Introduction to Microarray Data Analysis and Gene Networks lecture 8. Alvis Brazma European Bioinformatics Institute

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1 Introduction to Microarray Data Analysis and Gene Networks lecture 8 Alvis Brazma European Bioinformatics Institute

2 Lecture 8 Gene networks part 2 Network topology (part 2) Network logics Network dynamics

3 Gene Networks - four levels of hierarchical description Parts list genes, transcription factors, promoters, binding sites, Topology a graph describing the connections between the parts Control logics how combinations of regulatory signals interact (e.g., promoter logics) Dynamics how does it all work in real time

4 Gene Networks - four levels of hierarchical description Parts list genes, transcription factors, promoters, binding sites, Topology a graph describing the connections between the parts Control logics how combinations of regulatory signals interact (e.g., promoter logics) Dynamics how does it all work in real time

5 The arcs can have different meaning G1 G2 - The product of gene G1 is a transcription factor, which binds to the promoter of gene G2 (in Chip-chip experiment) physical interaction network (direct network) G1 G2 - The disruption of gene G1 changes the expression level of gene G2 data interpretation network (indirect network)

6 How both networks compare How much the two networks have in common We can look at the intersection of the networks whether the common parts have evidence in our existing knowledge If the target sets of the transcription factors present in both networks are similar Are the network topology (e.g., connectivity) properties similar

7 How both networks compare How much the two networks have in common We can look at the intersection of the networks whether the common parts have evidence in our existing knowledge If the target sets of the transcription factors present in both networks are similar Are the network topology (e.g., connectivity) properties similar

8 A couple of simple notions Any gene (node in the graph) with outgoing edges is called a source gene Any gene with incoming edges is a target gene Target set target node source node target set

9 A problem: Both network depend on the chosen significance threshold - i.e., what level of microarray signal to use to draw and edge in the network

10 The size of the networks for different significance thresholds ChIP network (p<0.01) ChIP network (p<0.001) mutant network (γ=2.0) mutant network (γ=2.5) mutant network (γ=3.0) source genes target genes genes edges edges where source gene and target gene have the same cellular role annotation in YPD ( ) 3694 (19.6%) 857 (13.9%) 4096 (12.8%) 2425 (13.9%) 1507 (14.6%) edges per source gene

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12 How both networks compare How much networks have in common We can look at the intersection of the networks whether the common parts have evidence in our existing knowledge If the target sets of the transcription factors present in both networks are similar Are the network topology (e.g., connectivity) properties similar

13 Intersection of the networks many connections are consistent with out a priori knowledge ARG5 LEU4 ECM40 ARG10 GCN4 HOM3 ARO1 CPA2 MET22 GIC2 YLR104W SPT21 MUT5 RFA2 YJR030C PDS1 YNL313C YOX1 UFE1 YDR115W CDC21 FUS1 RAD27 PDS5 IRR1 DIN7 ERP3 GPA1 STE12 SST2 GSH1 KAR4 STE2 YBR070C YHR149C YJL073W GIN4 YAP1 SGA1 MNN5 SW I6 SMC3 DUN1 YLR460C PCL1 YLR103C PCL2 YER079W RNR1 MBP1 YHR150W YDR528W YLR297W YER128W YPL267W SWE1 PRY2 PLB3 SVS1 SWI4 ABF1 HCM1 MCD1 SIC1 YKL185W YPL158C YGR086C SWI5 YLR194C CHS1 PST1 CCW6 YLR049C YPR157W YER078C SCW10 CLB2 MNN1 CIS3

14 Figure 6 YGR086C CCW6 SIC1 YLR194C CHS1 ARO1 CPA2 ARG10 MET22 STE12 FUS1 KAR4 STE2 GPA1 SST2 YAP1 GSH1 YLR460C SW I5 ARG5 ECM40 LEU4 GCN4 HOM3 CLB2 MBP1 SCW 10 CIS3 MNN1 SW I4 GIC2 SWI6 YKL185W YPL158C YLR049C PST1 YHR149C YBR070C MNN5 SGA1 PCL1 PCL2 YER079W YHR150W YDR528W YLR297W YER128W SWE1 YPR157W YER078C PRY2 PLB3 SVS1 ABF1 RNR1 HCM1 MCD1 YLR103C DUN1 SMC3 RFA2 MUT5 SPT21 YLR104W YJR030C PDS1 YNL313C YOX1 UFE1 YDR115W CDC21 RAD27 PDS5 IRR1 DIN7 ERP3 YJL073W GIN4 YPL267W

