Harries AD, Dye C: Tuberculosis. Ann Trop Med Parasitol. 2006, 100: 415-431.
PubMed
CAS
Google Scholar
Shenoi S, Friedland G: Extensively drug-resistant tuberculosis: a new face to an old pathogen. Annu Rev Med. 2009, 60: 307-320. 10.1146/annurev.med.60.053107.103955.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kuijl C, Savage NDL, Marsman M, Tuin AW, Janssen L, Egan DA, Ketema M, van den Nieuwendijk R, van den Eeden SJF, Geluk A, Poot A, van der Marel G, Beijersbergen RL, Overkleeft H, Ottenhoff THM, Neefjes J: Intracellular bacterial growth is controlled by a kinase network around PKB/AKT1. Nature. 2007, 450: 725-730. 10.1038/nature06345.
Article
PubMed
CAS
Google Scholar
Tiwari S, Choi H-P, Matsuzawa T, Pypaert M, MacMicking JD: Targeting of the GTPase Irgm1 to the phagosomal membrane via PtdIns(3,4)P(2) and PtdIns(3,4,5)P(3) promotes immunity to mycobacteria. Nat Immunol. 2009, 10: 907-917. 10.1038/ni.1759.
Article
PubMed
CAS
PubMed Central
Google Scholar
Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Müller T: Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinforma Oxf Engl. 2008, 24: i223-i231. 10.1093/bioinformatics/btn161.
Article
CAS
Google Scholar
Suter B, Kittanakom S, Stagljar I: Two-hybrid technologies in proteomics research. Curr Opin Biotechnol. 2008, 19: 316-323. 10.1016/j.copbio.2008.06.005.
Article
PubMed
CAS
Google Scholar
Gavin A-C, Maeda K, Kühner S: Recent advances in charting protein-protein interaction: mass spectrometry-based approaches. Curr Opin Biotechnol. 2011, 22: 42-49. 10.1016/j.copbio.2010.09.007.
Article
PubMed
CAS
Google Scholar
Lee H, Deng M, Sun F, Chen T: An integrated approach to the prediction of domain-domain interactions. BMC Bioinforma. 2006, 7: 269-10.1186/1471-2105-7-269.
Article
Google Scholar
Singhal M, Resat H: A domain-based approach to predict protein-protein interactions. BMC Bioinforma. 2007, 8: 199-10.1186/1471-2105-8-199.
Article
Google Scholar
Sprinzak E, Margalit H: Correlated sequence-signatures as markers of protein-protein interaction. J Mol Biol. 2001, 311: 681-692. 10.1006/jmbi.2001.4920.
Article
PubMed
CAS
Google Scholar
Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M: Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res. 2004, 14: 1107-1118. 10.1101/gr.1774904.
Article
PubMed
CAS
PubMed Central
Google Scholar
Sanchez C, Lachaize C, Janody F, Bellon B, Roder L, Euzenat J, Rechenmann F, Jacq B: Grasping at molecular interactions and genetic networks in Drosophila melanogaster using FlyNets, an Internet database. Nucleic Acids Res. 1999, 27: 89-94. 10.1093/nar/27.1.89.
Article
PubMed
CAS
PubMed Central
Google Scholar
Brun C, Chevenet F, Martin D, Wojcik J, Guénoche A, Jacq B: Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network. Genome Biol. 2003, 5: R6-10.1186/gb-2003-5-1-r6.
Article
PubMed
PubMed Central
Google Scholar
Dutkowski J, Tiuryn J: Phylogeny-guided interaction mapping in seven eukaryotes. BMC Bioinforma. 2009, 10: 393-10.1186/1471-2105-10-393.
Article
Google Scholar
Li H, Liang S: Local network topology in human protein interaction data predicts functional association. Plos One. 2009, 4: e6410-10.1371/journal.pone.0006410.
Article
PubMed
PubMed Central
Google Scholar
Sharan R, Ulitsky I, Shamir R: Network-based prediction of protein function. Mol Syst Biol. 2007, 3: 88-
Article
PubMed
PubMed Central
Google Scholar
Tu K, Yu H, Li Y-X: Combining gene expression profiles and protein-protein interaction data to infer gene functions. J Biotechnol. 2006, 124: 475-485. 10.1016/j.jbiotec.2006.01.024.
Article
PubMed
CAS
Google Scholar
Wu Y, Lonardi S: A linear-time algorithm for predicting functional annotations from PPI networks. J Bioinform Comput Biol. 2008, 6: 1049-1065. 10.1142/S0219720008003916.
