Annotation Exercise for LIA1
For this exercise, we will annotate the gene LIA1 using a published article:
Rexer CH, Chalker DL.
Lia1p, a novel protein required during nuclear differentiation for
genome-wide DNA rearrangements in Tetrahymena thermophila.
Eukaryot Cell. 2007 Aug;6(8):1320-9.
PubmedID:17586719
1. Which gene model number should receive the annotation for LIA1? Are there
any discrepancies to note between the MANATEE gene model and the published
sequence? (We can discuss if and how to note gene sequence or boundary
discrepancies, and how these should be noted in the future.)
2. Published (Standardized) name of the gene is LIA1. What are some other
names that would have been appropriate? Are any of these names more
appropriate than LIA1?
3. Write a description of the gene in 240 characters or less. Try to avoid
mentioning facts that may go stale. Note that the genome browser will be set
to show any information up to the first semicolon.
4. Gene Ontology annotations:
There are three separate Gene Ontologies: Biological Process, Molecular
Function, and Cellular Component. Identify terms from each ontology to
associate with the LIA1 gene based on the data presented in the paper. The
gene may receive more than one term from each ontology, or it may not
receive one based on this article. You can begin searching through the GO
from this website:
http://db.ciliate.org/cgi-bin/GO/go.pl?goid=8150
You can click through the ontology, or you can use the TGD Quick Search to
find terms.
Once you have chosen a term, two other things are necessary to
complete a GO annotation. The first is a publication ID (Pubmed ID), which we
already have for this paper. The other is an Evidence Code. There are a few
to choose from based on the data used to assign the term to the gene. This
complete list is from http://www.geneontology.org/GO.evidence.shtml :
Experimental Evidence Codes
- EXP: Inferred from Experiment
- IDA: Inferred from Direct Assay
- IPI: Inferred from Physical Interaction
- IMP: Inferred from Mutant Phenotype
- IGI: Inferred from Genetic Interaction
- IEP: Inferred from Expression Pattern
Computational Analysis Evidence Codes
- ISS: Inferred from Sequence or Structural Similarity
- ISO: Inferred from Sequence Orthology
- ISA: Inferred from Sequence Alignment
- ISM: Inferred from Sequence Model
- IGC: Inferred from Genomic Context
- RCA: inferred from Reviewed Computational Analysis
Author Statement Evidence Codes
- TAS: Traceable Author Statement
- NAS: Non-traceable Author Statement
Curator Statement Evidence Codes
- IC: Inferred by Curator
- ND: No biological Data available
Automatically-assigned Evidence Codes
- IEA: Inferred from Electronic Annotation
5. Think about what kind of data files you would like to show associated with
this gene – tables, gel pictures, fluorescence, etc.
6. Write a paragraph about the LIA1 gene, or edit an existing paragraph to
contain information about this gene. For example, Paragraph 5 on the
following page is about programmed DNA elimination; adding a section about
LIA1 may or may not be appropriate – your call.
https://playground.bradley.edu/wiki/index.php5/TTHERM_00046310
Be sure to include references in the paragraph where applicable. When the
TGD Wiki is fully functioning, we will be able to add links to these references
at the bottom of the page.