{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,6]],"date-time":"2025-05-06T23:54:11Z","timestamp":1746575651174},"reference-count":50,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2010,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Identifying candidate genes in genetic networks is important for understanding regulation and biological function. Large gene expression datasets contain relevant information about genetic networks, but mining the data is not a trivial task. Algorithms that infer Bayesian networks from expression data are powerful tools for learning complex genetic networks, since they can incorporate prior knowledge and uncover higher-order dependencies among genes. However, these algorithms are computationally demanding, so novel techniques that allow targeted exploration for discovering new members of known pathways are essential.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Here we describe a Bayesian network approach that addresses a specific network within a large dataset to discover new components. Our algorithm draws individual genes from a large gene-expression repository, and ranks them as potential members of a known pathway. We apply this method to discover new components of the cAMP-dependent protein kinase (PKA) pathway, a central regulator of <jats:italic>Dictyostelium discoideum<\/jats:italic> development. The PKA network is well studied in <jats:italic>D. discoideum<\/jats:italic> but the transcriptional networks that regulate PKA activity and the transcriptional outcomes of PKA function are largely unknown. Most of the genes highly ranked by our method encode either known components of the PKA pathway or are good candidates. We tested 5 uncharacterized highly ranked genes by creating mutant strains and identified a candidate cAMP-response element-binding protein, yet undiscovered in <jats:italic>D. discoideum<\/jats:italic>, and a histidine kinase, a candidate upstream regulator of PKA activity.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>The single-gene expansion method is useful in identifying new components of known pathways. The method takes advantage of the Bayesian framework to incorporate prior biological knowledge and discovers higher-order dependencies among genes while greatly reducing the computational resources required to process high-throughput datasets.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-11-163","type":"journal-article","created":{"date-parts":[[2010,5,14]],"date-time":"2010-05-14T18:14:04Z","timestamp":1273860844000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data"],"prefix":"10.1186","volume":"11","author":[{"given":"Anup","family":"Parikh","sequence":"first","affiliation":[]},{"given":"Eryong","family":"Huang","sequence":"additional","affiliation":[]},{"given":"Christopher","family":"Dinh","sequence":"additional","affiliation":[]},{"given":"Blaz","family":"Zupan","sequence":"additional","affiliation":[]},{"given":"Adam","family":"Kuspa","sequence":"additional","affiliation":[]},{"given":"Devika","family":"Subramanian","sequence":"additional","affiliation":[]},{"given":"Gad","family":"Shaulsky","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,3,31]]},"reference":[{"issue":"8","key":"3620_CR1","doi-asserted-by":"publisher","first-page":"599","DOI":"10.1038\/35085068","volume":"2","author":"B Mayr","year":"2001","unstructured":"Mayr B, Montminy M: Transcriptional regulation by the phosphorylation-dependent factor CREB. Nat Rev Mol Cell Biol 2001, 2(8):599\u2013609. 10.1038\/35085068","journal-title":"Nat Rev Mol Cell Biol"},{"key":"3620_CR2","volume-title":"Dictyostelium discoideum. A developmental system","author":"WF Loomis","year":"1975","unstructured":"Loomis WF: Dictyostelium discoideum. A developmental system. New York: Ac. Press; 1975."