Volume 9 Supplement 1
Ontology integration to identify protein complex in protein interaction networks
© Xu et al; licensee BioMed Central Ltd. 2011
Published: 14 October 2011
Protein complexes can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the complex connectivity of the network. The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of protein complexes detection algorithms.
We have developed novel semantic similarity method, which use Gene Ontology (GO) annotations to measure the reliability of protein-protein interactions. The protein interaction networks can be converted into a weighted graph representation by assigning the reliability values to each interaction as a weight. Following the approach of that of the previously proposed clustering algorithm IPCA which expands clusters starting from seeded vertices, we present a clustering algorithm OIIP based on the new weighted Protein-Protein interaction networks for identifying protein complexes.
The algorithm OIIP is applied to the protein interaction network of Sacchromyces cerevisiae and identifies many well known complexes. Experimental results show that the algorithm OIIP has higher F-measure and accuracy compared to other competing approaches.
In the post-genomic era, one of the most important issues is to systematically analyze and comprehensively understand the topology of biological networks and biochemical progress in cells. The current knowledge base of protein-protein interactions has been built from the heterogeneous data sources generated by high-throughput techniques [1–4].Protein complexes can help us to understand certain biological progress and to predict the functions of proteins. A wide range of graphtheoretic approaches have been employed for detecting protein complexes from protein interaction networks. However, they have been limited in accuracy due to the presence of unreliable interactions and the complex connectivity patterns of the networks. The experimental data sets are susceptible to false positives, i.e., some fraction of the putative interactions detected must be considered spurious because they cannot be confirmed to occur in vivo.
To resolve the inaccuracy resulting from false connections, other functional knowledge can be integrated into the protein interaction networks. For example, many groups [6–8] have investigated the integration of gene expression data from microarray experiments to improve protein complexes identification. However, gene expression data are also susceptible to experimental sources of bias and noise. The correlations of mRNA levels with even cognate protein expression may be modest at best. These factors limit the usefulness of microarray data for assessing the reliability of protein-protein interactions. Gene Ontology (GO)  is another useful data source to combine with the protein interaction networks. The GO is currently one of the most comprehensive and well-curated ontology databases in the bioinformatics community. It provides a collection of well-defined biological terms, called GO terms, spanning biological processes, molecular functions and cellular components. The GO has been used to facilitate the analysis of gene expression data [10–12].
In this work, we integrate protein-protein interactions with the information content in the GO annotation database and topology weights to enhance the modularization of interaction networks. An unweighted protein interaction network can be converted into a weighted graph representation by assigning a weight to each interaction . The weight of each interaction is interpreted as its reliability, i.e., the probability of the interaction being a true positive. We propose a novel method to measure the reliability of protein-protein interactions using GO annotation data and topology weights. Following the approach of that of the previously proposed clustering algorithm IPCA which expands clusters starting from seeded vertices, we present a clustering algorithm OIIP based on the new large weighted protein interaction networks.
Weights quantify the likelihood of the interaction between every pair of proteins, and they can be estimated by encoding the proteins using gene ontology (GO) consortium. “Ontology” is a specification of a conceptualization that refers to the subject of existence. GO is established by the following three criteria: (I) biological process referring to a biological objective to which the gene or gene product contributes; (II) molecular function defined as the biochemical activity of a gene product; (III) cellular component referring to the place in the cell where a gene product is active. It is very common for the same protein or proteins in the same subfamily to form protein complexes, for example, protein Ste2p and Ste3p from a complex that is among activated G protein-coupled receptors in yeast cellular mating. It is also common for proteins in heterofamilies to form protein complexes if they share a conservative motif, for example, protein Ctf19, Mcm21, and Okp1 from a heterocomplex in the budding yeast kinetochore. Complicated protein complexes may be formed by multiple proteins, some of which share same biological processes and some are from the same subfamily, for example, Dsl1p complex, involved in Golgi-ER retrograde transport, includes Dsl1p, Dsl3p, Q/t-SNARE proteins, and so forth. Thus GO consortium is considered to be a very helpful vehicle for investigating protein-protein interactions, because these three criteria reflect the attribute of gene, gene product, gene-product groups and the subcellular localization[19–21].
