray data Nicola Ancona*1, Rosalia Maglietta1, Annarita D'Addabbo1, Sabino Liuni2 and Graziano Pesole2,3 Address: 1Istituto di Studi sui Sistemi Intelligenti per I'Automazione, CNR, Via Amendola 122/D-I, 70126 Bari, Italy, 2Istituto di Tecnologie Biomediche-Sezione di Bari, CNR, Via Amendola 122/D, 70126 Bari Italy and 3Dipartimento Scienze Biomolecolari e Biotecnologie, Universitá di Milano, Via Caloria 26, 20133 Milano, Italy Email: Nicola Ancona* - ancona@ba.issia.cnr.it; Rosalia Maglietta - maglietta@ba.issia.cnr.it; Annarita D'Addabbo - daddabbo@ba.issia.cnr.it; Sabino Liuni - sabino.liuni@ba.itb.cnr.it; Graziano Pesole - graziano.pesole@unimi.it * Corresponding author from Italian Society of Bioinformatics (BITS): Annual Meeting 2005 Milan, Italy, 17–19 March 2005 Published: 1 December 2005 </supplement> <supplement> <title> <p>Italian Society of Bioinformatics (BITS): Annual Meeting 2005</p> </title> <editor>Rita Casadio, Alessandro Guffanti, Manuela Helmer-Citterich, Giancarlo Mauri, Luciano Milanesi, Graziano Pesole, Cecilia Saccone and Giorgio Valle</editor> <note>Research articles</note> BMC Bioinformatics 2005, 6(Suppl 4):S2 Abstract doi:10.1186/1471-2105-6-S4-S2 05/12/2013   Background: The advent of the technology of DNA microarrays constitutes an epochal change
  • 10. size is adequate for accurate and significant prediction estimates. The strength of this methodology, in contrast to classical statistical methods, is that it accounts simultaneously for the effect of several genetics markers and their possible interactions. The findings of this study show that RLS methodology is able to increase the diagnostic accuracy of CD prediction by contemporary evaluation of a large number of gene polymorphisms. This approach may be particularly useful in large-scale population screening programs, and when evaluating large datasets of gene polymorphisms (i.e. chips, microarrays). Moreover, it could shed more light on possible candidate genes with a weak genetic contribution, and for evaluating gene-gene and gene-phenotype interactions by analyzing populations with doi: 10.1111/j.1469-1809.2007.00349.x a reasonably small sample size. Predizione  del  morbo  di  Crohn   Regularized Least Squares Classifiers may Predict Keywords: SingleCrohn’s Disease from Profiles of Single Nucleotide Nucleotide Polymorphisms, Crohn’s disease, CARD15, prediction Polymorphisms It has recently been recognized that CD is a complex genetic disorder where susceptibility alleles and environCrohn’s Disease (CD) is an inflammatory bowel disease mental exposure are required for disease development. (IBD) that can affect any part of the gastrointestinal tract, Association studies have proposed several loci and genes Summary with a maximum occurrence in teenagers and young In this paper we focus on the prediction of Crohn’s disease (CD) susceptibility with CD, with NOD2 (NOD2/CARD15) correlated by analyzing SNP profiles for a adults from Western number of definedIt is a life-long diseaseWe assess the correlation between genetic markers and the countries. or suggested gene polymorphisms. being the best validated gene phenotype by using well-founded methods and procedures developed in the field of statistical learning theory. To(reviewed in Gaya et al. which affects about one million people in the world, composed of 178 CD patients and 127 healthy controls. this end, we use a sample generated by a case-control study 2006). In particular three mutations in this gene are asThe profile of with a chronic, relapsinggeneticleast squares each subject is composed (re- disease with a statistically significant accuracy We62% ( pthat course and(RLS) classifiers predict Crohn’s genetic variants distributed over 11 genes. of find = complications of 16 regularized sociated with CD (R702W, G908R, and L1007fsinsC), viewed in Shanahan, 0.018), significantly increasing the diagnostic accuracy by at least 10% compared to that obtained with the more 2002). largely confirmed gene involved in CD predisposition, namely and are This also frequentthat our sample ileal disease, young ageCARD15. more demonstrates in cases of size is adequate for accurate and significant prediction estimates. The strength of this methodology, in contrast to of-onset, and complications (reviewed in Economou classical statistical methods, is that it accounts simultaneously for the effect of several genetics markers and their possible interactions. The findings of this study show that RLS methodology is able to increase theof other candidate genes based et al. 2004). A number diagnostic accuracy of CD