TY - JOUR AU - McCarroll, S. A. AU - Murphy, C. T. AU - Zou, S. AU - Pletcher, S. D. AU - Chin, C. S. AU - Jan, Y. N. AU - Kenyon, C. AU - Bargmann, C. I. AU - Li, H. PY - 2004 DA - 2004// TI - Comparing genomic expression patterns across species identifies shared transcriptional profile in aging. JO - Nat Genet VL - 36 UR - https://doi.org/10.1038/ng1291 DO - 10.1038/ng1291 ID - McCarroll2004 ER - TY - JOUR AU - Jiao, Y. AU - Ma, L. AU - Strickland, E. AU - Deng, X. W. PY - 2005 DA - 2005// TI - Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis. JO - Plant Cell VL - 17 UR - https://doi.org/10.1105/tpc.105.035840 DO - 10.1105/tpc.105.035840 ID - Jiao2005 ER - TY - JOUR AU - Bergmann, S. AU - Ihmels, J. AU - Barkai, N. PY - 2004 DA - 2004// TI - Similarities and differences in genome-wide expression data of six organisms. JO - PLoS Biol VL - 2 UR - https://doi.org/10.1371/journal.pbio.0020009 DO - 10.1371/journal.pbio.0020009 ID - Bergmann2004 ER - TY - JOUR AU - Stuart, J. M. AU - Segal, E. AU - Koller, D. AU - Kim, S. K. PY - 2003 DA - 2003// TI - A gene-coexpression network for global discovery of conserved genetic modules. JO - Science VL - 302 UR - https://doi.org/10.1126/science.1087447 DO - 10.1126/science.1087447 ID - Stuart2003 ER - TY - JOUR AU - Rifkin, S. A. AU - Kim, J. AU - White, K. P. PY - 2003 DA - 2003// TI - Evolution of gene expression in the Drosophila melanogastersubgroup. JO - Nat Genet VL - 33 UR - https://doi.org/10.1038/ng1086 DO - 10.1038/ng1086 ID - Rifkin2003 ER - TY - JOUR AU - Carroll, S. B. PY - 2000 DA - 2000// TI - Endless forms: the evolution of gene regulation and morphological diversity. JO - Cell VL - 101 UR - https://doi.org/10.1016/S0092-8674(00)80868-5 DO - 10.1016/S0092-8674(00)80868-5 ID - Carroll2000 ER - TY - JOUR AU - Sparrow, D. B. AU - Cai, C. AU - Kotecha, S. AU - Latinkic, B. AU - Cooper, B. AU - Towers, N. AU - Evans, S. M. AU - Mohun, T. J. PY - 2000 DA - 2000// TI - Regulation of the tinman homologues in Xenopus embryos. JO - Dev Biol VL - 227 UR - https://doi.org/10.1006/dbio.2000.9891 DO - 10.1006/dbio.2000.9891 ID - Sparrow2000 ER - TY - BOOK AU - Wolpert, L. AU - Beddington, R. AU - Jessell, T. AU - Lawrence, P. AU - Meyerowitz, E. AU - Smith, J. PY - 2002 DA - 2002// TI - Principles of Development PB - Oxford University Press CY - Oxford ID - Wolpert2002 ER - TY - JOUR AU - Wang, Z. AU - Gerstein, M. AU - Snyder, M. PY - 2009 DA - 2009// TI - RNA-Seq: a revolutionary tool for transcriptomics. JO - Nat Rev Genet VL - 10 UR - https://doi.org/10.1038/nrg2484 DO - 10.1038/nrg2484 ID - Wang2009 ER - TY - JOUR AU - Song, J. AU - Xu, Q. AU - Olsen, R. AU - Loomis, W. AU - Shaulsky, G. AU - Kuspa, A. AU - Sucgang, R. PY - 2005 DA - 2005// TI - Comparing the Dictyostelium and Entamoebagenomes reveals an ancient split in the Conosa lineage. JO - PLoS Comput Biol VL - 1 UR - https://doi.org/10.1371/journal.pcbi.0010071 DO - 10.1371/journal.pcbi.0010071 ID - Song2005 ER - TY - JOUR AU - Raper, K. B. AU - Thom, C. PY - 1941 DA - 1941// TI - Interspecific Mixtures in the Dictyosteliaceae. JO - American