Annotation Conf. Call, February 24, 2015
Annotation Consistency Exercise
Here is a link to the paper that I've chosen for the first annotation consistency exercise/discussion:
It describes studies on C. elegans bcl-7 (http://www.wormbase.org/species/c_elegans/gene/WBGene00016192) and human BCL7B (http://www.uniprot.org/uniprot/Q9BQE9).
The main thing I'd like to focus on for the annotation exercise is what Biological Process annotations curators make, noting that, at the moment, the all-encompassing Biological Process terms might not yet exist for what is described in the paper. In particular, I'd like to discuss annotating to a process vs. regulation of a process, and the use of annotation extensions to provide more context for the BP terms.
I've included some links to entries on the anatomy terms and phenotypes described in the paper, in case they're helpful:
- Seam cells
- During larval development, seam cells divide to generate new seam cells renew as well as a number of differentiated cell types (hypodermal/epidermal cell, neuron, glia). They stop renewing once the animals reach adulthood and do not appear to reside in a stem cell-like 'niche'.
- Somatic gonad development
- Egl phenotype
- Pvl phenotype
- Burst phenotype
- Alae morphology phenotype
Note that the paper starts with gross anatomical defects and then progresses to a more detailed characterization of the phenotype. This is fairly typical.
Summary of Molecular Markers Affected in bcl-7 Mutant Animals
|Gene/Marker Name||Molecular Identity||Anatomical Expression Pattern||Result|
|scm::gfp||not known||nuclei of seam cells, all larval stages||reduced number except for early L1 larval stage|
|cdh-3::gfp||cadherin||cytoplasm of seam cells||reduced number|
|col-19::gfp||collagen||hypodermal syncytium (hyp7) and seam cells in adult stage||decreased in hyp7 (not significant), decreased in seam cells (significant)|
|des-2::gfp||nicotinic acetylcholine receptor||PVD neurons||no extra neurons|
|dat-1::gfp||dopamine transporter||PDE neurons||no extra neurons|
|egl-27::mCherry||MTA1 homolog, NODE complex||strong in intestine, weak in epidermis in L4 larval stage||increased expression ubiquitously, but especially in seam cells and hyp7; increased expression - qRT-PCR|
|ceh-6||POU-homeodomain transcription factor, NODE complex||not reported in this paper, but head and tail region, excretory cell, neurons, vulva - dynamic expression pattern||increased expression - qRT-PCR|
|histone H3 (anti-phospho-histone, PH3)||chromatin||mitotic germ line||decreased number of mitotic cells, further from source of proliferative signal (distal tip cells, DTCs)|
|lag-2||Notch ligand DSL (Delta, Serrate, LAG-2)||2 distal tip cells (DTCs)||loss of expression in one distal tip cell|
|wrm-1||beta-catenin||seam cells, somatic gonad precursors (SGPs, distal tip cell parents)||increased expression (not significant) - qRT-PCR|
|bar-1||beta-catenin||not discussed in this paper||increased expression (significant) - qRT-PCR|
|sys-1||beta-catenin||not discussed in this paper||increased expression (significant) - qRT-PCR|
|WRM-1::GFP||beta-catenin||anterior cortex of mother seam cell at L2; higher in posterior daughter cell||anterior daughter cells higher or equal to posterior daughter cell (50% of animals)|
|POP-1::GFP||TCF/LEF transcription factor|