Discovery of small protein complexes from PPI networks with size-specific supervised weighting

Size-specific supervised weighting (SSS) of the PPI network

SSS uses supervised learning to weight each edge of the reliable PPI network with two posterior probabilities, that of being a small-co-complex edge (ie. of belonging to a small complex), and that of being a large-co-complex edge, given the edge's features. These features consist of diverse data sources, their topological characteristics, and an isolatedness feature derived from an initial calculation of the posterior. We first describe the data sources and features we use, then describe our weighting approach.

Size-specific supervised weighting of the PPI network (SSS)

In this step, we weight the edges of the PPI network with our size-specific supervised weighting (SSS) approach. We use a highly-reliable subset of the PPI network, by keeping only the top k edges with the highest PPI reliability scores. In our experiments we set k = 10000, but similar results are obtained for other values of k. SSS uses supervised learning to weight each edge with three scores: its posterior probability of being a small-co-complex edge (ie. of belonging to a small complex), of being a large-co-complex edge, and of not being a co-complex edge, given the features of the edge. These features consist of the twelve features described above (PPI, STRING, LIT , and nine topological features), as well as an isolatedness feature which is derived from an initial calculation of the posterior probabilities. We use a naive-Bayes maximum-likelihood model to derive the posterior probabilities.

Each edge (a, b) in the network is cast as a data instance, with its set of features F. Using a reference set of protein complexes, each edge (a, b) in the training set is given a class label lg-comp if both a and b are in the same large complex; it is labelled sm-comp if both a and b are in the same small complex; otherwise it is labelled non-comp. Learning proceeds by the following steps (illustrated in Figure 1):

1 Minimum description length (MDL) supervised discretization [16] is performed to discretize the features (excluding the isolatedness feature). MDL discretization recursively partitions the range of each feature to minimize the information entropy of the classes. If a feature cannot be discretized, that means it is not possible to find a partition that reduces the information entropy, so the feature is removed. Thus this step also serves as simple feature selection.

2 The maximum-likelihood parameters are learned for the three classes lg-comp, sm-comp, and non-comp:

$P\left(F=f|sm\text{-}comp\right)=\frac{n_{sm,F=f}}{n_{sm}}$

$P\left(F=f|lg\text{-}comp\right)=\frac{n_{lg,F=f}}{n_{lg}}$

$P\left(F=f|non\text{-}comp\right)=\frac{n_{non,F=f}}{n_{non}}$

for each discretized value f of each feature F (excluding the isolatedness feature). n _sm is the number of edges with class label sm-comp, n _{sm,F = f} is the number of edges with class label sm-comp and whose feature F has value f ; n _lg is the number of edges with class label lg-comp, n _{lg,F = f} is the number of edges with class label lg-comp and whose feature F has value f ; n _non is the number of edges with class label non-comp, and n _{non,F = f} is the number of edges with class label non-comp and whose feature F has value f .

3 Using the learned models, the class posterior probabilities are calculated for each edge (a, b) using the naive-Bayes formulation:

$P\left(\left(a,b\right)issm\text{-}comp|F_1=f_1,F_2=f_2,...\right)=\frac{\prod _{i}P\left(F_i=f_i|\left(a,b\right)issm\text{-}comp\right)P\left(sm\text{-}comp\right)}{{\sum }_{class\in \left\{sm\text{-}comp,lg\text{-}comp,non\text{-}comp\right\}}\prod _{i}P\left(F_i=f_i|\left(a,b\right)isclass\right)P\left(class\right)}$

The posterior probabilities are calculated in a similar fashion for the other two classes lg-comp and non-comp. We abbreviate the posterior probability of edge (a, b) being in each of the three classes as P_(a,b),sm, P_(a,b),lg, and P_(a,b),non.

