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In this study, we wished to elucidate how proteins encoded by human house-keeping genes and tissue-specific genes are organized in human protein-protein interaction networks. We constructed protein-protein interaction networks for different tissue types using two gene expression datasets and one protein-protein interaction database. We then calculated three network indices of topological importance, the degree, closeness, and betweenness centralities, to measure the network position of proteins encoded by house-keeping and tissue-specific genes, and quantified their local connectivity structure.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Compared to a random selection of proteins, house-keeping gene-encoded proteins tended to have a greater number of directly interacting neighbors and occupy network positions in several shortest paths of interaction between protein pairs, whereas tissue-specific gene-encoded proteins did not. In addition, house-keeping gene-encoded proteins tended to connect with other house-keeping gene-encoded proteins in all tissue types, whereas tissue-specific gene-encoded proteins also tended to connect with other tissue-specific gene-encoded proteins, but only in approximately half of the tissue types examined.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>Our analysis showed that house-keeping gene-encoded proteins tend to occupy important network positions, while those encoded by tissue-specific genes do not. The biological implications of our findings were discussed and we proposed a hypothesis regarding how cells organize their protein tools in protein-protein interaction networks. Our results led us to speculate that house-keeping gene-encoded proteins might form a core in human protein-protein interaction networks, while clusters of tissue-specific gene-encoded proteins are attached to the core at more peripheral positions of the networks.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1752-0509-3-32","type":"journal-article","created":{"date-parts":[[2009,3,11]],"date-time":"2009-03-11T07:12:10Z","timestamp":1236755530000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":28,"title":["Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks"],"prefix":"10.1186","volume":"3","author":[{"given":"Wen-hsien","family":"Lin","sequence":"first","affiliation":[]},{"given":"Wei-chung","family":"Liu","sequence":"additional","affiliation":[]},{"given":"Ming-jing","family":"Hwang","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2009,3,11]]},"reference":[{"issue":"6822","key":"300_CR1","doi-asserted-by":"publisher","first-page":"860","DOI":"10.1038\/35057062","volume":"409","author":"International Human Genome Sequencing Consortium","year":"2001","unstructured":"International Human Genome Sequencing Consortium: : Initial sequencing and analysis of the human genome. 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