LEADER 05902nam 22007933u 450 001 9910346695703321 005 20240613144242.0 010 $a981-4447-97-8 035 $a(CKB)3280000000002179 035 $a(EBL)1109719 035 $a(OCoLC)821772805 035 $a(SSID)ssj0001075100 035 $a(PQKBManifestationID)11959813 035 $a(PQKBTitleCode)TC0001075100 035 $a(PQKBWorkID)11213811 035 $a(PQKB)11695282 035 $a(MiAaPQ)EBC6383185 035 $a(Au-PeEL)EBL6383185 035 $a(OCoLC)1165177092 035 $a(oapen)https://directory.doabooks.org/handle/20.500.12854/42143 035 $a(EXLCZ)993280000000002179 100 $a20140421d2012|||| u|| | 101 0 $aeng 135 $aur|n|---||||| 181 $ctxt 182 $cc 183 $acr 200 10$aBiocomputing 2013 - Proceedings of the Pacific Symposium 210 $aSingapore $cWorld Scientific Publishing Company$d2012 215 $a1 online resource (471 p.) 300 $aDescription based upon print version of record. 311 $a981-4596-36-1 327 $aModeling cell heterogeneity: from single-cell variations to mixed cells populations445; Computational Challenges of Mass Phenotyping454; The Future of Genome-Based Medicine456; 0session-intro-cdr.pdf; 1cheng; 1. Introduction; 2. Methods; 2.1. Data sources and data processing; 2.2. Pair-wise similarity scores; 2.3. Method nomenclature; 2.4. AUCs and p-values; 2.5. Expression signal strength; 3. Results; 4. Discussion; 5. Acknowledgments; 2felciano; 3phatak; 4shi; 5wang; 0intro-epigenomics.pdf; 1ahn; 2luo; 3sahu; 1gabr; 2gevaert; 3kim; 1. Introduction; 2. Methods 327 $a2.1. Introduction of the Module Cover Problem2.2. Integrated Module Cover; 2.3. Two-Step Module Cover; 3. Results; 3.1. Analysis of Glioblastoma Multiforme Data from GMDI; 3.1.1. Comparison of the Module Cover approaches. 327 $aFor an association to be specific in a given module, only a few regulatory associations should have highly significant p-values while the remaining loci are expected to have insignificant p-values. Thus, we defined the specificity of a module M as the area of a cumulative histogram of association significance values. Specifically, we partitioned the range from 0 to strength (M) into 10 bins of equal sizes and defined cj to be the cumulative percentage of j-th bin. Then the specificity is defi...3.1.2. Analysis of GBM data; 3.1.3. Analysis of Ovarian Cancer Data; 4. Discussion 327 $aUncovering modules that are associated with genomic alterations in a disease is a challenging task as well as an important step to understand complex diseases. To address this challenge we introduced a novel technique - module cover - that extends the concept of set cover to network modules. We provided a mathematical formalization of the problem and developed two heuristic solutions: the Integrated Module Cover approach, which greedily selects genes to cover disease cases while simultaneousl... 327 $aIn general, the module cover approach is especially helpful in analyzing and classifying heterogeneous disease cases by exploring the way different combinations of dys-regulated of modules relate to a particular disease subcategory. Indeed, our analysis indicated that the gene set selected by module cover approach may be used for classification. Equally important, the selected module covers may help to interpret classifications that were obtained with other methods.5. Materials; 5.1 Data Treatment for Glioblastoma Multiforme Data from GMDI 327 $aDifferentially Expressed Genes: Briefly, all samples were profiled using HG-U133 Plus 2.0 arrays that were normalized at the probe level with dChip (16, 19). Among probes representing each gene, we chose the probeset with the highest mean intensity in the tumor and control samples. We determined genes that are differentially expressed in each disease case compared to the non-tumor control cases with a Z-test. For a gene g and case c, we define cover(c, g) to be 1 if nominal p-value < 0.01 and... 330 $aThe Pacific Symposium on Biocomputing (PSB) 2013 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2013 will be held on January 3 - 7, 2013 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference.PSB 2013 will bring together top researchers from the US, the Asian Pacific nations, and around the world t 606 $aBiology -- Computer simulation -- Congresses 606 $aBiology -- Mathematical models -- Congresses 606 $aBiology -- Mathematical models 606 $aBiology$2HILCC 606 $aHealth & Biological Sciences$2HILCC 606 $aBiology - General$2HILCC 610 $aProtein Interactions 610 $aMetabolomics 610 $aBiocomputing 610 $aComputational Genetics 610 $aOntology 610 $aComputational Proteomics 610 $aBioinformatics 615 4$aBiology -- Computer simulation -- Congresses. 615 4$aBiology -- Mathematical models -- Congresses. 615 4$aBiology -- Mathematical models. 615 7$aBiology 615 7$aHealth & Biological Sciences 615 7$aBiology - General 676 $a574.310724 700 $aAltman$b Russ$0903258 702 $aAltman$b Russ 712 02$aebrary, Inc 801 0$bAU-PeEL 801 1$bAU-PeEL 801 2$bAU-PeEL 906 $aBOOK 912 $a9910346695703321 996 $aBiocomputing 2013 - Proceedings of the Pacific Symposium$92019220 997 $aUNINA