A new feature ISO (isolatedness) is calculated for each edge (a, b), based on the probability that the edge is isolated (not adjacent to any other edges), or is part of an isolated triangle:

$ISO\left(a,b\right)=ISO2\left(a,b\right)+ISO3\left(a,b\right)$

$\begin{array}{c}ISO2\left(a,b\right)=P_{\left(a,b\right),sm}{\displaystyle \prod _{x\in \left\{a,b\right\},y\in N_{a,b}}}{P}_{\left(x,y\right),non}\hfill \end{array}$

$ISO3\left(a,b\right)={\displaystyle \sum _{c\in N_a\cap N_b}}\left(P_{\left(a,b\right),sm}{P}_{\left(a,c\right),sm}{P}_{\left(b,c\right),sm}{\displaystyle \prod _{x\in \left\{a,b,c\right\},y\in N_{a,b,c}}}{P}_{\left(x,y\right),non}\right)$

where N _x denotes the neighbours of x, excluding x. The ISO feature is discretized with MDL.

5 The maximum-likelihood parameters for the ISO feature are learned for the three classes.

6 The posterior probabilities for the three classes, P_(a,b),sm, P_(a,b),lg, and P_(a,b),non, are recalculated for each edge (a, b), this time incorporating the new ISO feature.

Extracting small complexes

After using SSS to weight the PPI network, the small complexes are extracted. This stage, called Extract, consists of two steps (see Figure 1): first, the small-co-complex probability weight of each edge is disambiguated into size-2 and size-3 complex components; next, each candidate complex is scored by its cohesiveness-weighted density, which is based on both its internal and outgoing edges.

Experimental setup

In our main experiments, we compare our two-stage approach (weighting with SSS, small complex extraction with Extract) against using the original PPI reliability (PPIREL) weighted network with standard clustering approaches to derive small complexes:

Markov Cluster Algorithm (MCL) [1] simulates stochastic flow to enhance the contrast between regions of strong and weak flow in the graph. The process converges to a partition with a set of high-flow regions (the clusters) separated by boundaries with no flow.

Restricted Neighborhood Search Clustering (RNSC) [2] is a local search algorithm that explores the solution space to minimize a cost function, calculated according to the number of intra-cluster and inter-cluster edges. RNSC first composes an initial random clustering, and then iteratively moves nodes between clusters to reduce the clustering's cost. It also makes diversification moves to avoid local minima. RNSC performs several runs, and reports the clustering from the best run.

IPCA [3] expands clusters from seeded vertices, based on rules that encode prior knowledge of the topological structure of protein complexes' PPI subgraphs. Whether a cluster is expanded to include a vertex is determined by the diameter of the resultant cluster and the connectivity between the vertex and the cluster.

Clustering by Maximal Cliques (CMC) [4] first generates all the maximal cliques from a given network, and then removes or merges highly overlapping clusters based on their inter-connectivity as follows. If the overlap between two maximal cliques exceeds a threshold overlap thres, then CMC checks whether the interconnectivity between the two cliques exceeds a second threshold merge thres. If it does, then the two cliques are merged; otherwise, the clique with lower density is removed.

Clustering with Overlapping Neighborhood Expansion (ClusterONE) [5] greedily expands clusters from seeded vertices to maximize a cohesiveness function, which is based on the edge weights within a cluster and the edge weights connecting the cluster to the rest of the network. It then merges highly-overlapping clusters.

Proteins' Partition Sampler v2.3 (PPSampler2) [6] partitions the PPI network into clusters using a Markov-chain Monte-Carlo approach to optimize an objective function. Novelly, it incorporates the size distribution of clusters in the objective function, and thus accounts for the sizes of complexes found in actual biological systems, where most of the complexes are small.

We also investigate the performance of using our SSS-weighted network with standard clustering approaches, and using the PPIREL network with our Extract approach.

We perform random sub-sampling cross-validation, repeated over ten rounds, using manually curated complexes as reference complexes for training and testing. For yeast, we use the CYC2008 [17] set which consists of 408 complexes, of which 259 are small (composed of two or three proteins). For human, we use the CORUM [18] set (filtered to remove duplicates and small complexes that are subsets of large ones), which consists of 1352 complexes, of which 701 are small. In each cross-validation round, t% of the complexes (large and small) are selected for testing, while all the remaining complexes are used for training. Each edge (a, b) in the network is given a class label lg-comp if a and b are in the same large training complex; otherwise it is labeled sm-comp if a and b are in the same small training complex; otherwise its class label is non-comp. Learning in SSS is performed using these labels, and the edges of the network are weighted using the learned models. Small complexes are then extracted from the weighted network. The predicted complexes are evaluated by matching them with only the small test complexes.