Semantic similarity has been used in Information Science to evaluate the similarity between two concepts in a taxonomy, and we applied it to protein-protein interactions to estimate the similarity between two proteins. Based on the previous method , we proposed our semantic similarity method. We define an annotation size of a GO term as the number of annotated proteins on the GO term. The semantic similarity between two proteins is then calculated based on the annotation size of the GO term, on which both proteins are annotated. According to the transitivity property of GO annotation, if a protein x is annotated on a GO term gi, it is also annotated on the GO terms on the path from gi to the root GO term in the GO structure. Thus, the proportion of the annotation size of a GO term to the total number of annotated proteins can quantify the specificity of the GO term. If two proteins are annotated on a more specific GO term and have more common GO terms, then they are functionally more similar.
Suppose a protein x is annotated on m different GO terms. Si(x) denotes a set of annotated proteins on the GO term gi, whose annotation includes x, where 1≤i≤m. In the same way, suppose both x and y are annotated on n different GO terms, where n≤m. Sj(x, y) denotes a set of annotated proteins on the GO term gj, whose annotation includes x and y, where 1≤j≤n. Then, the minimum size of Si(x), mini|Si(x)|, is less than or equal to minj|Sj(x, y)|.C(x,y) denotes the sets of GO terms, whose annotation includes x and y. |C(x,y)| is the number of common GO terms which x and y both have.
Smax is the maximum size of annotation among all GO terms in a DAG structure. If two proteins x and y are annotated on a more specific GO term and more common GO terms than x and z, then x is semantically more similar to y than z.
Considering the graph topology, we also involve the topology weight. For an input graph G = (V, E), we assign the topology weight of an edge [u, v] to be the number of neighbors shared by the vertices u and v. Then we assigned the sum of Ssem(u, v) and topology weight to the edge between u and v as a weight.
Weighted vertex and selecting seed
We define the weight of each vertex to be the sum of the weights of its incident edges. After all vertices are assigned weights, we also sort in non-increasing order the vertices by their weights and store them in a queue Sq (vertices of the same weight are ordered in terms of their degrees). The complexity of calculating edge weights and vertex weights is O(|V||E|), and the complexity of sorting all vertices by their weights is O(|V| log |V|).
The notion that vertex weight is a good measure for selecting seeds has been adopted by DPClus  and MCODE. Here, we also pick the highest weighted vertices as the seeds. Our procedure proceeds as follows. We pick the first vertex in the queue Sq and use it as a seed to grow a new cluster. Once the cluster is completed, all vertices in the cluster are removed from the queue Sq and we pick the first vertex remaining in the queue Sq as the seed for the next cluster. There is an important difference between this seed selection procedure and the one used in the IPCA algorithm . Our procedure computes the vertex weight for each vertex based on the weighted networks; while the IPCA algorithm computes the vertex weight based on the original networks. We feel that our approach is biologically more meaningful because a complex is not only a dense structure in the original protein network but also have biological function.
Where evk is the sum of the weights of edges between the vertex v and K, and wk is the sum of weights of edges in K. We discuss the relationship between the parameter Evk and INvK introduced in the algorithm IPCA. According to , INvK is defined as , where mvK is the number of edges between the vertex v and K, and nK is the number of vertices in K. By the expressions, our parameter Evk is similar to the parameter INvK. While our parameter considers with the biological weights, it have more biological meaning.
A cluster K is extended by adding vertices recursively from its neighbors according to the priority. The priority of a neighbor v of K is determined by the value Evk. This procedure is similar to the one proposed in IPCA , except that we do not use INvk to judge the extending. So whether a high priority vertex v is added to the cluster is determined by the Extend-judgment test below.
Only when the candidate vertex v is satisfied the conditions, can it be added to the cluster. Once the new vertex v is added to the cluster, the cluster is updated.
Before we present the results of our comparative experiments, let us first introduce the various evaluation metrics that have been used to evaluate their computational methods for complex detection. We will then present the experimental results of comparing different state-of-the-art techniques using these evaluation metrics.
Overall, there are three types of evaluation metrics used to evaluate the quality of the predicted complexes and compute the overall precision of the prediction methods.
Precision, recall and f-measure
Sensitivity, positive predictive value and accuracy
P-values (functional homogeneity)
Where a predicted complex C contains k proteins in the functional group F and the whole PPI network contains |V| proteins. The functional homogeneity of a predicted complex is the smallest p-value over all the possible functional groups. A predicted complex with a low functional homogeneity indicates it is enriched by proteins from the same function group and it is thus likely to be true protein complex. By setting a common threshold which specifies the acceptable level of statistical significance, the numbers of predicted complexes with functional homogeneity under this threshold for the various methods can then be used for evaluating their respective overall performance.