Journal of Botany VL - 28 UR - https://doi.org/10.2307/2437063 DO - 10.2307/2437063 ID - Raper1941 ER - TY - BOOK AU - Kessin, R. H. PY - 2001 DA - 2001// TI - Dictyostelium - Evolution, cell biology, and the development of multicellularity PB - Cambridge Univ. Press CY - Cambridge, UK UR - https://doi.org/10.1017/CBO9780511525315 DO - 10.1017/CBO9780511525315 ID - Kessin2001 ER - TY - STD TI - Supplementary Material. [http://dictygenome.bcm.tmc.edu/~anup/RNAseq/] UR - http://dictygenome.bcm.tmc.edu/~anup/RNAseq/ ID - ref13 ER - TY - JOUR AU - Hughes, T. R. AU - Marton, M. J. AU - Jones, A. R. AU - Roberts, C. J. AU - Stoughton, R. AU - Armour, C. D. AU - Bennett, H. A. AU - Coffey, E. AU - Dai, H. AU - He, Y. D. AU - Kidd, M. J. AU - King, A. M. AU - Meyer, M. R. AU - Slade, D. AU - Lum, P. Y. AU - Stepaniants, S. B. AU - Shoemaker, D. D. AU - Gachotte, D. AU - Chakraburtty, K. AU - Simon, J. AU - Bard, M. AU - Friend, S. H. PY - 2000 DA - 2000// TI - Functional discovery via a compendium of expression profiles. JO - Cell VL - 102 UR - https://doi.org/10.1016/S0092-8674(00)00015-5 DO - 10.1016/S0092-8674(00)00015-5 ID - Hughes2000 ER - TY - JOUR AU - Rot, G. AU - Parikh, A. AU - Curk, T. AU - Kuspa, A. AU - Shaulsky, G. AU - Zupan, B. PY - 2009 DA - 2009// TI - dictyExpress: a Dictyostelium discoideumgene expression database with an explorative data analysis web-based interface. JO - BMC Bioinformatics VL - 10 UR - https://doi.org/10.1186/1471-2105-10-265 DO - 10.1186/1471-2105-10-265 ID - Rot2009 ER - TY - STD TI - dictyExpress. [http://www.ailab.si/dictyexpress/] UR - http://www.ailab.si/dictyexpress/ ID - ref16 ER - TY - JOUR AU - Booth, E. O. AU - Van Driessche, N. AU - Zhuchenko, O. AU - Kuspa, A. AU - Shaulsky, G. PY - 2005 DA - 2005// TI - Microarray phenotyping in Dictyosteliumreveals a regulon of chemotaxis genes. JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti726 DO - 10.1093/bioinformatics/bti726 ID - Booth2005 ER - TY - BOOK AU - Loomis, W. F. PY - 1975 DA - 1975// TI - Dictyostelium discoideum. A Developmental System PB - Academic Press CY - New York ID - Loomis1975 ER - TY - JOUR AU - Jordan, I. K. AU - Marino-Ramirez, L. AU - Koonin, E. V. PY - 2005 DA - 2005// TI - Evolutionary significance of gene expression divergence. JO - Gene VL - 345 UR - https://doi.org/10.1016/j.gene.2004.11.034 DO - 10.1016/j.gene.2004.11.034 ID - Jordan2005 ER - TY - JOUR AU - Khaitovich, P. AU - Hellmann, I. AU - Enard, W. AU - Nowick, K. AU - Leinweber, M. AU - Franz, H. AU - Weiss, G. AU - Lachmann, M. AU - Paabo, S. PY - 2005 DA - 2005// TI - Parallel Patterns of Evolution in the Genomes and Transcriptomes of Humans and Chimpanzees. JO - Science VL - 309 UR - https://doi.org/10.1126/science.1108296 DO - 10.1126/science.1108296 ID - Khaitovich2005 ER - TY - JOUR AU - Yanai, I. AU - Graur, D. AU - Ophir, R. PY - 2004 DA - 2004// TI - Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control. JO - OMICS VL - 8 UR - https://doi.org/10.1089/153623104773547462 DO - 10.1089/153623104773547462 ID - Yanai2004 ER - TY - JOUR AU - Mortazavi, A. AU - Williams, B. A. AU - McCue, K. AU - Schaeffer, L. AU - Wold, B. PY - 2008 DA - 2008// TI - Mapping and quantifying mammalian transcriptomes by RNA-Seq. JO - Nat Methods VL - 5 UR - https://doi.org/10.1038/nmeth.1226 DO - 10.1038/nmeth.1226 ID - Mortazavi2008 ER - TY - JOUR AU - Nagalakshmi, U. AU - Wang, Z. AU - Waern, K. AU - Shou, C. AU - Raha, D. AU - Gerstein, M. AU - Snyder, M. PY - 2008 DA - 2008// TI - The transcriptional landscape of the yeast genome defined by RNA sequencing. JO - Science VL - 320 UR - https://doi.org/10.1126/science.1158441 DO - 10.1126/science.1158441 ID - Nagalakshmi2008 ER - TY - JOUR AU - Biswas, M. AU - O'Rourke, J. F. AU - Camon, E. AU - Fraser, G. AU - Kanapin, A. AU - Karavidopoulou, Y. AU - Kersey, P. AU - Kriventseva, E. AU - Mittard, V. AU - Mulder, N. AU - Phan, I. AU - Servant, F. AU - Apweiler, R. PY - 2002 DA - 2002// TI - Applications of InterPro in protein annotation and genome analysis. JO - Brief Bioinform VL - 3 UR - https://doi.org/10.1093/bib/3.3.285 DO - 10.1093/bib/3.3.285 ID - Biswas2002 ER - TY - JOUR AU - Drummond, D. A. AU - Bloom, J. D. AU - Adami, C. AU - Wilke, C. O. AU - Arnold, F. H. PY - 2005 DA - 2005// TI - Why highly expressed proteins evolve slowly. JO - Proc Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0504070102 DO - 10.1073/pnas.0504070102 ID - Drummond2005 ER - TY - JOUR AU - Maeda, M. AU - Sakamoto, H. AU - Iranfar, N. AU - Fuller, D. AU - Maruo, T. AU - Ogihara, S. AU - Morio, T. AU - Urushihara, H. AU - Tanaka, Y. AU - Loomis, W. F. PY - 2003 DA - 2003// TI - Changing patterns of gene expression in dictyostelium prestalk cell subtypes recognized by in situ hybridization with genes from microarray analyses. JO - Eukaryot Cell VL - 2 UR - https://doi.org/10.1128/EC.2.3.627-637.2003 DO - 10.1128/EC.2.3.627-637.2003 ID - Maeda2003 ER - TY - JOUR AU - King, M. AU - Wilson, A. PY - 1975 DA - 1975// TI - Evolution at Two Levels Humans and Chimpanze. JO - Science VL - 188 UR - https://doi.org/10.1126/science.1090005 DO - 10.1126/science.1090005 ID - King1975 ER - TY - JOUR AU - Knecht, D. A. AU - Cohen, S. M. AU - Loomis, W. F. AU - Lodish, H. F. PY - 1986 DA - 1986// TI - Developmental regulation of Dictyostelium discoideumactin gene fusions carried on low-copy and high-copy transformation vectors. JO - Mol Cell Biol VL - 6 UR - https://doi.org/10.1128/MCB.6.11.3973 DO - 10.1128/MCB.6.11.3973 ID - Knecht1986 ER - TY - JOUR AU - Eichinger, L. AU - Pachebat, J. A. AU - Glockner, G. AU - Rajandream, M. A. AU - Sucgang, R. AU - Berriman, M. AU - Song, J. AU - Olsen, R. AU - Szafranski, K. AU - Xu, Q. AU - Tunggal, B. AU - Kummerfeld, S. AU - Madera, M. AU - Konfortov, B. A. AU - Rivero, F. AU - Bankier, A. T. AU - Lehmann, R. AU - Hamlin, N. AU - Davies, R. AU - Gaudet, P. AU - Fey, P. AU - Pilcher, K. AU - Chen, G. AU - Saunders, D. AU - Sodergren, E. AU - Davis, P. AU - Kerhornou, A. AU - Nie, X. AU - Hall, N. AU - Anjard, C. PY - 2005 DA - 2005// TI - The genome of the social amoeba Dictyostelium discoideum. JO - Nature VL - 435 UR - https://doi.org/10.1038/nature03481 DO - 