We design our experiments to simulate a real-use scenario of complex prediction in an organism where a few complexes might already be known, and novel complexes are to be predicted: in each round of cross-validation, the training complexes are those that are known and leveraged for learning to discover new complexes, while the test complexes are used to evaluate the performance of each approach at this task. Thus we use a large percentage of test complexes t = 90%. In yeast, this gives about 233 small test complexes and 26 small training complexes per cross-validation iteration; in human, this gives about 631 small test complexes and 70 small training complexes.

Evaluation methods

The precision of clusters is calculated only among those clusters that do not match a training complex, to eliminate the bias of the supervised approach (SSS) for predicting training complexes well. As a summarizing statistic of a precision-recall graph, we also calculate the area under the curve (AUC) of a precision-recall graph.

To measure the quality of a predicted complex, we derive the semantic coherence of its Gene Ontology (GO [19]) annotations across the three GO classes, biological process (BP), cellular compartment (CC), and molecular function (MF). First, we derive the BP semantic similarity between two proteins as the information content of their BP annotations' most informative common ancestor [20]. Then we define the BP semantic coherence of a predicted complex as the average BP semantic similarity between every pair of proteins in that complex (likewise for CC and MF).

Prediction of small complexes

In this section we compare the performance of small complex prediction using our weighting approach (SSS) versus PPI reliability (PPIREL), and using our complex extraction algorithm (Extract) versus other clustering algorithms (CMC, ClusterOne, IPCA, MCL, RNSC, PPSampler2). Figure 2a shows the performance of prediction of yeast small complexes, in terms of precision-recall AUC. Our 2-stage approach (SSS + Extract) outperforms all other approaches tested here, including using the PPIREL or SSS-weighted networks with standard clustering algorithms, or the PPIREL-weighted network with Extract. Furthermore, when using standard clustering algorithms to discover small complexes, weighting the network with SSS gives improved performance compared to using PPIREL (especially for ClusterOne, MCL, RNSC, and PPSampler2).

Figure 2b shows the precision-recall graphs comparing our approach (SSS + Extract) to the baselines of standard clustering algorithms applied on a PPIREL network. While our approach has lower precision among the initial top predictions (at recall less than 5%), beyond that we attain substantially greater precision: for example, at 40% recall, our approach attains more than three times the precision than the other clustering approaches (28% versus 9%). Furthermore, we attain substantially higher recall as well. Figure 2c shows the precision-recall graphs when the standard clustering algorithms are applied on the SSS-weighted network. Using the SSS-weighted network, most of the clustering algorithms achieve improved precision in the mid-recall ranges, as well as gains in recall. However, our approach (SSS + Extract) still maintains greater precision in most of the recall range.

Figure 3 shows the performance of prediction of human small complexes. The prediction of complexes in human is much more challenging than in yeast, so the AUCs achieved here are correspondingly lower. Nonetheless, our approach (SSS + Extract) still outperforms all the other approaches, including using the PPIREL or SSS-weighted networks with standard clustering algorithms, or the PPIREL-weighted network with Extract. When using standard clustering algorithms to discover small complexes, weighting the network with SSS gives improved performance only for CMC and IPCA, while performance remains the same or decreases for the other clustering algorithms.

Figure 3b and 3c show the corresponding precision-recall graphs. As in yeast, our approach (SSS + Extract) outperforms the standard clustering algorithms applied on the PPIREL-weighted network by achieving substantially higher recall, as well as greater precision in almost the whole recall range (Figure 3b). Using the SSS instead of the PPIREL-weighted network, CMC and IPCA achieve higher precision, while the other clustering algorithms suffer from lower precision or recall (Figure 3c).

In the following section we investigate how the various techniques incorporated in SSS and Extract improve the performance of small complex prediction.

How do SSS and Extract improve performance?