prediction by contemporary evaluation ∗ Corresponding Author: Ancona Nicola, Istituto di Studi sui of a large number of gene polymorphisms. This approach on positional or functional plausibility, have been tested, may be particularly useful in large-scale population screening programs, and when evaluating large datasets of gene Sistemi Intelligenti per polymorphisms (i.e. chips, microarrays). Moreover, it could shed more light on possible candidate genes with a weak l’Automazione, CNR, Via Amendola with interactions by analyzing populations can genetic contribution, and for evaluating Fax: +39122/D-I, 70126 Bari, Italy. Tel: +39-080-5929428; gene-gene and gene-phenotype conflicting results that with be explained by differa reasonably small sample size. ent genetic backgrounds and insufficient power of the 080-5929460. E-mail: ancona@ba.issia.cnr.it Introduction A. D’Addabbo1 , A. Latiano2 , O. Palmieri2 , R. Maglietta1 , V. Annese2 and N. Ancona1, ∗ 1 Istituto di Studi sui Sistemi Intelligenti per l’Automazione, CNR, Via Amendola 122/D-I, 70126 Bari, Italy. 2 U.O. Gastroenterologia, Ospedale CSS-IRCCS, San Giovanni Rotondo, Italy. Keywords: Single Nucleotide Polymorphisms, Crohn’s disease, CARD15, prediction C 2007 The Authors Introduction Journal compilation C 2007 University College London 05/12/2013   Crohn’s Disease (CD) is an inflammatory bowel disease (IBD) that can affect any part of the gastrointestinal tract, with a maximum occurrence in teenagers and young Annals of Human Genetics (2007) 71,537–549 It has recently been recognized that CD is a complex genetic disorder where susceptibility alleles and environmental exposure are required for disease development. Association studies have proposed several loci and genes 537
  • 11. Pathways  deregola/  in  neoplasie   BIOINFORMATICS ORIGINAL PAPER Vol. 23 no. 16 2007, pages 2063–2072 doi:10.1093/bioinformatics/btm289 Gene expression Statistical assessment of functional categories of genes deregulated in pathological conditions by using microarray data R. Maglietta1, A. Piepoli2, D. Catalano3, F. Licciulli3, M. Carella4, S. Liuni3, G. Pesole3,5, F. Perri2 and N. Ancona1,* 1 ` Istituto di Studi sui Sistemi Intelligenti per l’Automazione, CNR, Via Amendola 122/D-I, 70126 Bari, 2Unita Operativa di Gastroenterologia, IRCCS, ‘Casa Sollievo della Sofferenza’-Ospedale, Viale Cappuccini, 71013 San Giovanni Rotondo (FG), 3Istituto di Tecnologie Biomediche-Sezione di Bari, CNR, Via Amendola 122/D, 70126 Bari, 4Servizio di Genetica Medica, IRCCS, ‘Casa Sollievo della Sofferenza’-Ospedale, Viale Cappuccini, 71013 San Giovanni Rotondo (FG) and 5 ` Dipartimento di Biochimica e Biologia Molecolare - Universita di Bari, Via E. Orabona 4, 70126 Bari, Italy Received on April 5, 2007; revised on May 14, 2007; accepted on May 21, 2007 Advance Access publication May 31, 2007 Associate Editor: Trey Ideker ABSTRACT Motivation: A major challenge in current biomedical research is the identification of cellular processes deregulated in a given pathology through the analysis of gene expression profiles. To this end, 05/12/2013   predefined lists of genes, coding specific functions, are compared with a list of genes ordered according to their values of differential belonging to two distinct categories (e.g. diseased patients versus healthy controls, or patients in two different stages of the same pathology) are collected (Alon et al., 1999; Barrier et al., 2006). Successively, suitable univariate statistics are used for finding those genes which are differentially expressed in the experimental conditions analyzed (Golub et al., 1999; Guyon et al.,
  • 12. Gene  set  enrichment  analysis   BMC Bioinformatics BioMed Central Open Access Research article Comparative study of gene set enrichment methods Luca Abatangelo1, Rosalia Maglietta1, Angela Distaso1, Annarita D'Addabbo1, Teresa Maria Creanza1, Sayan Mukherjee2 and Nicola Ancona*1 Address: 1Istituto di Studi sui Sistemi Intelligenti per l'Automazione, CNR, Via Amendola 122/D-I, Bari, Italy and 2Institute for Genome Science and Policy, Duke University, Durham, NC, USA Email: Luca Abatangelo - abatangelo@ba.issia.cnr.it; Rosalia Maglietta - maglietta@ba.issia.cnr.it; Angela Distaso - distaso@ba.issia.cnr.it; Annarita D'Addabbo - daddabbo@ba.issia.cnr.it; Teresa Maria Creanza - creanza@ba.issia.cnr.it; Sayan Mukherjee - sayan@stat.duke.edu; Nicola Ancona* - ancona@ba.issia.cnr.it * Corresponding author Published: 2 September 2009 BMC Bioinformatics 2009, 10:275 doi:10.1186/1471-2105-10-275 Received: 11 November 2008 Accepted: 2 September 2009 This article is available from: http://www.biomedcentral.com/1471-2105/10/275 © 2009 Abatangelo et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract 05/12/2013   Background: The analysis of high-throughput gene expression data with respect to sets of genes rather than individual genes has many advantages. A variety of methods have been developed for
