BioInformaticsAnalysis of Cancer Pathways

Using Spotfire

Michael Moorhouse, PhD.

Peter van der Spek, PhD.

Erasmus Medical Center, Rotterdam,Department of Bioinformatics

with material supplied by:

Making Decisions in a Clinical Environment

Forensics Diagnostic Classification& Clinical Trials

Genome Research & Epidemiology

Erasmus Medical CenterRotterdam, The Netherlands

New opportunities for disease

management

•Classifying biological subgroups

•Identifying novel targets for therapy

•Companion diagnostics for directed therapy

•Assessing and managing risk

Disease Management - the future

Morphological Differences are Characterized by Different

Gene Signatures

Dataset: Pomeroy et al. Nature 415, 436-442 (2002)

M93119 INSM1 Insulinoma-associated 1M30448 Casein kinase II beta subunit S82240 RhoED80004 KIAA0182 geneD76435 Zic proteinX83543 APXL Apical proteinX62534 HMG2 High-mobility group M96739 NSCL-1 U26726 11 beta-hydroxysteroid dehydrogenase type IIHG311-HT311 Ribosomal Protein L30X86693 High endothelial venuleM93426 PTPRZ Protein tyrosine phosphataseU48705 DDR geneX86809 Major astrocytic phosphoprotein PEA-15U45955 Neuronal membrane glycoprotein M6bU53204 Plectin (PLEC1) X13916 LDL-receptor related proteinD87258 Serin protease with IGF-binding motifZ31560 SOX2 SRY (sex determining region Y)-box 2M32886 SRI SorcinJ04164 RPS3 Ribosomal protein S3M12125 Skeletal beta-tropomyosinD29958 KIAA0116 geneD17400 PTS 6-pyruvoyltetrahydropterin synthaseD83174 CBP1 Collagen-binding protein 1D83735 Adult heart mRNA for neutral calponinD84454 UDP-galactose translocatorL38969 Thrombospondin 3 (THBS3) U12465 RPS11 Ribosomal protein S11D80005 KIAA0183 geneD87463 KIAA0273 geneU90902 Clone 23612 mRNA sequenceD26070 Type 1 inositol 1,4,5-trisphosphate receptorX63578 ParvalbuminZ15108 PRKCZ Protein kinase C, zetaL35592 Germline mRNA sequenceL10338 SCN1B Sodium channelL33243 PKD1 Polycystic kidney disease protein 1L77864 Stat-like protein (Fe65) J04469 Mitochondrial creatine kinase (CKMT) M80397 POLD1 Polymerase (DNA directed), delta 1X14830 CHRNB1 Cholinergic receptor, nicotinic, beta polypeptide 1U97018 Echinoderm microtubule-associated protein homolog HuEMAP HG4178-HT4448 Af-17K02882 IGHD gene X52228 MUC1 Mucin 1, transmembraneU22314 Neural-restrictive silencer factorD29675 Inducible nitric oxide synthase geneS82471 SSX3 M54951 Human atrial natriuretic factor gene

AT/RT CNS

Ncer

MDMGlio

PNET

AT/RT Renal/Extrarenal

MD Mglio Rhab Ncer PNET

-3 -2 -1 0 +1 +2 +3standard deviation from mean

Brain Tumour Classification

Dataset: Pomeroy et al. Nature 415, 436-442 (2002)