Figures 2 and 3 showed that weighting the network with SSS improves yeast small complex prediction in four of six clustering algorithms, while it only improves human complex prediction in two clustering algorithms. To investigate the benefits of SSS weighting, we compare the performance of the weighting approaches in classifying edges as belonging to small complexes. Each weighting approach is used to weight the edges of the network, and the precision-recall graph is obtained by varying a threshold on the edge weights. Figure 4a shows the precision-recall graph for classification of yeast small complex edges. SSS achieves much higher precision than classifying by PPIREL, as the SSS weights more accurately reflect membership in small complexes. This leads to improved performance by clustering algorithms when applied to the SSS-weighted network to predict small yeast complexes. On the other hand, when classifying edges in small human complexes, Figure 4b shows that SSS has lower precision than PPIREL at the lower recall range, with only similar or marginally better precision at higher recall ranges. Thus, only two clustering algorithms obtain improved performance from clustering the SSS-weighted network. Figure 4 also shows the poor performance of a previously proposed supervised weighting approach SWC [8], which learns a model for all co-complex edges in general, as opposed to distinct models for small and large complexes. As the number of edges in a complex grows quadratically with its number of proteins, the edges from large complexes far outnumber those from small complexes, so SWC's learned model reflects the characteristics of large complexes. Thus, SWC suffers from poor performance in classifying edges from small complexes, demonstrating the importance of the size-specific modeling of SSS.

The SSSno_iso graph in Figure 4 shows that if the isolatedness feature is not incorporated into SSS (in other words, steps 4 to 6 of SSS are skipped), precision drops substantially in yeast, showing the utility of the isolatedness function in predicting small complex edges. However, in human, incorporating the isolatedness feature gives only marginal improvement in precision. Figure 5 shows the performance of small complex prediction, when SSS is used with and without the isolatedness feature, with the complexes derived by Extract. Incorporating isolatedness gives a noticeable boost to precision in both yeast and human, demonstrating that isolatedness benefits the prediction of small complexes by improving the SSS weighting of edges.

Figures 2 and 3 showed that using Extract to derive small complexes from the PPIREL network does not perform better than using most of the other clustering algorithms (Extract achieves higher recall, at the expense of precision). We investigate the effect of cohesiveness weighting in Extract, applied on the SSS network versus the PPIREL network. Figure 6a shows the performance of the clustering algorithms applied on the SSS network, with and without scoring by cohesiveness weighting, for predicting yeast small complexes. For Extract (where cohesiveness weighting is used by default), scoring without cohesiveness weighting means a cluster's score is its weighted density. For the other clustering algorithms (where weighted density is used by default), scoring with cohesiveness weighting means a cluster's score is the product of its weighted density and its cohesiveness (ratio of sum of internal edges over internal and outgoing edges). With the SSS network, scoring by cohesiveness weighting improves performance across all clustering algorithms. On the other hand, Figure 6b shows that, with the PPIREL network, scoring by cohesiveness weighting decreases performance across most clustering algorithms. Thus, cohesiveness weighting appears useful only when edges are weighted using SSS.

Figure 6c and 6d show the corresponding charts for human complexes, with and without cohesiveness weighting. With the SSS network, cohesiveness weighting improves performance in four of seven clustering algorithms; whereas with the PPIREL network, cohesiveness weighting decreases performance in all clustering algorithms. Thus, in human complexes as well, cohesiveness weighting appears useful only when edges are weighted using SSS.

Example complexes

In this section we present some example complexes that are difficult to predict using the PPIREL network with any standard clustering algorithm, but can be predicted with our approach (SSS + Extract). Since the various clustering approaches output different numbers of predictions, we consider only the top scoring predicted clusters with a cross-validation precision level greater than some threshold. For yeast we use a precision threshold of 10%, but for human we use a lower precision threshold of 2%, since fewer human complexes are predicted with high precision.

The DNA replication factor A complex in yeast consists of three proteins, Rfa1p, Rfa2p, and Rfa3p. Figure 7a shows the PPIREL network around this complex, with edge widths scaled to PPI reliability scores. The complex is embedded within two size-4 cliques (with Rad52p, and Mec1p), with high PPIREL weights. Moreover, Rfa1p is also connected via high PPIREL weights to many external proteins, some of which form size-3 cliques as well. As a result, none of the standard clustering algorithms applied on the PPIREL network predicted this complex, in any cross-validation round. Figure 7b shows the SSS network, with edge widths scaled to the small co-complex posterior probability scores. The three proteins in the complex remain interconnected with high edge weights, while the extraneous edges' weights are now markedly lowered. Thus, our Extract algorithm is able to retrieve this complex from the SSS network consistently across all cross-validation rounds where it is tested.