},{"issue":"3","key":"3620_CR3","doi-asserted-by":"crossref","first-page":"684","DOI":"10.1128\/MMBR.62.3.684-694.1998","volume":"62","author":"WF Loomis","year":"1998","unstructured":"Loomis WF: Role of PKA in the timing of developmental events in Dictyostelium cells. Microbiol Mol Biol Rev 1998, 62(3):684\u2013694.","journal-title":"Microbiol Mol Biol Rev"},{"key":"3620_CR4","first-page":"707","volume-title":"Genetic network inference: from co-expression clustering to reverse engineering","author":"P D'Haeseleer","year":"2000","unstructured":"D'Haeseleer P, Liang S, Somogyi R: Genetic network inference: from co-expression clustering to reverse engineering. Volume 16. Oxford Univ Press; 2000:707\u2013726."},{"issue":"25","key":"3620_CR5","doi-asserted-by":"publisher","first-page":"14863","DOI":"10.1073\/pnas.95.25.14863","volume":"95","author":"MB Eisen","year":"1998","unstructured":"Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95(25):14863\u201314868. 10.1073\/pnas.95.25.14863","journal-title":"Proc Natl Acad Sci USA"},{"key":"3620_CR6","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1038\/10343","volume":"22","author":"S Tavazoie","year":"1999","unstructured":"Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM: Systematic determination of genetic network architecture. Nature genetics 1999, 22: 281\u2013285. 10.1038\/10343","journal-title":"Nature genetics"},{"issue":"2","key":"3620_CR7","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1093\/bioinformatics\/18.2.261","volume":"18","author":"I Shmulevich","year":"2002","unstructured":"Shmulevich I, Dougherty ER, Kim S, Zhang W: Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 2002, 18(2):261\u2013274. 10.1093\/bioinformatics\/18.2.261","journal-title":"Bioinformatics"},{"issue":"4","key":"3620_CR8","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1038\/ng1532","volume":"37","author":"K Basso","year":"2005","unstructured":"Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A: Reverse engineering of regulatory networks in human B cells. Nat Genet 2005, 37(4):382\u2013390. 10.1038\/ng1532","journal-title":"Nat Genet"},{"issue":"1","key":"3620_CR9","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1038\/msb4100120","volume":"3","author":"M Bansal","year":"2007","unstructured":"Bansal M, Belcastro V, Ambesi-Impiombato A, di Bernardo D: How to infer gene networks from expression profiles. Molecular Systems Biology 2007, 3(1):78.","journal-title":"Molecular Systems Biology"},{"issue":"5659","key":"3620_CR10","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1126\/science.1094068","volume":"303","author":"N Friedman","year":"2004","unstructured":"Friedman N: Inferring cellular networks using probabilistic graphical models. Science 2004, 303(5659):799\u2013805. 10.1126\/science.1094068","journal-title":"Science"},{"key":"3620_CR11","volume-title":"Learning in Graphical Models","author":"D Heckerman","year":"1999","unstructured":"Heckerman D: A Tutorial on Learning with Bayesian Networks. In Learning in Graphical Models. Edited by: Jordan M. Cambridge, MA,: MIT Press; 1999."},{"issue":"5721","key":"3620_CR12","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1126\/science.1105809","volume":"308","author":"K Sachs","year":"2005","unstructured":"Sachs K, Perez O, Pe'er D, Lauffenburger DA, Nolan GP: Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data. Science 2005, 308(5721):523\u2013529. 10.1126\/science.1105809","journal-title":"Science"},{"key":"3620_CR13","volume-title":"Proceedings of the 23nd Annual Conference on Uncertainty in Artificial Intelligence (UAI-07): 2007","author":"D Eaton","year":"2007","unstructured":"Eaton D, Murphy K: Bayesian structure learning using dynamic programming and MCMC. Proceedings of the 23nd Annual Conference on Uncertainty in Artificial Intelligence (UAI-07): 2007 2007."},{"key":"3620_CR14","volume-title":"1999: Citeseer","author":"N Friedman","year":"1999","unstructured":"Friedman N, Nachman I, Pe\u00eder D: Learning Bayesian network structure from massive datasets: The \u00ecsparse candidate\u00ee algorithm. 1999: Citeseer 1999."