Classic DesmoplasticHG1980-HT2023 Tubulin, Beta 2U63842 NeuroD3 geneX67951 PAGA Proliferation-associated gene A X64330 ATP-citrate lyaseJ03241 TGFB3 Transforming growth factor, beta 3U44839 Putative ubiquitin C-terminal hydrolase (UHX1) Z27113 H.Sapiens gene for RNA polymerase II subunit X12447 ALDOA Aldolase AU73328 DLX7 Distal-less homeobox 7U59913 SMAD5 Z75190 Apolipoprotein E receptor 2X15183 Human mRNA for 90-kDa heat-shock proteinU61263 Acetolactate synthase homolog L07515 Human heterochromatin protein homologue (HP1)M34677 Human nested gene protein gene (coag. factorVIII)U40391 Serotonin N-acetyltransferase geneD16611 CPO Coproporphyrinogen oxidase L37127 RNA polymerase IIU33839 No description available X81817 BAP31X51804 Human PMI gene for a putative receptor proteinY09305 Protein kinase, Dyrk4X14885 Transforming growth factor-beta 3 (TGF-beta 3) X57398 NME1 Non-metastatic cells 1 (NM23A) X02152 LDHA Lactate dehydrogenase AX64364 BSG BasiginU04806 FLT3/FLK2 ligand mRNAU52191 SMCY (H-Y) mRNAM35296 Tyrosine kinase arg geneD50840 Ceramide glucosyltransferaseS69189 Peroxisomal acyl-coenzyme A oxidaseL03785 MYL5 Myosin, light polypeptide 5M82919 GABRB3 Gamma-aminobutyric acid (GABA) A receptor, beta 3U65092 Melanocyte-specific gene 1 (msg1) S49592 Transcription factor E2F like protein D79994 KIAA0172 geneX95586 PSMB5 Proteasome subunit, beta type, 5U79299 Human neuronal olfactomedin-related ER localized proteinX71973 GPX4 Phospholipid hydroperoxide glutathione peroxidaseU31342 Human nucleobindin geneU48437 Amyloid precursor-like protein 1 D86957 KIAA0202 geneHG2279-HT2375 Triosephosphate IsomeraseZ19585 THBS4 Thrombospondin 4M16405 Human m4 muscarinic acetylcholine receptor geneU32315 Syntaxin 3 U11701 LIM-homeobox domain protein (hLH-2) Y11251 Novel member of serine-arginine domain protein, SRrp129U68018 Mad protein homolog (hMAD-2) M81181 ATP1B2 ATPase, Na+/K+ transporting, beta 2 polypeptideU58334 Bcl2, p53 binding protein Bbp/53BP2 L38490 ARF4L ADP-ribosylation factor 4-like

HG3543-HT3739 Insulin-Like Growth Factor 2X53331 MGP Matrix protein glaX65724 NDP Norrie disease proteinD14530 40S Ribosomal protein S23Y00757 SGNE1 Secretory granule, neuroendocrine protein 1 U25789 Ribosomal protein L21 L27560 Insulin-like growth factor binding protein 5 (IGFBP5) X83543 APXL Apical protein (Xenopus laevis-like)X52966 RPL35A Ribosomal protein L35aL06797 Human (clone L5) orphan G protein-coupled receptorM14745 BCL2 B HG3431-HT3616 DecorinD79205 Ribosomal protein L39D82345 NB thymosin betaD38549 KIAA0068 geneU14972 Ribosomal protein S10X59841 PBX3J03242 IGF2 Insulin-like growth factor 2 (somatomedin A)HG3214-HT3391 Metallopanstimulin 1X06617 RPS11 Ribosomal protein S11J02611 APOD Apolipoprotein DX16064 Human mRNA for translationally controlled tumor proteinZ74616 COL1A2 Collagen, type I, alpha-2L40386 DP2 (Humdp2)X04741 Human mRNA for protein gene product (PGP)M55210 LAMC1 Laminin, gamma 1 M96739 NSCL-1 U73304 CB1 cannabinoid receptor (CNR1) geneM65292 HFL1 H factor (complement)-like 1HG311-HT311 Ribosomal Protein L30M83233 TCF12 Transcription factor 12 U07919 ALDH6 Aldehyde dehydrogenase 6 X57959 RPL17 Ribosomal protein L7J04080 C1S Complement component 1, s subcomponentX76029 Neuromedin UU14973 40S ribosomal protein S29U24576 Breast tumor autoantigen L41066 NF-AT3X60489 Elongation factor-1-betaM62843 Paraneoplastic encephalomyelitis antigen HUDHG662-HT662 Epstein-Barr Virus Small Rna-Associated ProteinHG613-HT613 Ribosomal Protein S12L42379 Quiescin (Q6) mRNAM13241 N-MYC U12404 HSPB1 Heat shock 27kD protein 1M55998 Alpha-1 collagen type I geneS82240 RhoEU78027 L44L gene X06700 COL3A1 Alpha-1 type 3 collagenD13413 Tumor-associated 120 kDa nuclear protein p120M74719 SEF2-1A protein (SEF2-1A) M93119 INSM1 Insulinoma-associated 1 M92287 CCND3 Cyclin D3HG33-HT33 Ribosomal Protein S4