15 How both networks compare How much networks have in common We can look at the intersection of the networks whether the common parts have evidence in our existing knowledge If the target sets of the transcription factors present in both networks are similar Are the network topology (e.g., connectivity) properties similar

16 How Chip-chip and disruption networks relate? All genes All genes t Transcription factors Regulation set of t h Disrupted genes Effectual set of h

17 How Chip-chip and disruption networks relate? All genes All genes Transcription factors Regulation set of g Disrupted genes Effectual set of g

18 How to estimate that the overlap is more than expected by random? G R E R E We assume that the elements of the set E are marked, and pick the set of size R at random. Then the size x= R E of the intersection are distributed according to hypergeometric distribution. The probability of observing an intersection of size k or larger can be computed according to formula: = = k i R G i R E G i E k x P 0 1 ) (

19 How Chip-chip and disruption networks relate? All genes All genes 146 Transcription factors 23(9) Disrupted genes 213 Regulation set of g Effectual set of g From 23 transcription factors studied in both networks only 9 have their target sets overlapping more than expected by chancel

20 From 23 transcription factors studied in both networks only 9 have their target sets overlapping more than expected by chance Is it as bad as my look? We will expect many indirect connections in the disruption network that are not present in Chip network is this the case?

21 Direct vs. indirect interactions Y Direct Direct X Z Indirect

22 GLN3 RTG1 YAP1 LYS2 GCN4 YHM1 ARO3 ARO1 ARG4 YJL200C CPA2 BAS1 HIS4 ADE3 ADE13 ADE17 ADE4 YOL158C YAP6 FET4 ROX1 MBP1 SWI6 SWI4 RNR1 NDD1 YBR070C GIC2 SVS1 SOK2 YNL058C GDH3 ECM33 SWI5 SLY1 YDR451C YER189W YER190W PMA1 YGL114W YHL029C YIL158W YJL051W CIS3 SUR7 CDC5 CLN1 SRL1 YOR248W YOR315W CLB2 NCE102 YBL029W UTR2

23 From 23 transcription factors studied in both networks only 9 have their target sets overlapping more than expected by chance Is it as bad as my look? We will expect many indirect connections in the disruption network that are not present in Chip network is this the case? There is an anecdotal evidence that this is the case What about the connections present in the Chip network, but not in the disruption network? can be explained by nonfunctional relationships in the chip network and combinatorial regulatory effects

24 Conclusions We want to think that networks share enough in common both to be meaningful, but at the same time apparently there is a lots of noise in at least one of them present

25 How both networks compare How much networks have in common We can look at the intersection of the networks whether the common parts have evidence in our existing knowledge If the target sets of the transcription factors present in both networks are similar Are the network topology (e.g., connectivity) properties similar and what are they

26 Degree of a node in a graph The central node has degree = 7 indegree = 3 outdegree = 4

27 Important genes and genes with complex regulation Most genes have only a few incoming / outgoing edges, but some have high numbers (>500) Indegree Outdegree

28 Genes with highest in- and out-degree γ outdegree m n indegree m n 2.0 Carbohydrate metabolism Amino-acid metabolism RNA turnover Nucleotide metabolism 6 82 Meiosis Energy generation Cellstress Small molecule transport Protein translocation Other metabolism RNA turnover Amino-acid metabolism Cellstress 62 8 Nucleotide metabolism 3 67 Meiosis 54 3 Energy generation Proteinsynthesis 53 7 Differentiation 2 43 Cellwallmaintenance 47 6 Small molecule transport RNA turnover 48 4 Small molecule transport RNA processing/ modification 41 4 Other metabolism 2 96 Cellstress 27 8 Nucleotide metabolism 2 58 Small molecule transport 19 8 Matingresponse 2 57 Cellwallmaintenance 19 6 Amino-acid metabolism Cellular role table showing the top 5 groups with the highest median degrees for the networks with γ=2.0, 2.8 and 3.6 with a minimum group size of 3 for outdegree and 40 for the indegree (m median degree, n number of genes per group)

29 Node degree distributions for both networks roughly follow power-law ChIP network mutant network connections per gene connections per gene proportion of genes proportion of genes

30 Yeast network topology properties ChIP network connections per gene mutant network connections per gene proportion of genes proportion of genes Power-law property on logarithmic scale approximately linear relationship Whether this is so is still open to debate what is clear however is that most genes have relatively few connections, a few have many

31 Why topology is important? Reduce hypothesis space when analysing next layers of model complexity instead of default all genes depend on all, topology tells us which genes are independent What is the complexity of gene regulation Given a transcription factor T how many genes does T regulate? Given a gene A, how many transcription factors regulate A? Are networks modular?

