Mining breast cancer genes with a network based noise-tolerant approach

Rationale for data integration

A network-based score (S _N ) and an expression-based score (S _E ) were respectively derived for each gene, which were then integrated into a final score (S) by weighting them with a coefficient λ. A P-score was computed to represent performance of the proposed method when λ was changed from 0 to 1. P-score was the average ranking of known breast cancer genes in top 10% of the final gene ranking list (see Methods). Smaller P-score (ranked higher) meant better performance (Figure 2). As shown in Figure 2, better performance was achieved when λ=0 (i.e., using only network-based ranking) compared with λ=1 (i.e., using only expression-based ranking); the best performance was obtained when λ=0.2, which suggested that utilizing genes’ complex relations in the PPI network can help cancer gene mining tasks. It also confirmed that multiple data sources can complement each other in ranking cancer genes. Final ranking results were listed in Additional file 1: Table S1.

Evaluation of performance in ranking known cancer genes

Robustness with respect to realistic data noise

In general, a method based on multiple types of knowledge is more objective than those utilizing singular information; combining independent data sources can alleviate effects of biases inherent in single data types [32]. Most data sets, especially genome wide data, tend to contain appreciable amount of noise. For instance, GO is a powerful tool which provides a controlled vocabulary to describe biological functions on multiple levels [33]. It was also widely used on cancer research (there are about 39,000 citations for GO in Google Scholar by Oct. 16, 2012). However, not all GO annotations are equally credible [34]. As of October 2012, there were over 3 million GO annotations for Homo sapiens genes. Each GO annotation includes an evidence code to indicate how the annotation was inferred. All evidence codes (except IEA, which is automatically derived) are manually assigned. They can be divided into four categories: experimental (EXP, IDA, IPI, IMP, IGI, and IEP), computational analysis (ISS, ISO, ISA, ISM, IGC, IBA, IBD, IKR, IRD, and RCA), author statements (TAS and NAS), and curatorial statements (IC and ND). For Homo sapiens, 16 evidence codes were used to describe GO annotations [35]. The vast majority of GO annotations were found to be computationally derived and not manually curated (IEA evidence code) (Figure 3). GO annotations therefore contain appreciable amount of noise within themselves.

Approaches that exhibit robust performance with regard to noise are needed if they are to prove useful in cancer gene hunting endeavours. Nevertheless, as mentioned before, few projects had specifically analysed data noise effects quantitatively. A network based noise tolerant method was proposed here to mine breast cancer genes. Its performance was compared with that of the well performing random walk approach by five-fold cross-validation. The results confirmed the proposed method’s robust performance with respect to data noise.

The set of known breast cancer genes (KnownSet, see Methods) was enlarged by including genes sharing GO annotations with those in the KnownSet. The enlarged set was called the GOSet (GO enriched gene set, see Methods), which was adopted as a noisy set of likely breast cancer genes. The GOSet was utilized to check an algorithm’s robustness with respect to data noise. Data were sampled from the GOSet, and combined with the KnowSet to generate a noisy set of training data. This way of synthesizing noisy data set is unique in that it doesn’t simply using random data as noise, which is too artificial. The GOSet contains enriched but still imperfect data, which can better mimic data noise in real life scenarios. An algorithm’s ability to retain its performance was checked when fraction of noisy data in the training set went up.

The proposed method did not work quite as well as random walk approach when input data was 100% accurate, however, when noise level in input data increased, we observed the following phenomena (Figure 4).

1. 1.

   Random walk approach exhibited a sharp decrease in its performance, while our method was able to maintain a relatively stable performance.

    
2. 2.

   When noise increased to a large extent, the proposed method was able to perform about twice as well as random walk approach did.

    

It can thus be stated that the proposed method was more robust with respect to noise in input data, compared to the state-of-art random walk based approach. The results also confirmed the power of data integration, which was able to let different data sets complementing each other [22, 23].