  • 13. Pathway  anaysis  in  colon  cancer  progression   Maglietta et al. BMC Cancer 2012, 12:608 http://www.biomedcentral.com/1471-2407/12/608 RESEARCH ARTICLE Open Access Molecular pathways undergoing dramatic transcriptomic changes during tumor development in the human colon Rosalia Maglietta1, Vania Cosma Liuzzi1, Elisa Cattaneo2, Endre Laczko3, Ada Piepoli4, Anna Panza4, Massimo Carella5, Orazio Palumbo5, Teresa Staiano6, Federico Buffoli6, Angelo Andriulli4, Giancarlo Marra2† and Nicola Ancona1*† Abstract Background: The malignant transformation of precancerous colorectal lesions involves progressive alterations at 05/12/2013   both the molecular and morphologic levels, the latter consisting of increases in size and in the degree of cellular
  • 14. Riproducibilità  dei  risulta/   Journal of Biomedical Informatics 43 (2010) 397–406 Contents lists available at ScienceDirect Journal of Biomedical Informatics journal homepage: www.elsevier.com/locate/yjbin On the reproducibility of results of pathway analysis in genome-wide expression studies of colorectal cancers Rosalia Maglietta a, Angela Distaso a, Ada Piepoli b, Orazio Palumbo c, Massimo Carella c, Annarita D’Addabbo a, Sayan Mukherjee d, Nicola Ancona a,* a Istituto di Studi sui Sistemi Intelligenti per l’Automazione, CNR, Via Amendola 122/D-I, Bari, Italy Unità Operativa di Gastroenterologia, IRCCS, ‘‘Casa Sollievo della Sofferenza”-Ospedale, 71013 San Giovanni Rotondo (FG), Italy c Servizio di Genetica Medica, IRCCS, ‘‘Casa Sollievo della Sofferenza”-Ospedale, 71013 San Giovanni Rotondo (FG), Italy d Institute for Genome Science and Policy, Duke University, Durham, NC, USA b a r t i c l e i n f o a b s t r a c t Article history: Received 26 June 2009 Available online 29 September 2009 Keywords: Bioinformatics Microarray data Pathway Colorectal cancer One of the major problems in genomics and medicine is the identification of gene networks and pathways deregulated in complex and polygenic diseases, like cancer. In this paper, we address the problem of assessing the variability of results of pathways analysis identified in different and independent genome wide expression studies, in which the same phenotypic conditions are assayed. To this end, we assessed the deregulation of 1891 curated gene sets in four independent gene expression data sets of subjects affected by colorectal cancer (CRC). In this comparison we used two well-founded statistical models for evaluating deregulation of gene networks. We found that the results of pathway analysis in expression studies are highly reproducible. Our study revealed 53 pathways identified by the two methods in all the four data sets analyzed with high statistical significance and strong biological relevance with the pathology examined. This set of pathways associated to single markers as well as to whole biological processes altered constitutes a signature of the disease which sheds light on the genetics bases of CRC. Ó 2009 Elsevier Inc. All rights reserved. 05/12/2013   1. Introduction two distinct statistical methods: Statistical Analysis of Microarray (SAM) [7] and Mixed Model Analysis (MMA) [8]. Both methods
  • 15. RS-­‐SNP:  GWAS  in  morbo  di  Crohn   D’Addabbo et al. BMC Genomics 2011, 12:166 http://www.biomedcentral.com/1471-2164/12/166 SOFTWARE Open Access RS-SNP: a random-set method for genome-wide association studies Annarita D’Addabbo1, Orazio Palmieri2, Anna Latiano2, Vito Annese2, Sayan Mukherjee3 and Nicola Ancona1* Abstract Background: The typical objective of Genome-wide association (GWA) studies is to identify single-nucleotide polymorphisms (SNPs) and corresponding genes with the strongest evidence of association (the ‘most-significant SNPs/genes’ approach). Borrowing ideas from micro-array data analysis, we propose a new method, named RS-SNP, for detecting sets of genes enriched in SNPs moderately associated to the phenotype. RS-SNP assesses whether the number of significant SNPs, with p-value P ≤ a, belonging to a given SNP set S is statistically significant. The rationale of proposed method is that two kinds of null hypotheses are taken into account simultaneously. In the first null model the genotype and the phenotype are assumed to be independent random variables