Results and discussion
The protein interaction database is downloaded from the Gavin database  and BioGrid (version yeast HC-BIOGRID-2.0.31). The protein-complex dataset CYC2008  which we used is a comprehensive catalogue of 408 manually curated heterometic protein complexes reliably backed by small-scale experiment reported. We apply the proposed algorithm OIIP to this two databases. In the following subsections, we discuss the effect of the value Tin on clustering, compare the predicted clusters with the known complexes, evaluate the significance of the predicted clusters. We will also compare the algorithm OIIP to eight competing previous methods for their performance of identifying protein complexes. Since most proteins in the same complex have same or correlative function and involve in the same biological process, we employ biological annotation information, including Go cellular component annotation , GO Molecular Function annotation  and GO Biological process annotation  to assess the predicted protein-complexes.
The effect of Tin on clustering
Figure 1(a) shows that the total number of the predicted clusters is increasing as Tin increases. However, there is a abrupt decrease at Tin = 0.5. This is probably caused by the Hub structures in the protein interaction network. When Tin = 0.5, these Hub structures are decomposed into complexes that consist of only 2 proteins. Figure 1(b) shows that the size of the biggest cluster is decreasing as Tin increases. With the increasing of Tin, the probability of neighbors added to the cluster is decreasing. Thus, the size of the predicted clusters is also decreasing.
The Precision, Recall, F-measure, sensitivity, PPV and Accuracy of the predicted complexes by OIIP using different parameters
Comparison of OIIP and other methods
Performance comparison of Identify protein complexes methods on Gavin dataset
And we count the number of clusters with p-value less than 0.01, a threshold which represents significant biological sense and compute the proportion of clusters which achieve low p-value. The proportion of clusters from various methods with low p-value is shown in Table 2. Table 2 also shows that the clusters predicted by our method have achieved highest biological significance than predicted clusters from others on all the three biological annotation datasets when T is set to 0.5. Compare to the IPCA, we have better performance in all evaluation measurements. So the ontology interaction to the PPI network is valuable to predict protein complexes.
Examples of predicted complexes
Some predicted clusters which matched with benchmark complexes
Benchmark complexes ID in CYC2008
YBR123C YOR110W YPL007C YDR362C YAL001C YGR047C
YLR208W YGL092W YDL116W YJR042W YKL057C YGL100W
YLR166C YBR102C YPR055W YIL068C YER008C YDR166C YGL233W YJL085W
YBR234C YLR370C YJR065C YDL029W YIL062C YNR035C YKL013C
YER157W YGR120C YPR105C YNL051W YML071C YGL223C YNL041C YGL005C
YHR081W YHR069C YOL021C YGR095C YGR195W YDR280W YGR158C YCR035C YDL111C YNL232W YOR001W YOL142W YOR076C
YGL048C YKL145W YHR027C YHL030W YLR421C YHR200W YDR427W YDL147W YFR052W YDL097C YPR108W YIL075C YFR004W
YPL210C YDL092W YML105C YPR088C YPL243W YDL051W YKL122C
YOR179C YDR195W YGR156W YER133W YAL043C YKL059C YPR107C YLR115W YDR301W YNL317W YKR002W YKL018W YLR277C
YMR223W YGL066W YBR081C YGR252W YDR448W YGL112C YDR145W YMR236W YDR167W YBR198C YOL148C YLR055C YPL254W YDR392W YCL010C YDR176W YHR099W YML007W
Some predicted complexes which don’t match with benchmark complexes
YOR201C YNL284C YCR046C YBL038W YDR237W YDR462W YDR296W YDR322W YNL005C YMR024W
YIL070C YNL137C YHL004W YPL013C YBR251W YDR041W YDR036C
YNL112W YDR091C YMR309C YPR041W YBR079C YDR429C YOR096W YML063W
YDR164C YOR204W YBL038W YML025C YGR220C YCR046C YNL005C YDR296W YDR237W YNL284C YDR322W YDR462W YLR439W
It is believed that identification of protein complexes is useful to explain certain biological progress and to predict functions of proteins. In this paper, we developed an algorithm OIIP to identify protein complexes based on the new large weighted protein interaction networks. Experimentally generated protein-protein interaction data includes an enormous amount of false positives. So we introduced a semantic similarity method to measure the reliability of interactions. For this measurement, we use the annotations in Gene Ontology (GO), which provides the comprehensive functional information. When we implemented the OIIP algorithm with weighted networks, the overall F-measure and accuracy of complexes is substantially improved. This result strongly appeals the necessity of integrating of functional information for the analysis of protein-protein interaction data.