},{"key":"3620_CR15","doi-asserted-by":"crossref","first-page":"1543","DOI":"10.1242\/dev.129.7.1543","volume":"129","author":"N Van Driessche","year":"2002","unstructured":"Van Driessche N, Shaw C, Katoh M, Morio T, Sucgang R, Ibarra M, Kuwayama H, Saito T, Urushihara H, Maeda M: A transcriptional profile of multicellular development in Dictyostelium discoideum. Development 2002, 129: 1543\u20131552.","journal-title":"Development"},{"issue":"9","key":"3620_CR16","doi-asserted-by":"publisher","first-page":"2067","DOI":"10.1093\/bioinformatics\/bti270","volume":"21","author":"GK Smyth","year":"2005","unstructured":"Smyth GK, Michaud J, Scott HS: Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 2005, 21(9):2067\u20132075. 10.1093\/bioinformatics\/bti270","journal-title":"Bioinformatics"},{"issue":"4","key":"3620_CR17","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/30.4.e15","volume":"30","author":"YH Yang","year":"2002","unstructured":"Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30(4):e15. 10.1093\/nar\/30.4.e15","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"3620_CR18","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1016\/S1046-2023(03)00155-5","volume":"31","author":"GK Smyth","year":"2003","unstructured":"Smyth GK, Speed T: Normalization of cDNA microarray data. Methods 2003, 31(4):265\u2013273. 10.1016\/S1046-2023(03)00155-5","journal-title":"Methods"},{"issue":"3-4","key":"3620_CR19","doi-asserted-by":"publisher","first-page":"601","DOI":"10.1089\/106652700750050961","volume":"7","author":"N Friedman","year":"2000","unstructured":"Friedman N, Linial M, Nachman I, Pe'er D: Using Bayesian networks to analyze expression data. J Comput Biol 2000, 7(3\u20134):601\u2013620. 10.1089\/106652700750050961","journal-title":"J Comput Biol"},{"key":"3620_CR20","first-page":"2001","volume":"33","author":"KP Murphy","year":"2001","unstructured":"Murphy KP: The Bayes Net Toolbox for Matlab. Computing Science and Statistics 2001, 33: 2001.","journal-title":"Computing Science and Statistics"},{"issue":"3","key":"3620_CR21","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1242\/dev.00939","volume":"131","author":"CR Thompson","year":"2004","unstructured":"Thompson CR, Fu Q, Buhay C, Kay RR, Shaulsky G: A bZIP\/bRLZ transcription factor required for DIF signaling in Dictyostelium. Development 2004, 131(3):513\u2013523. 10.1242\/dev.00939","journal-title":"Development"},{"issue":"24","key":"3620_CR22","doi-asserted-by":"publisher","first-page":"4371","DOI":"10.1093\/bioinformatics\/bti726","volume":"21","author":"EO Booth","year":"2005","unstructured":"Booth EO, Van Driessche N, Zhuchenko O, Kuspa A, Shaulsky G: Microarray phenotyping in Dictyostelium reveals a regulon of chemotaxis genes. Bioinformatics 2005, 21(24):4371\u20134377. 10.1093\/bioinformatics\/bti726","journal-title":"Bioinformatics"},{"issue":"13","key":"3620_CR23","doi-asserted-by":"publisher","first-page":"2953","DOI":"10.1242\/dev.00523","volume":"130","author":"JR Good","year":"2003","unstructured":"Good JR, Cabral M, Sharma S, Yang J, Van Driessche N, Shaw CA, Shaulsky G, Kuspa A: TagA, a putative serine protease\/ABC transporter of Dictyostelium that is required for cell fate determination at the onset of development. Development 2003, 130(13):2953\u20132965. 10.1242\/dev.00523","journal-title":"Development"},{"issue":"18","key":"3620_CR24","doi-asserted-by":"publisher","first-page":"7005","DOI":"10.1073\/pnas.0306983101","volume":"101","author":"M Katoh","year":"2004","unstructured":"Katoh M, Shaw C, Xu Q, Van Driessche N, Morio T, Kuwayama H, Obara S, Urushihara H, Tanaka Y, Shaulsky G: An orderly retreat: Dedifferentiation is a regulated process. Proc Natl Acad Sci USA 2004, 101(18):7005\u20137010. 10.1073\/pnas.0306983101","journal-title":"Proc Natl Acad Sci USA"},{"issue":"2","key":"3620_CR25","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1016\/j.ydbio.2003.08.025","volume":"264","author":"K Kibler","year":"2003","unstructured":"Kibler K, Svetz J, Nguyen TL, Shaw C, Shaulsky G: A cell-adhesion pathway regulates intercellular communication during Dictyostelium development. Dev Biol 2003, 264(2):506\u2013521. 