AninditaVarshneya BIOL368 Week 14

Database Profile

1. What database did you access? (link to the home page of the database)
   • I accessed the eggNOG database
2. What is the purpose of the database?
   • The purpose of this database is to provide orthologous groups (OGs) of proteins at different taxonomic levels, and provide functional annotations. The annotations in eggNOG were recently expanded to include Gene Ontology terms, KEGG pathways, and SMART/Pfam domains.
   • https://academic.oup.com/nar/article/44/D1/D286/2503059/eggNOG-4-5-a-hierarchical-orthology-framework-with
3. What biological information does it contain?
   • It contains information about orthologous groups and functional annotations called evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) using graph-based clustering algorithm.
   • https://academic.oup.com/nar/article/44/D1/D286/2503059/eggNOG-4-5-a-hierarchical-orthology-framework-with
4. What species are covered in the database?
   • 2031 eukaryotic and prokaryotic organisms are organisms are included in the database with an additional 1655 prokaryotes. Some key groups of species it had information on include Drosophilidae, Chordata, Fungi, Methanobacteria, and many more.
   • https://academic.oup.com/nar/article/44/D1/D286/2503059/eggNOG-4-5-a-hierarchical-orthology-framework-with
5. What biological questions can it be used to answer?
   • The data in this database could be used to analyze functional divergence of different sequences because evolutionary forces affect class of sequences differently.
   • https://academic.oup.com/nar/article/44/D1/D286/2503059/eggNOG-4-5-a-hierarchical-orthology-framework-with
6. What type (or types) of database is it (sequence, structure model organism, or specialty [what?]; primary or “meta”; curated electronically, manually [in-house], manually [community])?
   • It is a sequence database with additional information regarding annotations of that sequence, raw algs, trimmed algs, trees, and hmm. Sequences are collected from other public databases (meta). Sequences are curated manually in-house using quality controls (that they did not explicitly specify). Algs is the abbreviation that eggNOG uses to refer to alignments. HMM is an abbreviation for hidden Markov models which is a statistical model used by the database.
   • https://academic.oup.com/nar/article/44/D1/D286/2503059/eggNOG-4-5-a-hierarchical-orthology-framework-with
7. What individual or organization maintains the database?
   • The database is maintained by the Computational Biology group - EMBL, Heidelberg and the EggNOG database Team. The main researcher in the eggNOG database is Sean Powell.
   • http://eggnogdb.embl.de/#/app/home
8. What is their funding source(s)?
   • European Commission MetaCardis [FP7-HEALTH-305312]; International Human Microbiome [HEALTH-FP7-2010-261376]; LTFCOFUND2013 [PCOFUND-GA-2013-609409]; European Research Council CancerBiome project [contract number 268985]; European Molecular Biology Organization [ALTF 721-2015]; CellNetworks (Excellence Initiative of the University of Heidelberg); Novo Nordisk Foundation [NNF14CC0001]; European Molecular Biology Laboratory (EMBL)
   • https://academic.oup.com/nar/article/44/D1/D286/2503059/eggNOG-4-5-a-hierarchical-orthology-framework-with
9. Is there a license agreement or any restrictions on access to the database?
   • There is no license agreement or restrictions on access to the database. It is funded for open access via EMBL. eggNOG data is available through the Creative Commons Attribution License which means that no restrictions can occur that prevent users from using, distributing, or reproducing any data in this database, so long as the original work is cited.
   • https://academic.oup.com/nar/article/44/D1/D286/2503059/eggNOG-4-5-a-hierarchical-orthology-framework-with
   • http://eggnogdb.embl.de/#/app/downloads
10. How often is the database updated? When was the last update?
    • The database is updated every couple months to a year. The last update was for version 4.5 in October 2015. Before that, updates came out on May 2015, Dec 2013, and Nov 2011.
    • http://eggnogdb.embl.de/#/app/home
11. Are there links to other databases?
    • This database links to a couple other databases. Databases that they link to as "Featured tools" include the ETE Toolkit, iTOL, and FetchMG. Databases that they link to as EggNOG-db partners include STRING, STITCH, SMART, and SIMAP.
    • http://eggnogdb.embl.de/#/app/methods
12. Can the information be downloaded? And in what file formats?
    • For each organism, members, annotations, raw_algs, trimmed_algs, trees, and hmm data can be downloaded. All data is downloaded with a .fa file type, which is a FASTA format file type. All files come double compressed.
    • http://eggnogdb.embl.de/#/app/downloads
13. Evaluate the “user-friendliness” of the database.
    • Is the Web site well-organized?
      • The site is very well-organized. It is easy to access the sequence data from any page on the website because they have several different search menu options, including one in the top bar of the page that is there no matter which page you are on. The website also provides an opportunity to do specific sequence searches in FASTA format by copying and pasting the sequence or by uploading a compatible file. Unfortunately, multiple-sequence FASTA files are not allowed. Even though the website is easy to maneuver through, it doesn't make itself accessible to non-specialist scientists because it uses several abbreviations and acronyms throughout the website, but does not provide any documentation regarding what those abbreviations/acronyms mean. However, in defense of the database, those who are using the database for OGs must have some level of background knowledge so the database doesn't necessarily need
      • http://eggnogdb.embl.de/#/app/seqscan
      • http://eggnogdb.embl.de/#/app/methods
    • Does it have a help section or tutorial?
      • This database does provide a brief tutorial that outlines major methods that users should use to access annotations from the various programs with which the database is interacting.
      • http://eggnogdb.embl.de/#/app/methods
    • Run a sample query. Do the results make sense?
      • Running a sample query is incredibly simple. The search menu in the top bar of the page provides options for similar OGs when you start typing a query. The results from the search provide information about the number of proteins and species with that OG as well as details about which ortholog different organisms have. Clicking on the tabs underneath the results summary provides more detail. For example, selecting the taxonomic profile tab provides users with GO terms, KEGG pathways, and domains that are associated with their search. My only criticism of this feature is that the database doesn't link the GO terms and KEGG pathways to the original website so users can learn more about those terms and pathways. Users can also access functional profiles, alignment data, and phylogenetic tree data. Directly from search results, users can also choose to download particular types of data.
      • http://eggnogdb.embl.de/#/app/results#COG5028_datamenu
      • 
      • The following data is provided directly under the results summary.
      • 
      • 
      • 