Figure 8 shows two yeast complexes, with an overlapping protein (Sir2p), involved in transcriptional silencing: the chromatin silencing complex, consisting of Sir2p, Sir3p, and Sir4p, and the RENT complex, consisting of Sir2p, Cdc14p, and Net1p. In the PPIREL network (Figure 8a), each of the two complexes are connected via highly-weighted extraneous edges to many external proteins. Once again, none of the standard clustering algorithms applied on the PPIREL network could predict either of these complexes, in any cross-validation round. In the SSS network (Figure 8b), the chromatin silencing complex remains connected with high edge weights, with a marked reduction in the weights of the extraneous edges. Thus our Extract algorithm retrieves this complex from the SSS network consistently across all cross-validation rounds where it is tested. On the other hand, in the RENT complex, the weights of two edges (from Sir2p to the other two proteins) are now even lower than some of its extraneous edges. As a result, our Extract algorithm retrieves this complex in only 33% of the cross-validation rounds where it is tested. Nonetheless, this is still an improvement over using the PPIREL network with standard clustering algorithms.

Figure 9 shows two human ubiquitin ligase heterodimer complexes with an over-lapping protein: the UBE2V1-UBE2N and UBE2V2-UBE2N complexes. In the PPIREL network (Figure 9a), UBE2N is connected via highly-weighted edges to many other external proteins, forming a number of size-3 cliques with them. The UBE2V1-UBE2N complex is embedded within two size-3 cliques, making it difficult to discover: none of the standard clustering algorithms predicted this complex in any cross-validation round. On the other hand, the UBE2V2-UBE2N complex is relatively isolated as UBE2V2 is not connected to any other external protein, allowing CMC and IPCA to predict this complex consistently. In our SSS network (Figure 9b), all extraneous edges' weights have been dramatically lowered, leaving the co-complex edges with high weights. Thus our Extract algorithm retrieved UBE2V1-UBE2N 78% of the time, and UBE2V2-UBE2N 100% of the time.

Quality of novel complexes

In this section we compare the number and quality of high-confidence novel complexes predicted by our approach (SSS + Extract), against using standard clustering algorithms on the PPI reliability network. When weighting the network with SSS, the entire set of reference complexes is used for training. We filter the predicted complexes to remove those that match any reference complex, and to keep only high-confidence predictions: the score of each predicted complex is mapped to a precision value, using the cross-validation results, and only predicted complexes with estimated precision greater than a confidence threshold are kept. For yeast, this confidence threshold is 0.5; for human, a lower threshold of 0.1 is used, since much fewer complexes are predicted with high precision.

Figure 10a shows the number of high-confidence novel complexes predicted in yeast, and their average BP, CC, and MF semantic coherence, using the different approaches. Compared to the other approaches, SSS with Extract generates more than twice as many high-confidence novel predictions, with equal or greater quality: our predicted complexes have greater coherence than ClusterOne, MCL, or PPSampler2 (p <.05 in at least one of BP, CC, or MF), and similar coherence with the other approaches. The CYC2008 reference complexes have much higher BP and CC coherence, but lower MF coherence.

Figure 10b shows the corresponding charts for human predictions. Again, our approach generates more high-confidence novel predictions than the other approaches, with equal or greater quality: our predicted complexes have greater coherence than ClusterOne, MCL, RNSC, or PPSampler2 (p <.05 in at least one of BP, CC, or MF), and similar coherence with the other approaches. Our predicted complexes have similar semantic coherence compared to the Corum reference complexes.

Finally, we briefly mention two novel complexes, predicted by our approach, that we have validated via a literature scan. Our approach predicts a high-scoring yeast cluster consisting of Cap1p and Cap2p, which is not found in our reference database of complexes. However, a literature scan revealed this to be the capping protein heterodimer, which binds to actin filaments to control filament growth [21]. Our approach also predicts a novel high-scoring human cluster consisting of PKD1 and PKD2. A literature scan revealed that these two proteins, which are involved in autosomal polycystic kidney disease, have been found to form a PKD1-PKD2 heterodimer [22].