![]() HumanNet (older versions for other organisms at and FunctionalNet), which provides interactive searches of a human functional gene network.Reactome), which we've seen before, links human genes according to reactions and pathways, and also calculated functional linkages from various high-throughput data.For example, can you find enolase?), the human metabolic reaction network, a review of mapping transcriptional networks by Chip-SEQ (with the current record holder in this regard probably held by ENCODE), and a review of protein interaction mapping in humans and how it is informing disease genetics. Metabolic networks: The wall chart (it's interactive.All (well, at least some) of your ortholog definition questions answered!.For example, we use EggNOG in the lab for annotating genes in new genomes/transcriptomes because the EggNOG HMM ortholog models are easily downloadable/re-run on any set of genes you happen to be interested in. The various algorithms basically have different trade-offs with regard to precision vs recall, and ease of use. Approaches with higher precision include OMA (introduced in this paper), PhylomeDB, and EggNOG. InParanoid tends towards higher recall, lower precision for finding orthologs. Note: InParanoid annotation lags a bit, so you'll need to find the Ensembl protein id, or try a text search for the common name. One good tool for discovering orthologs is InParanoid. ![]() Search among the known diseases for "Waardenburg", or enter the human genes linked to Waardenburg (Entrez gene IDs 4286, 5077, 6591, 7299) to get a feel for how this works. You can get started by rediscovering the plant model of Waardenburg syndrome. This is a fun example of the power of opportunistic data mining aka "research parasitism" in biomedical research. Phenologs and the drug discovery story we'll discuss in class.Also, note that late days can't be used for the final project Please indicate in the email if you are willing to let us post the project to the course web site. Remember: The final project web page is due by 10PM April 12, 2023, turned in as a URL emailed to the TA+Professor.Bacterial photography, and UT's 2012 iGEM entry.iGEM, and an example part ( the light sensor).Sc 2.0, as of 2017, with the computational genome design.1/2 a synthetic yeast chromosome and Build-A-Genome.A new cell from a chemically synthesized genome, SOM.Turn them in as a URL to the web site you created, sent by email to the TA AND PROFESSOR.Ī collection of further reading, if you're so inclined: Reminder: All projects are due by 10PM, April 12.TA Office hours: Wed 1 - 2 PM / Thu 12:30 - 1:30 in MBB 1.448BA or by appointment on Zoom.Office hours: Mon 4 – 5 PM on the class Zoom channel (available on Canvas). ![]() BCH394P/BCH364C Systems Biology & Bioinformatics ![]()
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