and the null distribution is the probability of the number of significant SNPs in S greater than observed by chance. The second null model assumes the number of significant SNPs in S depends on the size of S and not on the identity of the SNPs in S . Statistical significance is assessed using non-parametric permutation tests. Results: We applied RS-SNP to the Crohn’s disease (CD) data set collected by the Wellcome Trust Case Control Consortium (WTCCC) and compared the results with GENGEN, an approach recently proposed in literature. The enrichment analysis using RS-SNP and the set of pathways contained in the MSigDB C2 CP pathway collection highlighted 86 pathways rich in SNPs weakly associated to CD. Of these, 47 were also indicated to be significant by GENGEN. Similar results were obtained using the MSigDB C5 pathway collection. Many of the pathways found to be enriched by RS-SNP have a well-known connection to CD and often with inflammatory diseases. Conclusions: The proposed method is a valuable alternative to other techniques for enrichment analysis of SNP sets. It is well founded from a theoretical and statistical perspective. Moreover, the experimental comparison with GENGEN highlights that it is more robust with respect to false positive findings. Background The objective of genome-wide association studies 05/12/2013   (GWAS) is to identify genetic variants, a subset of single nucleotide polymorphisms (SNPs), associated with the onset and progression of complex disease phenotypes at For polygenic diseases focusing the analysis on only the most significant SNPs is particularly problematic as no particular gene may have a large effect [1] but genic regions weakly associated to the phenotype are important when susceptibility is conferred by a large number
  • 16. Inferring  gene  regulatory  networks  from   expression  profiles   05/12/2013  
  • 17.   The  Gaussian  concentration  graph  models   to   describe   interac/ons   between   genes   in   a   Gene   Regulatory  Network  (GRN).       G  =  (V,E)   GRAPH   VERTICES   EDGES   Genes   Condi0onal  dependencies   ABSENCE  OF  EDGE   The  covariance  selec0on  models:  a  zero  entry  in  the  concentra0on  matrix  indicates  the   condi0onal  independence  between  the  two  random  normal  variables.   Dempster,  1972   Cox  &  Wermuth,  1996.  
  • 18. APPLICATIONS  OF    L2C  ON  REAL  DATA   The  isoprenoid  biosynthesis     pathways  in  A.  thaliana     Evidence  of  two  modules  (plastidial  and  cytosolic  pathways)   with  strongly    interconnected  and  positively  correlated  genes   within  them.     Identification  of  negative  correlated    nodes    as  candidates     for  the  cross-­‐talk    between    the  two  pathways:     HMGS  and  HDS.   A  signature  of  HRAS  oncogene  in  human     cell  cultures  (Bild  et  al.,  2006)       Identification  of  a  common  transcriptional  regulator   of  the  direct  interactors  of  Ras:  RREB1  
  • 19. Ruolo  di  elemen/  non  codifican/  nello   studio  delle  patologie  complesse   Utilizzo  di  miRNA  circolanti  come  potenziali   biomarcatori  per  la  diagnostica  precoce  del  cancro   colorettale.     Studio  del  ruolo  dei  long  non-­‐coding  RNA  come   modulatori  dell’attività  dei  miRNA  nel  controllo   dell’insorgenza  di  neoplasie.   05/12/2013  
  • 20. Systems  medicine   Il  principale  obiettivo  è  affrontare  e  risolvere  questioni   clinicamente  rilevanti.  In  particolare,  si  occupa  di:     —  Fornire  spiegazioni  dei  meccanismi  patologici;   —  Utilizzare  il  sangue  come  una  finestra  diagnostica  per   monitorare  lo  stato  di  salute  di  un  individuo;   —  Catalogare  e  distinguere  sottotipi  di  patologie   complesse  al  fine  di  a)  studiare  i  meccanismi  biologici   responsabili  della  loro  insorgenza  e  progressione,  b)   individuare  appropriati  farmaci;   05/12/2013  
  • 21. Systems  medicine   —  Fornire  nuovi  approcci  per  la  scoperta  di  target   farmaceutici;   —  Generare  metriche  per  valutare  lo  stato  di  salute  di  un   individuo.   Interessante  il  consorzio   Coordinating  Action  Systems  Medicine  www.casym.eu   sviluppato  nell’ambito  del  FP7-­‐Directorate-­‐General  for   Research  and  Innovation  of  the  European  Commission.   05/12/2013  
  • 22. Conclusioni   Siamo  disponibili  a:   —  nuove  collaborazioni  con  gruppi  di  ricerca  operanti   sul  territorio;   —  affrontare  nuove  problematiche;   —  partecipare  a  nuove  iniziative  di  ricerca  in  ambito   nazionale  ed  internazionale.   05/12/2013