Evaluating Functional Annotations of Enzymes Using the Gene Ontology

Autor: Holliday, Gemma L, Davidson, Rebecca, Akiva, Eyal, Babbitt, Patricia C

Publikováno v: Methods in molecular biology (Clifton, N.J.)

The Gene Ontology (GO) (Ashburner et al., Nat Genet 25(1):25-29, 2000) is a powerful tool in the informatics arsenal of methods for evaluating annotations in a protein dataset. From identifying the nearest well annotated homologue of a protein of int

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid_dedup__::cf73e7e98ec04b3a5746bb88cecd56b0
http://europepmc.org/articles/PMC5837055

Identification of sample annotation errors in gene expression datasets

Autor: Karolina Edlund, Jan G. Hengstler, Marcus Schmidt, Miriam Lohr, Birte Hellwig, Jörg Rahnenführer, Patrick Micke, Johan Botling, Johanna Sofia Margareta Mattsson

Publikováno v: Archives of toxicology, 89(12): 2265-2272
Archives of Toxicology

The comprehensive transcriptomic analysis of clinically annotated human tissue has found widespread use in oncology, cell biology, immunology, and toxicology. In cancer research, microarray-based gene expression profiling has successfully been applie

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5462dce3a3dd2b39f4738236eef24d3f
https://doi.org/10.1007/s00204-015-1632-4

An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences

Autor: Knutson, Stacy T, Westwood, Brian M, Leuthaeuser, Janelle B, Turner, Brandon E, Nguyendac, Don, Shea, Gabrielle, Kumar, Kiran, Hayden, Julia D, Harper, Angela F, Brown, Shoshana D, Morris, John H, Ferrin, Thomas E, Babbitt, Patricia C, Fetrow, Jacquelyn S

Publikováno v: Knutson, ST; Westwood, BM; Leuthaeuser, JB; Turner, BE; Nguyendac, D; Shea, G; et al.(2017). An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences. PROTEIN SCIENCE, 26(4), 677-699. doi: 10.1002/pro.3112. UC San Francisco: Retrieved from: http://www.escholarship.org/uc/item/1gp574hh
Protein science : a publication of the Protein Society, vol 26, iss 4

Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification-amino acids that distinguish details between functional families within a superfa

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::4dd03e35f028280acb626a3ffb41f4ee
http://www.escholarship.org/uc/item/1gp574hh

DASP3: identification of protein sequences belonging to functionally relevant groups

Autor: Patricia C. Babbitt, Angela F. Harper, Thomas E. Ferrin, Janelle B. Leuthaeuser, Jacquelyn S. Fetrow, John H. Morris

Publikováno v: Leuthaeuser, JB; Morris, JH; Harper, AF; Ferrin, TE; Babbitt, PC; & Fetrow, JS. (2016). DASP3: identification of protein sequences belonging to functionally relevant groups. BMC BIOINFORMATICS, 17. doi: 10.1186/s12859-016-1295-z. UC San Francisco: Retrieved from: http://www.escholarship.org/uc/item/60r7f4qk
BMC bioinformatics, vol 17, iss 1
BMC Bioinformatics

Background Development of automatable processes for clustering proteins into functionally relevant groups is a critical hurdle as an increasing number of sequences are deposited into databases. Experimental function determination is exceptionally tim

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0decc5b785a4a1bb1ac1d899f2dc2696
http://www.escholarship.org/uc/item/60r7f4qk

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