The fact that biological properties are poor at the identification reveals that the higher-level structures (e.g., secondary and tertiary structure) of proteins cannot be accurately represented by the primary structure under the current coding techniques. The experimentally determined protein interaction network has not been used in the research, and a possible future research could combine the experimentally determined protein interactions with the GO estimated interactions to further improve the identification.
This work is supported by grant from the Natural Science Foundation of China (No. 60673039 and 61070098), the National High Tech Research and Development Plan of China (No. 2006AA01Z151), the Fundamental Research Funds for the Central Universities (No. DUT10JS09) and Liaoning Province Doctor Startup Fund (No. 20091015).
This article has been published as part of Proteome Science Volume 9 Supplement 1, 2011: Proceedings of the International Workshop on Computational Proteomics. The full contents of the supplement are available online at http://www.proteomesci.com/supplements/9/S1.
- Uetz P: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000,403(1):623–627.PubMed
- Ito T: A comprehensive two-hybrid analysis to explore the yeast protein interactome. PNAS 2001,98(8):4569–4574. 10.1073/pnas.061034498PubMed CentralPubMed
- Gavin AC: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002,415(1):141–147.PubMed
- Ho Y: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 2002,415(1):180–183.PubMed
- von Mering C: Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002,417(1):399–403.PubMed
- Cho YR, Hwang W, Zhang A: Identification of overlapping functional modules in protein interaction networks: information flow-based approach. Proceedings of 6th IEEE International Conference on Data Mining Workshops 2006, 147–152.
- Ideker T, Ozier O, Schwikowski B, Siegel AF: Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 2002,18(1):S233-S240. 10.1093/bioinformatics/18.suppl_1.S233PubMed
- Tornow S, Mewes HW: Functional modules by relating protein interaction networks and gene expression. Nucleic Acids Res 2003,31(21):6283–6289. 10.1093/nar/gkg838PubMed CentralPubMed
- The Gene Ontology Consortium: The Gene Ontology (GO) project in 2006. Nucleic Acids Research 2006,34(1):322–326. 10.1093/nar/gkj439
- Hvidsten TR, Lagreid A, Komorowski J: Learning rule based models of biological process from gene expression time profiles using Gene Ontology. Bioinformatics 2003,19(9):1116–1123. 10.1093/bioinformatics/btg047PubMed
- Fang Z, Yang J, Li Y, Luo Q, Liu L: Knowledge guided analysis of microarray data. Journal of Biomedical Informatics 2006,39(1):401–411.PubMed
- Doherty JM, Carmichael LK, Mills JC: GOurmet: A tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions. BMC Bioinformatics 2006,7(151):332–365.
- Barrat A, Barthelemy M, Pastor-Satorras R, Vespignani A: The architecture of complex weighted networks. PNAS 2004,101(11):3747–3752. 10.1073/pnas.0400087101PubMed CentralPubMed
- Li Min, Chen Jianer, Wang Jianxin: Modifying the DPClus algorithm for identifying protein complexes based on new topological structures. BMC Bioinformatics 2008,9(398):345–352.
- Shi C, Kaminskyj S, Caldwell S, Loewen MC: A role for a complex between activated G protein-coupled receptors in yeast cellular mating. Proc. Natl. Acad. Sci. U.S.A 2007,104(13):5395–5400. 10.1073/pnas.0608219104PubMed CentralPubMed
- Ortiz J, Stemmann O, Rank J: Lechner: A putative protein complex consisting of Ctf19, Mcm21, and Okp1 represents a missing link in the budding yeast kinetochore. Genes Dev 1999,13(9):1140–1155. 10.1101/gad.13.9.1140PubMed CentralPubMed
- Kraynack BA, Chan A, Rosenthal E, Essid M, Umansky B, Waters MG, Schmitt HD: Dsl1p, Tip20p, and the novel Dsl3(Sec39) protein are required for the stability of the Q/t-SNARE complex at the endoplasmic reticulum in yeast. Mol. Biol. Cell 2005,16(9):3963–3977. 10.1091/mbc.E05-01-0056PubMed CentralPubMed
- Chou KC, Cai YD: Predicting Protein-Protein Interactions from Sequences in a Hybridization Space. Proteome Res 2006,5(1):316–322.