Journal Club

Vocabulary

1. Mannoproteins-mannoproteins are defined as glycoproteins that contain 15 to 90% mannose by weight.
   • http://link.springer.com/chapter/10.1007%2F978-3-642-68234-6_18.
2. Trehalose biosynthesis - is a two step process in which glucose 6-phosphate plus UDP-glucose is converted to alpha,alpha-trehalose 6-phosphate by trehalose-6-phosphate synthase (TPS), and then alpha,alpha-trehalose 6-phosphate and water are converted to trehalose and phosphate by trehalose-6-phosphate phosphatase (TPP).
   • http://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=TRESYN-PWY.
3. Prototrophic: “having the nutritional requirements of the normal or wild type”
   • http://www.merriam-webster.com/dictionary/prototrophic
4. Cryostat: “an apparatus for maintaining a constant low temperature especially below 0°C”
   • http://www.merriam-webster.com/dictionary/cryostat
5. Orthologues: A homologous gene that is related to those in different organisms by descent from the DNA of a common ancestor and that may or may not have the same function.
   • http://www.thefreedictionary.com/Orthologue
6. Permeases: Any of a group of membrane-bound carriers (enzymes) that effect the transport of solute through a semipermeable membrane; this term is not typically used to describe eukaryotes.
   • http://medical-dictionary.thefreedictionary.com/permease
7. chemostat:an apparatus for growing bacterial cultures at a constant rate bycontrolling the supply of nutrient medium
   • http://www.dictionary.com/browse/chemostat
8. trehalose: trehalose was visualized as a storage molecule, aiding the release of glucose for carrying out cellular functions
   • https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2708026/\
9. Hypergeometric distribution: “a probability function f(x) that gives the probability of obtaining exactly x elements of one kind and n − x elements of another if n elements are chosen at random without replacement from a finite population containing N elements of which M are of the first kind and N − M are of the second kind and that has the form”
   • http://www.merriam-webster.com/dictionary/hypergeometric%20distribution
10. Immunoprecipitation: “precipitation resulting from interaction of specific antibody and antigen.”
    • http://medical-dictionary.thefreedictionary.com/immunoprecipitation
11. Sphingolipids: Any of a group of lipids, such as the ceramides, that yield sphingosine or its derivatives upon hydrolysis. They are major components of cell membranes and play a role in signaling and regulatory functions.
    • http://www.thefreedictionary.com/sphingolipids
12. Desaturase: An enzyme that converts an unsaturated fatty acid chain to one that includes at least one carbon-carbon double bond.
    • http://medical-dictionary.thefreedictionary.com/desaturase
13. Diurnal: recurring every day, having a daily cycle
    • http://www.merriam-webster.com/dictionary/diurnal
14. Homeoviscous: A compositional adaptation of membrane lipids that serves to maintain the correct membrane fluidity under new conditions.
    • http://www.pnas.org/content/71/2/522.full.pdf
15. Ceramidase: catalyze hydrolysis of ceramides to generate sphingosine (SPH), which is phosphorylated to form sphingosine-1-phosphate (S1P).
    • https://www.ncbi.nlm.nih.gov/pubmed/18619555
16. DEAD-box proteins: proteins that are ubiquitous in RNA-mediated processes and function by coupling cycles of ATP binding and hydrolysis to changes in affinity for single-stranded RNA.
    • https://www.ncbi.nlm.nih.gov/pubmed/21297876
17. Nitrogen Catabolite Repression: A transcription regulation process in which the presence of one nitrogen source leads to a decrease in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other nitrogen sources.