Article
PubMed
CAS
Google Scholar
Baudot A, Jacq B, Brun C: A scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network. Genome Biol. 2004, 5: R76-10.1186/gb-2004-5-10-r76.
Article
PubMed
PubMed Central
Google Scholar
Makino T, Gojobori T: Evolution of protein-protein interaction network. Genome Dyn. 2007, 3: 13-29.
Article
PubMed
CAS
Google Scholar
Makino T, Suzuki Y, Gojobori T: Differential evolutionary rates of duplicated genes in protein interaction network. Gene. 2006, 385: 57-63.
Article
PubMed
CAS
Google Scholar
Baudot A, Angelelli JB, Guénoche A, Jacq B, Brun C: Defining a modular signalling network from the fly interactome. Bmc Syst Biol. 2008, 2: 45-10.1186/1752-0509-2-45.
Article
PubMed
PubMed Central
Google Scholar
Qian X, Yoon B-J: Effective identification of conserved pathways in biological networks using hidden Markov models. PloS One. 2009, 4: e8070-10.1371/journal.pone.0008070.
Article
PubMed
PubMed Central
Google Scholar
Venkatesan K, Rual JF, Vazquez A, Stelzl U, Lemmens I, Hirozane-Kishikawa T, Hao T, Zenkner M, Xin X, Goh KI, Yildirim MA, Simonis N, Heinzmann K, Gebreab F, Sahalie JM, Cevik S, Simon C, de Smet AS, Dann E, Smolyar A, Vinayagam A, Yu H, Szeto D, Borick H, Dricot A, Klitgord N, Murray RR, Lin C, Lalowski M, Timm J, Rau K, Boone C, Braun P, Cusick ME, Roth FP, Hill DE, Tavernier J, Wanker EE, Barabási AL, Vidal M: An empirical framework for binary interactome mapping. Nat Methods. 2009, 6: 83-90. 10.1038/nmeth.1280.
Article
PubMed
CAS
PubMed Central
Google Scholar
Bossi A, Lehner B: Tissue specificity and the human protein interaction network. Mol Syst Biol. 2009, 5: 260-
Article
PubMed
PubMed Central
Google Scholar
Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska BC, Basso K, Beltrao P, Krogan N, Gautier J, Dalla-Favera R, Califano A: A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol Syst Biol. 2010, 6: 377-
Article
PubMed
PubMed Central
Google Scholar
Rachlin J, Cohen DD, Cantor C, Kasif S: Biological context networks: a mosaic view of the interactome. Mol Syst Biol. 2006, 2: 66-
Article
PubMed
PubMed Central
Google Scholar
Myers CL, Chiriac C, Troyanskaya OG: Discovering biological networks from diverse functional genomic data. Methods Mol Biol Clifton Nj. 2009, 563: 157-175. 10.1007/978-1-60761-175-2_9.
Article
Google Scholar
Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, Forsberg M, Zwahlen M, Kampf C, Wester K, Hober S, Wernerus H, Björling L, Ponten F: Towards a knowledge-based human protein atlas. Nat Biotechnol. 2010, 28: 1248-1250. 10.1038/nbt1210-1248.
Article
PubMed
CAS
Google Scholar
Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TK, Gronborg M, Ibarrola N, Deshpande N, Shanker K, Shivashankar HN, Rashmi BP, Ramya MA, Zhao Z, Chandrika KN, Padma N, Harsha HC, Yatish AJ, Kavitha MP, Menezes M, Choudhury DR, Suresh S, Ghosh N, Saravana R, Chandran S, Krishna S, Joy M, Anand SK, Madavan V, Joseph A, Wong GW, Schiemann WP, Constantinescu SN, Huang L, Khosravi-Far R, Steen H, Tewari M, Ghaffari S, Blobe GC, Dang CV, Garcia JG, Pevsner J, Jensen ON, Roepstorff P, Deshpande KS, Chinnaiyan AM, Hamosh A, Chakravarti A, Pandey A: Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 2003, 13: 2363-2371. 10.1101/gr.1680803.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kumar P, Kumar D, Parikh A, Rananaware D, Gupta M, Singh Y, Nandicoori VK: The Mycobacterium tuberculosis protein kinase K modulates activation of transcription from the promoter of mycobacterial monooxygenase operon through phosphorylation of the transcriptional regulator VirS. J Biol Chem. 2009, 284: 11090-11099. 10.1074/jbc.M808705200.
