PPT-Genome-wide Prediction of Enhancers and Their Target Genes using ENCODE data

Zhiping Weng U Mass Medical School Simons Institute UC Berkeley March 10 2016 1 The Enc yclopedia  O f  D NA  E lements Consortium Goals Catalog all functional elements in the genome. Jeroen. . Raes. , Jan O . Korbel. , Martin J . Lercher. , Christian von . Mering. and Peer Bork. Presented by Daehwan Kim. Outline. Genome size. Genome sizes of Archaea, Bacteria, and Eukaryotes. Factors affecting genome and genome sizes . Presented by:. Dan Foreman. Dan Foreman. Progress User since 1984. Author of several Progress related Publications. Progress Performance Tuning Guide. Progress Database Administration Guide. Progress VST & System Tables. BCB 660. October 20, 2011. From Carson Holt. Annotations. Automated. Ab. initio. (based on genomic sequence alone). Involves comparisons to known proteins (BLAST similarity). Sequence motifs such as start/stop . On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE. AKA:. why the ENCODE . project is full of it. by Matthew . Oberhardt. What is ENCODE?. The Human Genome project sequenced “the human genome. ”. “the human genome” that we have labeled as such doesn’t actually . exist. What we call the human genome sequence is really just a . reference. Venter et. al (2004). Presented by. Ken . Vittayarukskul. Steven S. White.. Context of the Problem . Evolutionary history is directly tied to microbial genetics. Little is known. Until recently, microbial diversity was measured by PCR amplification and sequencing of only ribosomal genes. Presented by:. Dan Foreman. Dan Foreman. Progress User since 1984. Author of several Progress related Publications. Progress Performance Tuning Guide. Progress Database Administration Guide. Progress VST & System Tables. Dan Gilchrist. National Human Genome Research Institute. October 18, 2016. The ENCODE Project. 3D Data Access Through the ENCODE Portal. The ENCODE Encyclopedia. Tools for Investigating Genetic Variants. Genome: the total number of genes in an individual.. Human Genome- approx. 20,000 genes on the 46 human chromosomes.. Human Genome Project (HGP). Ongoing effort to completely map and sequence our genome.. and . evidence-based gene finding . 12/2021. Wilson Leung. Outline. Overview of computational gene predictions. Different types of eukaryotic gene predictors. Common types of gene prediction errors. Computational gene predictions. Hardison. . Genomics 2_2. 1/7/15. 1. Y Chromosome. 3 billion bp = 3 Gb. Chr1 247 Mb. Chr12 132 Mb. Chr22 50 Mb. A human . genome (. male). The . genome. is . all the DNA. in a cell.. All the DNA on all the chromosomes. Looking . out for the genes and each other. Sridhar Hannenhalli. Department of Cell Biology and Molecular Genetics. Center for Bioinformatics and Computational Biology. UM Institute for Advance Computer Studies. [22]. The pattern of blocks was assessed to see whether theirarrangement in the ancestral genome prior to duplicationarrangement in the ancestral genome prior to duplicationequally parsimonious series . Knowing how many genes determine a phenotype (Mendelian and/or QTL analysis), and where the genes are located (linkage mapping) is a first step in understanding the genetic basis of a phenotype . A second step is determining the sequence of the gene (or genes).