Robustness with respect to completely random noise

GOSet tried to simulate realistic data noise. However, it might be suspected that GOSet was biased toward the proposed method in one way or another. To make sure the comparison between the proposed method and the random walk approach was not done unfairly, randomly picked genes were added to the KnownSet (Figure 1, Box B, see Methods), and performances of the proposed method and random walk approach were then compared. Figure 5 again showed that random walk approach showed linear performance decline when noise increased in the source data, while the proposed method was able to maintain stable performance.

Deriving known breast cancer gene set

Ranking by PPI network

The human PPI data were derived from five sources: HPRD [41], BioGRID [42], homoMINT [43], IntAct [44] and a manually curated human signalling network [45]. Protein identifiers were mapped to uniform coding gene identifiers. Official gene symbols were used as identifier. Redundant interactions were removed, along with interactions with identifiers that could not be mapped to gene symbols (Table 1). The final PPI network was represented by an undirected graph where nodes representing genes and edges representing interactions. The graph contained 156,459 interactions connecting 15,494 genes.

Similarities between proteins were found to be correlated with their proximity in the PPI network [46]. It was assumed that when a gene in the PPI network exhibited topological features similar to known breast cancer genes, it’s more likely to be involved in breast cancer processes. Several papers had shown that cancer genes could be effectively distinguished from others by their topological attributes in the PPI network, such as node degree [47], betweenness centrality [48] and shortest path length [10]. The above three network topological indices were computed and used to assess gene similarity in the PPI network. Genes were then sorted according to values of the topological indices.

Let G(V,E) be the PPI network, where V is the set of genes, and E the set of interactions in the network.

where $\mathit{\sigma }$ _jk is the number of shortest paths from a source j∈V to a target k∈V, and $\mathit{\sigma }$ _jk (v) is the number of those paths passing through some node v other than j,k. If j=k, $\mathit{\sigma }$_jk =1, and if v∈j,k, $\mathit{\sigma }$ _jk (v)=0.

where G is the KnownSet, d(v,t) is the shortest path length between node v and t. n is the number of known breast cancer genes which can be reached by v.

The above topological attributes were computed with the Python package networkx [50]. To facilitate later integration step, they were transformed into rankings; that is, each list was sorted, and a gene was assigned a positive integer number for a specific attribute according to that attribute’s value in the sorted list (Figure 6). In the end, three rankings for each gene were obtained based on its topological attributes in the network. S _N (v) was the topology-based ranking score of a gene v, which was calculated from the three network topological attributes: node degree, shortest path length and node betweenness, S _N (v) = (c _d (v) + c _spl (v) + c _b (v))/3.

Deriving GO enriched gene set

GO provides a controlled vocabulary of terms for describing genes and gene products [17]. GO enrichment analysis assesses whether certain GO annotations are significantly over represented among a set of genes [51]. The level of enrichment can be represented by a p-value based on specific probability distribution. The p-value is calculated by randomly picking sets of genes from the genome and computing the probability of obtaining more genes with GO terms annotated to those in the study set [52]. The smaller the p-value, the more significant the GO term is enriched in the gene set. For the KnownSet, we used three tools (DAVID [53], GOstats [54], GOEAST [55]) to perform enrichment analyses in the BP (Biological Process) sub-ontology. DAVID and GOEAST are online tools and GOstats is an R package from Bioconductor [56]. The top 50 enriched terms were picked from results obtained by each of those tools. The three enriched GO term sets from the three tools were combined into one GO term set by taking their union. In addition, cancer-hallmark related GO terms are those characteristically related to cancers, they should also be included. The set of cancer-hallmark GO terms listed in Table 1 of [37] were added to the above obtained GO term set, which was then remapped to a set of corresponding genes based on human GO annotations. Genes not covered by our PPI network were removed. The obtained set of genes was enriched with BP terms annotated to known breast cancer genes; they thus were more likely to be involved in breast cancer than randomly selected genes. This set of genes was called the GO enriched gene set (GOSet) (Figure 7).