32 What does modular mean? Are there only one connected component or several In scale free graphs there are hub nodes (nodes with high degree keeping everything together) and there is a theory that networks fall into pieces (modules) if the hub nodes are removed is this the case for real netoworks

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37 Looking for modules full removed 1% 5% 10% largest ChIP network second total number in-silico network largest second total number largest mutant network second total number

38 Network modularity On static topology level there are no obvious modules in yeast transcription regulation network This does not mean however that there are no modules? there is evidence for modules More subtle methods may be needed to find them

39 What have we learned on the topology level? Comparison of different networks shows that we have some idea of what the true topology is like, but it is far from perfect The network topology is roughly scale free There are not obvious modules in these networks on the topology level one giant component

40 Gene Networks - four levels of hierarchical description Parts list genes, transcription factors, promoters, binding sites, Topology a graph describing the connections between the parts Control logics how combinations of regulatory signals interact (e.g., promoter logics) Dynamics how does it all work in real time

41 Gene Networks - four levels of hierarchical description Parts list genes, transcription factors, promoters, binding sites, Topology a graph describing the connections between the parts Control logics how combinations of regulatory signals interact (e.g., promoter logics) Dynamics how does it all work in real time

42 More complex interactions G1 G2 G3

43 Logics A A B & D B C & D C D = A & B & C

44 Control functions Discrete vs. continuous D = A & B & C D = w 1 A + w 2 B + w 3 C

45 Decision trees no A>5 no yes B>2 C>3 yes no yes if A>5 and B<=2 then D=1 if A>5 and B>2 then D=0 if A<=5 and C<=3 then E=1 if A<=5 and C>3 then E=0 D=1 D=0 E=1 E=0

46 Decision tree for CLN2 gene in yeast 1.1 > > >0.8

47 Logics high throughput data is only now beginning to have impact Predicting gene expression from combination of expression levels of other genes (Soinov et al, 2003) Limited to about 20 genes For instance, by choosing genes well known to be involved in yeast cell cycle regulation it is possible to derive decision trees describing the combinatorial regulatory effects for these genes At least some of the conclusions are supported by a priori knowledge

48 What is known about the regulatory logics from classical low throughput approaches? Yuh, C.H., Bolouri, H. and Davidson, E.H. (1998) Genomic cisregulatory logic: experimental and computational analysis of a sea urchin gene. Science 279, Boolean, linear and decision tree concepts are all used 12 input variables

49 Probabilistic approaches

50 Canalizing Boolean functions There is one input and one value for that input that determines the output regardless of the values of other inputs F = x V y canalizing x=1 -> F=1 F = x & y canalizing x= 0 -> F=0 F = x y not canalizing none of the values of none of the inputs can determine the value of F For Boolean functions of many inputs only a small number of the possible functions are canalizing

51 Gene Networks - four levels of hierarchical description Parts list genes, transcription factors, promoters, binding sites, Topology a graph depicting the connections of the parts Control logics how combinations of regulatory signals interact (e.g., promoter logics) Dynamics how does it all work in real time

52 Classification of dynamic network models Continuous versus discrete state (e.g, boolean) Deterministic versus probabilistic state transitions (e.g. differential equations versus Bayesian models); Ignoring spatial effects vs modelling spatial effects

53 Differential equation based models The basic assumption the rate of changes in gene product abundance at a particular time are determined by the abundance of gene products at the time g i (t) the abundance of the product of gene i at time t w ij the weight of the contribution of gene j to the expression of gene i

54 Differential equation based models Difference equation model: g 1 (t+ t) g 1 (t) = (w 11 g 1 (t) w 1n g n (t)) t... g n (t+ t) g n (t) = (w n1 g 1 (t) w nn g n (t)) t where: g i (t) the abundance of the product of gene i at time t w ij the weight of the contribution of gene j to the expression of gene I The main problem we don t know the constants w ij

55 Differential equation model for drosophila embryo development von Dassow, G., Meir, E., Munro, E.M. and Odell, G.M. (2000) The segment polarity network is a robust developmental module. Nature 406,

56 Synchronous Boolean networks the assumptions Each gene the system (cell) can be in one of two states expressed 1, not expressed 0 The genes can switch from state to state all simultaneously in synchronous manner The next state of each gene is determined by previous states of all genes by Boolean functions describing the network