10.1016\/j.ydbio.2003.08.025","journal-title":"Dev Biol"},{"issue":"39","key":"3620_CR26","doi-asserted-by":"publisher","first-page":"15406","DOI":"10.1073\/pnas.0705996104","volume":"104","author":"N Van Driessche","year":"2007","unstructured":"Van Driessche N, Alexander H, Min J, Kuspa A, Alexander S, Shaulsky G: Global transcriptional responses to cisplatin in Dictyostelium discoideum identify potential drug targets. Proc Natl Acad Sci USA 2007, 104(39):15406\u201315411. 10.1073\/pnas.0705996104","journal-title":"Proc Natl Acad Sci USA"},{"key":"3620_CR27","doi-asserted-by":"publisher","first-page":"471","DOI":"10.1038\/ng1545","volume":"37","author":"N Van Driessche","year":"2005","unstructured":"Van Driessche N, Demsar J, Booth EO, Hill P, Juvan P, Zupan B, Kuspa A, Shaulsky G: Epistasis analysis with global transcriptional phenotypes. Nature Genetics 2005, 37: 471\u2013477. 10.1038\/ng1545","journal-title":"Nature Genetics"},{"issue":"5","key":"3620_CR28","doi-asserted-by":"publisher","first-page":"1101","DOI":"10.1128\/EC.3.5.1101-1110.2004","volume":"3","author":"Q Xu","year":"2004","unstructured":"Xu Q, Ibarra M, Mahadeos D, Shaw C, Huang E, Kuspa A, Cotter D, Shaulsky G: Transcriptional Transitions during Dictyostelium Spore Germination. Eukaryotic Cell 2004, 3(5):1101\u20131110. 10.1128\/EC.3.5.1101-1110.2004","journal-title":"Eukaryotic Cell"},{"issue":"4","key":"3620_CR29","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1111\/j.1550-7408.2000.tb00058.x","volume":"47","author":"R Sucgang","year":"2000","unstructured":"Sucgang R, Shaulsky G, Kuspa A: Toward the functional analysis of the Dictyostelium discoideum genome. J Eukaryot Microbiol 2000, 47(4):334\u2013339. 10.1111\/j.1550-7408.2000.tb00058.x","journal-title":"J Eukaryot Microbiol"},{"issue":"7038","key":"3620_CR30","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1038\/nature03481","volume":"435","author":"L Eichinger","year":"2005","unstructured":"Eichinger L, Pachebat JA, Glockner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, Hemphill L, Bason N, Farbrother P, Desany B, Just E, Morio T, Rost R, Churcher C, Cooper J, Haydock S, van Driessche N, Cronin A, Goodhead I, Muzny D, Mourier T, Pain A, Lu M, Harper D, Lindsay R, Hauser H, James K, Quiles M, Madan Babu M, Saito T, Buchrieser C, Wardroper A, Felder M, Thangavelu M, Johnson D, Knights A, Loulseged H, Mungall K, Oliver K, Price C, Quail MA, Urushihara H, Hernandez J, Rabbinowitsch E, Steffen D, Sanders M, Ma J, Kohara Y, Sharp S, Simmonds M, Spiegler S, Tivey A, Sugano S, White B, Walker D, Woodward J, Winckler T, Tanaka Y, Shaulsky G, Schleicher M, Weinstock G, Rosenthal A, Cox EC, Chisholm RL, Gibbs R, Loomis WF, Platzer M, Kay RR, Williams J, Dear PH, Noegel AA, Barrell B, Kuspa A: The genome of the social amoeba Dictyostelium discoideum. Nature 2005, 435(7038):43\u201357. 10.1038\/nature03481","journal-title":"Nature"},{"key":"3620_CR31","doi-asserted-by":"publisher","first-page":"30859","DOI":"10.1074\/jbc.273.47.30859","volume":"273","author":"HJ Kim","year":"1998","unstructured":"Kim HJ, Chang WT, Meima M, Gross JD, Schaap P: A novel adenylyl cyclase detected in rapidly developing mutants of Dictyostelium. J Biol Chem 1998, 273: 30859\u201330862. 10.1074\/jbc.273.47.30859","journal-title":"J Biol Chem"},{"issue":"26","key":"3620_CR32","doi-asserted-by":"publisher","first-page":"15260","DOI":"10.1073\/pnas.93.26.15260","volume":"93","author":"G Shaulsky","year":"1996","unstructured":"Shaulsky G, Escalante R, Loomis WF: Developmental signal transduction pathways uncovered by genetic suppressors. Proc Natl Acad Sci USA 1996, 93(26):15260\u201315265. 