“The role of Bioinformatics in basic and applied research”

Carla Oliveira Expression Regulation in Cancer Group, IPATIMUP Medical Faculty of Porto University Porto, Portugal E-mail: carlaol@ipatimup.pt CEO Bioinf2Bio (www.frombioinformatics2biology.com)

Sessão de Apresentação do Mestrado em Bioinformática e Biologia Computacional Faculdade de Ciências da Universidade de Lisboa Lisbon, Portugal May 6th, 2014 Invitation by: Francisco Couto

Genomics Analysis of human genes Epigenomics DNA and histone-protein modifications Transcriptomics RNA expression Proteomics Protein expression and modifications Metabolomics Low molecular weight substances Toxicomics Toxic substance Cellomics Characteristics and functions of living cells

Ex: ArrayCGH, targeted DNAseq, ExomeSeq, WGS

Ex: miRNA microarray & RNAseq

Bioinformatics biological data storing, retrieving, organizing and analysis

What are OMICs?

Ex: MethylSeq, ChipSeq

Research question > Methodology > Platforms > Analysis

Cell/tissue

RNA

Protein

Metabolites

DNA

DA

TA G

ENER

ATI

ON

(Tb

)

DA

TA

INTE

GR

ATI

ON

Interpretation

VA

LID

ATI

ON

Integrative Approach

Methodology

Metabolomics

Proteomics

Transcriptomics

Genomics

Bioinformatics (Statistics, Pathway Analysis Tools...)

From questions to knowledge

…this knowledge was expected to allow accurate classification

of phenotypes, early detection of disease, discrimination

among disease sub-types, prediction of clinical outcomes,

characterization of disease progression, and personalize

therapeutic approaches. But…

“For every complex problem there is an answer that is clear, simple, and wrong.”

H. L. Mencken

From a health perspective...

How to use OMICs information to address and study specific genes and diseases?

1st Generate a relevant and appropriate scientific question or clinical problem

2nd Study and select the best OMICs strategy

3rd Find the right partners (omics and bioinformatics analysis)

4th Set up reliable bioinformatics analysis and wet lab validation

5th Go back to your original scientific question or clinical problem and fight against fascination

OMICs in practice

Technology: Data Mining and Data Analysis

Knowledge

Data Data Data

Data

Data

Data

Data Data

Question

+

Selection

Analysis

NGS & MICROARRAY DATA ANALYSIS

Bioinf2Bio

miRNA

Microarrays

Expression

Microarrays

Tiling

Microarrays

RNAseq

NGS

Methylseq

NGS

DNAseq

NGS

Cadherin intronic transcription

during mouse embryogenesis (in preparation)

Transcriptome signatures

during TGF-β-induced

EMT and MET (in preparation)

Novel and rare CDH1

intronic variants: relevance

for HDGC (in preparation)

Data mining

ERiC

Bioinf2Bio

techniques

Mistranslation

in/and Cancer (under analysis)

Gastric Cancer Genome &

Transcriptome alterations (sequencing ongoing @ BGI)

NGS & MICROARRAY DATA ANALYSIS

Bioinf2Bio www.frombioinformatics2biology.com

Silver Analysis

Gold Analysis

Platinum Analysis

Bronze Analysis