Ranking by gene expression and GO

All breast cancer-related gene expression datasets (keywords: Homo sapiens & breast cancer) were download from the GEO database [38]. Data sets with fewer than five samples or conditions were deleted. Data sets of normal versus cancer samples were used so those containing recurred versus non-recurred samples were deleted. 53 GDSes (GEO data sets) were thus obtained.

where n is the set of expression profiles for gene i in a GDS, m is the number of samples/conditions in one of those profiles, and e _k (j) is the corresponding expression value of sample j.

After the above mentioned preprocessing steps, genes in each GDS were clustered by the APCluster algorithm according to their expression profiles. APCluster is an algorithm based on affinity propagation which works by considering all data points as potential cluster centers at the same time and setting up messages of similarity between any two data points, messages are exchanged among data points until all clusters are determined. APCluster had been shown to perform well compared to other clustering approaches [58, 59]. Pearson correlation coefficient between gene expression profiles was used as the similarity metric for APCluster. It was assumed that genes within a cluster would have higher probability of being involved in certain biological processes than those across clusters.

Overlaps of expression clusters with the GOSet were next computed. To evaluate significance of the overlaps, the same number of genes was randomly sampled as those in the cluster from GDS, and its overlap with the GOSet was computed; the procedure was repeated 1000 times for each cluster. A p-value was then computed for the clusters (Figure 8). Rankings were assigned to clusters according to their p-values; that is, the lower the p-value, the higher the position in the ranking list. Genes in the same clusters were assigned the same ranking. A ranking score S _E (i) was thus obtained for genes in each GDS, where i represented a specific GDS. A score S _E was assigned for each gene by computing the average of S _E (i) from all relevant GDSes.

Ranking integration

S _E (v) was the expression-based ranking score of gene v, which was computed from breast cancer-related gene expression data and GO annotations. λ (0≤λ≤1) is a coefficient to weigh the contribution of topological attributes and expression information in ranking breast cancer genes. The average ranking of genes in the KnownSet that sorted into top 10% was computed as the P-score. A smaller P-score meant better performance, that is, it was more likely to find true breast cancer genes from the top of the sorted list. S(v) is the final ranking for a gene v, which reflected the belief that a specific gene was a potential breast cancer gene. The higher a gene was ranked, the more likely it was involved in breast cancer related processes.

Random walk approach

where p ⁰ is the initial probability, which is 1/37 for the 37 genes in the KnownSet and 0 for all others; r represents the probability of remaining at the same node at the next step. [30] showed that random walk worked robustly against different r values, which was also confirmed by our computation (data not shown). r was taken to be 0.7 in the current work. For details of random walk approach, see [13].

Ranking performance comparison

OMIMSet contained 26 known breast cancer genes, CGCSet contained additional 11. The 26 known breast cancer genes in the OMIMSet were used as the KnownSet. Procedure in Figure 1 was followed and the model built, which was then used to rank the 11 known breast cancer genes in the CGCSet. Ranking values in italic meant those genes were ranked in the top 10% of the final list. The row of “top 10% average” represented average rankings of those known breast cancer genes in CGCSet that ranked in top 10%, while “all 11 test genes average” represented the average rankings of all 11 genes in the CGCSet (Table 2). In later computation, OMIMSet and CGCSet were combined into a KnownSet of 37 genes.

Performance evaluation against realistic data noise

where A is the number of genes in the KnownSet, B is the number of genes ranked within top k.

One F-score was computed for each fold, averaging five F-scores (for five-fold cross validation) produced the final F-score.

Performance evaluation against completely random noise

Random genes were first sampled from the PPI network and added to the KnownSet. Procedure in Figure 1 and random walk computation were then performed. Figure 5 plotted the ratio of random genes to the number of genes in KnownSet (37) and the proportion of added random genes that ranked within top 10%.