10.1073\/pnas.93.26.15260","journal-title":"Proc Natl Acad Sci USA"},{"issue":"8","key":"3620_CR33","doi-asserted-by":"publisher","first-page":"1241","DOI":"10.1093\/bioinformatics\/bth074","volume":"20","author":"RF Hashimoto","year":"2004","unstructured":"Hashimoto RF, Kim S, Shmulevich I, Zhang W, Bittner ML, Dougherty ER: Growing genetic regulatory networks from seed genes. Bioinformatics 2004, 20(8):1241\u20131247. 10.1093\/bioinformatics\/bth074","journal-title":"Bioinformatics"},{"issue":"90002","key":"3620_CR34","doi-asserted-by":"publisher","first-page":"ii224","DOI":"10.1093\/bioinformatics\/bti1137","volume":"21","author":"JM Pena","year":"2005","unstructured":"Pena JM, Bjorkegren J, Tegner J: Growing Bayesian network models of gene networks from seed genes. Bioinformatics 2005, 21(90002):ii224-ii229. 10.1093\/bioinformatics\/bti1137","journal-title":"Bioinformatics"},{"key":"3620_CR35","first-page":"104","volume":"2","author":"S Imoto","year":"2003","unstructured":"Imoto S, Higuchi T, Goto T, Tashiro K, Kuhara S, Miyano S: Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks. Proc IEEE Comput Soc Bioinform Conf 2003, 2: 104\u2013113.","journal-title":"Proc IEEE Comput Soc Bioinform Conf"},{"issue":"Suppl 2","key":"3620_CR36","doi-asserted-by":"publisher","first-page":"ii227","DOI":"10.1093\/bioinformatics\/btg1082","volume":"19","author":"Y Tamada","year":"2003","unstructured":"Tamada Y, Kim S, Bannai H, Imoto S, Tashiro K, Kuhara S, Miyano S: Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. Bioinformatics 2003, 19(Suppl 2):ii227\u2013236.","journal-title":"Bioinformatics"},{"key":"3620_CR37","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1006\/dbio.2002.0715","volume":"248","author":"N Zhang","year":"2002","unstructured":"Zhang N, Long Y, Devreotes PN: EgeA, a novel C2 domain containing protein, is essential for GPCR-mediated gene expression in Dictyostelium. Dev Biol 2002, 248: 1\u201312. 10.1006\/dbio.2002.0715","journal-title":"Dev Biol"},{"issue":"8","key":"3620_CR38","doi-asserted-by":"publisher","first-page":"1480","DOI":"10.1093\/molbev\/msl022","volume":"23","author":"CD Deppmann","year":"2006","unstructured":"Deppmann CD, Alvania RS, Taparowsky EJ: Cross-species annotation of basic leucine zipper factor interactions: Insight into the evolution of closed interaction networks. Mol Biol Evol 2006, 23(8):1480\u20131492. 10.1093\/molbev\/msl022","journal-title":"Mol Biol Evol"},{"issue":"2","key":"3620_CR39","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1006\/dbio.1996.8499","volume":"183","author":"SK Mann","year":"1997","unstructured":"Mann SK, Brown JM, Briscoe C, Parent C, Pitt G, Devreotes PN, Firtel RA: Role of cAMP-dependent protein kinase in controlling aggregation and postaggregative development in Dictyostelium. Dev Biol 1997, 183(2):208\u2013221. 10.1006\/dbio.1996.8499","journal-title":"Dev Biol"},{"issue":"2","key":"3620_CR40","doi-asserted-by":"publisher","first-page":"358","DOI":"10.1016\/j.ydbio.2006.01.010","volume":"292","author":"PA Thomason","year":"2006","unstructured":"Thomason PA, Sawai S, Stock JB, Cox EC: The histidine kinase homologue DhkK\/Sombrero controls morphogenesis in Dictyostelium. Developmental Biology 2006, 292(2):358\u2013370. 10.1016\/j.ydbio.2006.01.010","journal-title":"Developmental Biology"},{"key":"3620_CR41","doi-asserted-by":"publisher","first-page":"502","DOI":"10.1101\/gad.8.4.502","volume":"8","author":"GR Schnitzler","year":"1994","unstructured":"Schnitzler GR, Fischer WH, Firtel RA: Cloning and characterization of the G-box binding factor, an essential component of the developmental switch between early and late development in Dictyostelium. Genes Devel 1994, 8: 502\u2013514. 10.1101\/gad.8.4.502","journal-title":"Genes Devel"},{"key":"3620_CR42","doi-asserted-by":"publisher","first-page":"R144","DOI":"10.1186\/gb-2007-8-7-r144","volume":"8","author":"S Sawai","year":"2007","unstructured":"Sawai S, Guan XJ, Kuspa A, Cox EC: High-throughput analysis of spatio-temporal dynamics in Dictyostelium. Genome Biol 2007, 8: R144. 