- Ashburner M: Gene Ontology: tool for the unification of biology. Nat. Genet 2000,25(1):25–29. 10.1038/75556PubMed CentralPubMed
- Chou JJ, Li H, Salvessen GS, Yuan J, Wagner G: Solution structure of BID, an intracellular amplifier of apoptotic signalling. Cell 1999,96(1):615–624.PubMed
- Oxenoid K, Chou JJ: The structure of phospholamban pentamer reveals a channel-like architecture in membranes. Proc. Natl. Acad. Sci., U.S.A 2005,102(1):10870–10875. 10.1073/pnas.0504920102PubMed CentralPubMed
- Resnik P: Using information content to evaluate semantic similarity in a taxonomy. The Proc. of 14th International Joint Conference on Artificial Intelligence 1995, 448–453.
- Cho Y-R, Hwang W, Ranmanathan M, Zhang A: Semantic integration to identify overlapping functional modules in protein interaction networks. BMC Bioinformatics 2007,265(8):147–160.
- Bader G, Hogue C: An Automated Method for Finding Molecular Complexes in Large Protein Interaction Networks. BMC Bioinformatics 2003,4(2):455–470.
- Chua HN, Ning K, Sung WK, Leong HW, Wong L: Using indirect protein-protein interactions for protein complex prediction. CSB 2007,2(1):97–109.
- Geva G, Sharan R: Identification of Protein Complexes from Co-immunoprecipitation Data. Bioinformatics 2009,74(3):1223–1146.
- Wu M, Li XL, Kwoh CK, Ng SK: A Core-Attachment based Method to Detect Protein Complexes in PPI Networks. BMC Bioinformatics 2009,10(169):122–142.
- Brohee S, van Helden J: Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 2006,7(1):488–502. 10.1186/1471-2105-7-488PubMed CentralPubMed
- Friedel CC, Krumsiek J, Zimmer R: Boostrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. RECOMB 2008,1(1):3–16.
- Bu D, Zhao Y, Cai L, Xue H, Zhu X, Lu H, Zhang J, Sun S, Ling L, Zhang N, Li G, Chen R: Topological structure analysis of the protein-protein interaction network in budding yeast. Nucleic Acids Res 2003,31(9):2443–2450. 10.1093/nar/gkg340PubMed CentralPubMed
- Gavin AC, Aloy P, Grandi P: Proteome survey reveals modularity of the yeast cell machinery. Nature 2006,440(1):631–636.PubMed
- Adamcsek B, Palla G, Farkas I, Derenyi I, Vicsek T: CFinder: locating cliques and overlapping modules in biological networks. Bioinformatics 2006,22(8):1021–1043. 10.1093/bioinformatics/btl039PubMed
- King A, Przulj N, Jurisica I: Protein Complex Prediction via Cost-based Clustering. Bioinformatics 2004,20(1):3013–3020. 10.1093/bioinformatics/bth351PubMed
- Pereira-Leal JB, Enright AJ, Ouzounis CA: Detection of functional modules from protein interaction networks. Protein Structure Function, and Bioinformatics 2004,54(1):49–57.
- Wu M, Li XL, Kwoh CK, Ng SK: A Core-Attachment based Method to Detect Protein Complexes in PPI Networks. BMC Bioinformatics 2009,10(1):169–181. 10.1186/1471-2105-10-169PubMed CentralPubMed
- Liu GM, Chua HN, Wong L: Complex discovery from weighted PPI networks. Bioinformatics 2009,25(15):1891–1897. 10.1093/bioinformatics/btp311PubMed
- Leung HC, Yiu SM, Xiang Q, Chin FY: Predicting Protein Complexes from PPI Data: A Core-Attachment Approach. Journal of Computational Biology 2009,16(2):133–144. 10.1089/cmb.2008.01TTPubMed
- Shuye Pu, Wong Jessica, Turner Brian: Up-to-data catalogues of yeast protein complexes. Nucleic Acids Research 2009,37(1):825–831.
- TG Consortium: The Gene Ontology Consortium: Creating the gene ontology resource: design and implementation. Genome Res 2001,11(1):1425–1433.
- Altaf-Ul-Amin M, Shinbo Y, Mihara K, Kurokawa K, Kanaya S: Development and implementation of an algorithm for detection of protein complexes in large interaction networks. BMC Bioinformatics 2006,207(3):134–163.
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