    • http://www.yeastgenome.org/go/GO:0090295/overview
18. Upregulation: An increase in the number of receptors on the surface of target cells, making the cells more sensitive to a hormone or another agent.
    • http://www.medicinenet.com/script/main/art.asp?articlekey=24470
19. Shake-flask Culture: Shake flask fermentation is nothing but the fermentation carried out in a shake flasks, in particular Erlenmeyer flask.
    • http://biotechequipments.blogspot.com/2007/07/what-is-shake-flask-fermentation.html
20. Cis-regulatory sequences: such as enhancers and promoters, control development and physiology by regulating gene expression.
    • http://www.nature.com/nrg/journal/v13/n1/full/nrg3095.html
21. Transcriptomics: the study of transcriptomes and their functions
    • http://www.nature.com/subjects/transcriptomics
22. Coordinate regulation: regulation of expression of several different genes at once
    • http://www.hyperdictionary.com/dictionary/coordinate+regulation
23. Translocation: 1. Transposition of two segments between nonhomologous chromosomes as a result of abnormal breakage and refusion of reciprocal segments. 2. Transport of a metabolite across a biomembrane.
    • http://medical-dictionary.thefreedictionary.com/translocation
24. Spargeing: is a technique which involves bubbling a chemically inert gas, such as nitrogen, argon, helium, through a liquid.
    • http://www.lindeus.com/en/processes/blanketing_inerting_sparging/index.html
25. Exogenous: developed or originating outside the organism.
    • http://medical-dictionary.thefreedictionary.com/exogenous.
26. Ergosterol: a sterol occurring mainly in yeast and forming ergocalciferol (vitamin D2) on ultraviolet irradiation or electronic bombardment.
    • http://medical-dictionary.thefreedictionary.com/ergosterol
27. Oleate: 1. A salt or ester of oleic acid. 2. A solution of an alkaloid or other basic drug in oleic acid.
    • http://medical-dictionary.thefreedictionary.com/oleate
28. DBP2: ATP-dependent RNA helicase of the DEAD-box protein family; has strong preference for dsRNA; interacts with YRA1; required for assembly of Yra1p, Nab2p and Mex67p onto mRNA and formation of nuclear mRNP; involved in mRNA decay and rRNA processing; may be involved in suppression of transcription from cryptic initiation sites
    • http://www.yeastgenome.org/locus/S000005056/overview
29. Transcriptomics: Transcriptomics is the study of the transcriptome—the complete set of RNA transcripts that are produced by the genome, under specific circumstances or in a specific cell—using high-throughput methods, such as microarray analysis.
    • http://www.nature.com/subjects/transcriptomics
30. Bonferroni Correction: The Bonferroni correction is an adjustment made to P values when several dependent or independent statistical tests are being performed simultaneously on a single data set. To perform a Bonferroni correction, divide the critical P value (α) by the number of comparisons being made.
    • http://www.aaos.org/AAOSNow/2012/Apr/research/research7/?ssopc=1

Acknowledgements

Thank you to Dr. Kam D. Dahlquist for helping me complete this assignment. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

References

• Huerta-Cepas, Jaime, et al. "eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences." Nucleic acids research (2015): gkv1248.
• EggNOG Database
• Week 14 Assignment

Other Links

User Page: Anindita Varshneya

Bioinfomatics Lab: Fall 2016

Class Page: BIOL 368-01: Bioinfomatics Laboratory, Fall 2016

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