10.1186\/gb-2007-8-7-r144","journal-title":"Genome Biol"},{"issue":"2","key":"3620_CR43","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1006\/dbio.1998.9049","volume":"203","author":"CK Singleton","year":"1998","unstructured":"Singleton CK, Zinda MJ, Mykytka B, Yang P: The histidine kinase dhkC regulates the choice between migrating slugs and terminal differentiation in Dictyostelium discoideum. Developmental Biology 1998, 203(2):345\u2013357. 10.1006\/dbio.1998.9049","journal-title":"Developmental Biology"},{"issue":"2","key":"3620_CR44","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1016\/S0012-1606(03)00204-5","volume":"259","author":"K Kibler","year":"2003","unstructured":"Kibler K, Nguyen TL, Svetz J, Driessche NV, Ibarra M, Thompson C, Shaw C, Shaulsky G: A novel developmental mechanism in Dictyostelium revealed in a screen for communication mutants. Developmental Biology 2003, 259(2):193\u2013208. 10.1016\/S0012-1606(03)00204-5","journal-title":"Developmental Biology"},{"key":"3620_CR45","doi-asserted-by":"crossref","first-page":"1203","DOI":"10.1242\/dev.124.6.1203","volume":"124","author":"P Balint-Kurti","year":"1997","unstructured":"Balint-Kurti P, Ginsburg G, Rivero-Lezcano O, Kimmel AR: rZIP, a RING-leucine zipper protein that regulates cell fate determination during Dictyostelium development. Development 1997, 124: 1203\u20131213.","journal-title":"Development"},{"key":"3620_CR46","doi-asserted-by":"publisher","first-page":"1715","DOI":"10.1242\/dev.02327","volume":"133","author":"M Fukuzawa","year":"2006","unstructured":"Fukuzawa M, Zhukovskaya NV, Yamada Y, Araki T, Williams JG: Regulation of Dictyostelium prestalk-specific gene expression by a SHAQKY family MYB transcription factor. Development 2006, 133: 1715\u20131724. 10.1242\/dev.02327","journal-title":"Development"},{"key":"3620_CR47","doi-asserted-by":"crossref","first-page":"2569","DOI":"10.1242\/dev.128.13.2569","volume":"128","author":"XQ Mu","year":"2001","unstructured":"Mu XQ, Spanos SA, Shiloach J, Kimmel A: CRTF is a novel transcription factor that regulates multiple stages of Dictyostelium development. Development 2001, 128: 2569\u20132579.","journal-title":"Development"},{"key":"3620_CR48","doi-asserted-by":"crossref","first-page":"2719","DOI":"10.1242\/dev.124.14.2719","volume":"124","author":"M Fukuzawa","year":"1997","unstructured":"Fukuzawa M, Hopper N, Williams J: cudA: A Dictyostelium gene with pleiotropic effects on cellular differentiation and slug behaviour. Development 1997, 124: 2719\u20132728.","journal-title":"Development"},{"key":"3620_CR49","doi-asserted-by":"publisher","first-page":"925","DOI":"10.1016\/j.ejcb.2006.04.002","volume":"85","author":"S Mattei","year":"2006","unstructured":"Mattei S, Klein G, Satre M, Aubry L: Trafficking and developmental signaling: Alix at the crossroads. Eur J Cell Biol 2006, 85: 925\u2013936. 10.1016\/j.ejcb.2006.04.002","journal-title":"Eur J Cell Biol"},{"issue":"3","key":"3620_CR50","first-page":"281","volume":"1743","author":"CH Lee","year":"2005","unstructured":"Lee CH, Jeong SY, Kim BJ, Choi CH, Kim JS, Koo BM, Seok YJ, Yim HS, Kang SO: Dictyostelium CBP3 associates with actin cytoskeleton and is related to slug migration. BBA-Molecular Cell Research 2005, 1743(3):281\u2013290.","journal-title":"BBA-Molecular Cell Research"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-163.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T12:08:19Z","timestamp":1630498099000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-11-163"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,3,31]]},"references-count":50,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["3620"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-11-163","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,3,31]]},"assertion":[{"value":"16 November 2009","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 March 2010","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 March 2010","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"163"}}