Classic Desmoplastic

IGF2

N-MYC

PTCH

GLI

-3 -2 -1 0 +1 +2 +3standard deviation from mean

Pathway Mapping Requires

GO Classification

GO-Viewer in Decisionsite portal

GO Classification I• Molecular function is what something does. It is a capability that a

physical gene product (or gene product group) carries as a potential. It describes only what it can do without specifying where or when this usage actually occurs. Examples of broad functional terms are "enzyme," "transporter," or "ligand." Examples of narrower functional terms are "adenylate cyclase," or "Toll receptor ligand."

• [There is a potential for semantic confusion between a gene product and its molecular function, because very often these are described in exactly the same words. For example, "alcohol dehydrogenase" can describe what you can put in an Eppendorf tube (gene product) or it can describe the function of this stuff. There is, however, a formal difference -- a "product" has a (potentially) many-to-many relationship with a "molecular function."

• An example: there are many gene products that have the function "alcohol dehydrogenase" (some of these may indeed be encoded by a gene with the name alcohol dehydrogenase, but many will not be); a particular gene product may have both (or more) the functions "alcohol dehydrogenase" and "acetaldehyde dismutase."] e.g. GPCR, Kinase

GO Classification II• Biological process is a biological objective. A biological process is

accomplished via one or more ordered assemblies of molecular functions. Usually there is some temporal aspect to it, although a process event may be essentially instantaneous. It often involves transformation, in the sense that something goes into a process and something different comes out of it. Examples of broad biological process terms are "cell growth and maintenance," or "signal transduction." Examples of more specific terms are "pyrimidine metabolism" or "cAMP biosynthesis."

• A biological process is not equivalent to a pathway. We are specifically not capturing or trying to represent any of the dynamics or dependencies that would be required to describe a pathway.

• [The semantic distinction between a biological process and a molecular function can, at times, be hard to draw, and GO takes a pragmatic, rather than dogmatic, approach: As a general rule a process must have >1 distinct steps.]

e.g. Apoptosis

GO Classification III

• A cellular component is just that, a component of a cell but with the proviso that the component is part of some larger object, which may be an anatomical structure, e.g. "rough endoplasmic reticulum" or "nucleus" or a gene product group, e.g. "ribosome," "proteasome" or a heterodimeric protein.

• Molecular function, biological process and cellular component are attributes of gene products. In principle these may all be assigned independently or may be inherited; in practice they are assigned independently, that is to say the three graphs, of function, process and cellular component, are independent.

• The relationships between gene product to molecular function, biological process and cellular component are all many to many.

e.g. Nucleus, Cytoplasm

Affymetrix uses GO terms since April 2003

NetAffx Gene Ontology Mining Tool

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GO viewer

GO-Tool Configuration

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2 Filter

3 Unfold & Explore…..

Gene Ontology Procedure

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Mark Selected Genes

Acknowledgements

• Johan Helmstad

• Tobias Fandriks• Niklas Lindgren• Christopher Ahlberg• Information Sources:

– GO Consortium– Dataset: Pomeroy et al. Nature 415, 436-442 (2002)

• OpenOffice.org