10.1038/nature03481 ID - Eichinger2005 ER - TY - JOUR AU - Raper, K. B. PY - 1935 DA - 1935// TI - Dictyostelium discoideum, a new species of slime mold from decaying forest leaves. JO - J Agr Res VL - 50 ID - Raper1935 ER - TY - JOUR AU - Ostrowski, E. A. AU - Katoh, M. AU - Shaulsky, G. AU - Queller, D. C. AU - Strassmann, J. E. PY - 2008 DA - 2008// TI - Kin discrimination increases with genetic distance in a social amoeba. JO - PLoS Biol VL - 6 UR - https://doi.org/10.1371/journal.pbio.0060287 DO - 10.1371/journal.pbio.0060287 ID - Ostrowski2008 ER - TY - JOUR AU - Sussman, M. PY - 1987 DA - 1987// TI - Cultivation and synchronous morphogenesis of Dictyosteliumunder controlled experimental conditions. JO - Methods Cell Biol VL - 28 UR - https://doi.org/10.1016/S0091-679X(08)61635-0 DO - 10.1016/S0091-679X(08)61635-0 ID - Sussman1987 ER - TY - JOUR AU - Iranfar, N. AU - Fuller, D. AU - Sasik, R. AU - Hwa, T. AU - Laub, M. AU - Loomis, W. F. PY - 2001 DA - 2001// TI - Expression patterns of cell-type-specific genes in Dictyostelium. JO - Mol Biol Cell VL - 12 UR - https://doi.org/10.1091/mbc.12.9.2590 DO - 10.1091/mbc.12.9.2590 ID - Iranfar2001 ER - TY - STD TI - Novocraft. [http://www.novocraft.com/] UR - http://www.novocraft.com/ ID - ref34 ER - TY - STD TI - dictyBase. [http://dictybase.org/] UR - http://dictybase.org/ ID - ref35 ER - TY - STD TI - TBrowse. [http://dictygenome.bcm.tmc.edu/~anup/RNAseq/RNA-seq-browser/] UR - http://dictygenome.bcm.tmc.edu/~anup/RNAseq/RNA-seq-browser/ ID - ref36 ER - TY - BOOK AU - Brown, T. A. PY - 2002 DA - 2002// TI - Genomes PB - BIOS Scientific Publishers Ltd CY - Oxford, UK ID - Brown2002 ER - TY - CHAP AU - Ihaka, R. AU - Gentleman, R. PY - 1996 DA - 1996// TI - R: A language for data analysis and graphics. BT - J Comput Graphical Stat ID - Ihaka1996 ER - TY - STD TI - Cytoscape. [http://www.cytoscape.org/] UR - http://www.cytoscape.org/ ID - ref39 ER - TY - JOUR AU - Maere, S. AU - Heymans, K. AU - Kuiper, M. PY - 2005 DA - 2005// TI - BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks. JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti551 DO - 10.1093/bioinformatics/bti551 ID - Maere2005 ER - TY - STD TI - gplots: Various R programming tools for plotting data. [http://cran.r-project.org/web/packages/gplots/index.html] UR - http://cran.r-project.org/web/packages/gplots/index.html ID - ref41 ER - TY - BOOK AU - Venables, W. AU - Ripley, B. PY - 2002 DA - 2002// TI - Modern applied statistics with S UR - https://doi.org/10.1007/978-0-387-21706-2 DO - 10.1007/978-0-387-21706-2 ID - Venables2002 ER - TY - CHAP AU - Smyth, G. ED - Gentleman, R. ED - Carey, V. ED - Huber, W. ED - Irizarry, R. ED - Dudoit, S. PY - 2005 DA - 2005// TI - Limma: linear models for microarray data. BT - Bioinformatics Computational Biology Solutions Using R and Bioconductor UR - https://doi.org/10.1007/0-387-29362-0_23 DO - 10.1007/0-387-29362-0_23 ID - Smyth2005 ER - TY - JOUR AU - Smyth, G. PY - 2004 DA - 2004// TI - Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. JO - Stat Appl Genet Mol Biol VL - 3 ID - Smyth2004 ER -