Article
PubMed
CAS
PubMed Central
Google Scholar
Lynn DJ, Winsor GL, Chan C, Richard N, Laird MR, Barsky A, Gardy JL, Roche FM, Chan THW, Shah N, Lo R, Naseer M, Que J, Yau M, Acab M, Tulpan D, Whiteside MD, Chikatamarla A, Mah B, Munzner T, Hokamp K, Hancock REW, Brinkman FSL: InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Mol Syst Biol. 2008, 4: 218-
Article
PubMed
PubMed Central
Google Scholar
Prieto C, De Las Rivas J: APID: Agile Protein Interaction DataAnalyzer. Nucleic Acids Res. 2006, 34 (Web Server issue): W298-W302.
Article
PubMed
CAS
PubMed Central
Google Scholar
Kohonen T: Self-Organizing Maps. 2000, Springer,http://www.springer.com/physics/complexity/book/978-3-540-67921-9,
Google Scholar
Souiai O, Becker E, Prieto C, Benkahla A, De las Rivas J, Brun C: Functional integrative levels in the human interactome recapitulate organ organization. PloS One. 2011, 6: e22051-10.1371/journal.pone.0022051.
Article
PubMed
CAS
PubMed Central
Google Scholar
Chaussabel D, Semnani RT, McDowell MA, Sacks D, Sher A, Nutman TB: Unique gene expression profiles of human macrophages and dendritic cells to phylogenetically distinct parasites. Blood. 2003, 102: 672-681. 10.1182/blood-2002-10-3232.
Article
PubMed
CAS
Google Scholar
Tailleux L, Waddell SJ, Pelizzola M, Mortellaro A, Withers M, Tanne A, Castagnoli PR, Gicquel B, Stoker NG, Butcher PD, Foti M, Neyrolles O: Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages. Plos One. 2008, 3: e1403-10.1371/journal.pone.0001403.
Article
PubMed
PubMed Central
Google Scholar
Lee J, Hartman M, Kornfeld H: Macrophage apoptosis in tuberculosis. Yonsei Med J. 2009, 50: 1-11. 10.3349/ymj.2009.50.1.1.
Article
PubMed
PubMed Central
Google Scholar
De Sousa AR, Penalva LO, Marcotte EM, Vogel C: Global signatures of protein and mRNA expression levels. Mol Biosyst. 2009, 5: 1512-1526.
Google Scholar
Nooren IMA, Thornton JM: Structural characterisation and functional significance of transient protein-protein interactions. J Mol Biol. 2003, 325: 991-1018. 10.1016/S0022-2836(02)01281-0.
Article
PubMed
CAS
Google Scholar
Huttenhower C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, Coller HA, Troyanskaya OG: Exploring the human genome with functional maps. Genome Res. 2009, 19: 1093-1106. 10.1101/gr.082214.108.
Article
PubMed
CAS
PubMed Central
Google Scholar
Tanay A, Sharan R, Kupiec M, Shamir R: Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proc Natl Acad Sci USA. 2004, 101: 2981-2986. 10.1073/pnas.0308661100.
Article
PubMed
CAS
PubMed Central
Google Scholar
Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R: The HUPO PSI’s molecular interaction format–a community standard for the representation of protein interaction data. Nat Biotechnol. 2004, 22: 177-183. 10.1038/nbt926.
Article
PubMed
CAS
Google Scholar
Finn RD, Marshall M, Bateman A: iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinforma Oxf Engl. 2005, 21: 410-412. 10.1093/bioinformatics/bti011.
Article
CAS
Google Scholar
Martin D, Brun C, Remy E, Mouren P, Thieffry D, Jacq B: GOToolBox: functional analysis of gene datasets based on Gene Ontology. Genome Biol. 2004, 5: R101-10.1186/gb-2004-5-12-r101.
Article
PubMed
PubMed Central
Google Scholar
Dice L: Measures of the amount of ecologic association between species. Ecology. 1945, 26: 297-302. 10.2307/1932409.
Article
Google Scholar
Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Edgar R: NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res. 2009, 37 (Database issue): D885-D890.
Article
PubMed
CAS
PubMed Central
Google Scholar
Eschrich SA, Hoerter AM: Libaffy: software for processing Affymetrix GeneChip data. Bioinforma Oxf Engl. 2007, 23: 1562-1564. 10.1093/bioinformatics/btm127.
Article
CAS
Google Scholar
Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA. 2001, 98: 5116-5121. 10.1073/pnas.091062498.
Article
PubMed
CAS
PubMed Central
Google Scholar
Huang DW, Sherman BT, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009, 4: 44-57.
Article
CAS
Google Scholar