57 Y=X&Z, X=Y, Z= X Y & X Z t t+1 X Y Z X Y Z State transitions State space

58 Reverse engineering: Given the state space transitions: Reconstruct the network:

59 Reverse engineering problem On one hand the problem is trivial the stage space immediately gives one a transition table, which is an equivalent representation to the wiring diagram However the problem of building the smallest wiring diagram from the table is NP-hard, i.e., it takes exponential time to do this For small networks (3 genes as above) this is not a problem, but for thousands of genes this is not a solution

60 Exponential algorithm Assume that all genes depend on all, i.e., in the wiring diagram connect each to all The Boolean function is the disjunctions of all vectors as given in the table This gives a hugely long Boolean functions for each gene (i.e, n2 n for a network of each gene) The minimisation of this Boolean function to the smallest equivalent one is a classic NP hard problem

61 Solution Instead of the minimal possible network look for simply small network Somogyi et al algorithm using mutual information not clear how good is this heuristics

62 Attractors in the state space

63 Canalizing Boolean functions There is one input and one value, which determines the output regardless of the values of other imputs F = x V y canalizing x=1 -> F=1 F = x & y canalizing x= 0 -> F=0 F = x y not canalizing none of the values of none of the inputs can determine the value of F For Boolean functions of many inputs only a small number of the possible functions are canalizing

64 Kaufman s simulations Randomly constructed Boolean networks such that the number of inputs of each gene is small the control functions are canalizing have a property that their state space consists of a relatively small number of attractors most of the time the spend in attractor states

65 Attractors in the state space

66 Kaufman s hypothesis Gene networks are predominantly controlled by canalizing functions Attractors are cell types He estimated that under certain conditions on network connectivity and assuming genes, there should be a few hundred different cell types

67 A hybrid models the finite state linear model B 1 F i B 2 & r i =(-1.5, 0.5) B 3

68 B 1 1 F i B 2 1 & r i =(-1.5, 0.5) B 3 0

69 B 1 1 F i B 2 1 & 1 r i =(-1.5, 0.5) B 3 0

70 c i B 1 1 F i t B 2 1 & 1 B 3 0

71 c i B 1 1 F i t B 2 1 & 0 B 3 1

72 0 1 r r r + b rep S rep b rep S rep b rep S rep asso rep concentration of repressor concentration of repressor concentration of repressor disso rep asso rep disso rep asso rep disso rep time t 1 time t 1 t 2 time

73 Simulations on a FSLM

74 Lac operon in E.coli bacteria There are two modes in E.coli glucose or lactose utilisation mode that is regulated by the presence or absence of lactose

75 Finite state model for Lac-Operon network FSLM representation Repressor Lactose + Galactose Glucose repressor galactose & repressor Promoter laci Promoter Operator Galactosidase lacz... activator glucose & activator galactosidase Activator galactosidase repressor see table galactosidase Glucose activator glucose galactose

76 0,1 N Finite state linear model for lambda phage lytic/lysogenic mode switch cro/ci cii Q P L P R P L1 P L1 N 0,1 Struc 0,1,2 N 0,1 P L2 ciii P L2 0,1 xis P int 0,1 int cii P E P E P ci ci O R1 O R2 O R3 ci/cro ci/cro ci/cro P M P R P M 0,1,2 cro 0,1,2,3 cii 0,1,2 stress Other ci N P R1 0,1,2,3, 4,5,6 O P ciii cii Other cii cell not implemented in the simulator P R2 Q N 0,1,2,3

77 Network dynamics the state of art Most of the current dynamic models include less than 10 genes, and the knowledge used in the modelling mostly comes from traditional biology studies There are no convincing examples where high throughput technologies had a substantial impact on network modelling on the dynamics level yet

78 Conclusions what have we learned on each level so far? Parts list we are dealing with thousands to tens of thousands of elements in these networks, and hundreds to thousands regulating elements; Topology may be tens of thousands of connections, it seems to be scale free, no obvious modules Control logics a gene can be controlled by dozens of transcription factors in a rather complex way Dynamics we are not yet able to model dynamics of genome scale transcription regulation networks

79 What do I hope you have learned in this course Some feel what real microarray data are like, some idea of the basic methods (if you didn t know this before) How to use ArrayExpress and Expression Profiler if you need this A flavour what is our current knowledge how genes are regulated and how little we know