Annotation Conf. Call, February 24, 2015: Difference between revisions
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Revision as of 17:53, 23 February 2015
Agenda
Annotation Consistency Exercise
Here is a link to the paper that I've chosen for the first annotation consistency exercise/discussion:
http://www.ncbi.nlm.nih.gov/pubmed/25569233
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'.
- http://www.wormatlas.org/hermaphrodite/seam%20cells/mainframe.htm
- http://www.wormatlas.org/hermaphrodite/seam%20cells/Images/Seamfig3leg.htm
- 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 Phenotypes Observed
Process | Phenotype - C. elegans bcl-7 | Phenotype - Human BCL7B |
---|---|---|
Apoptosis | increased expression of anti-apoptotic factor in mutant animals; no organismal changes | increased apoptosis from overexpression; increased survival with knockdown and actinomycin D treatment |
Cell Cycle | decreased number of mitotic germ cells | increased number of cells in G0/G1 phase |
Cell Differentiation | increased expression of markers associated with undifferentiated state | increased expression of markers associated with undifferentiated state |
Gene Expression | increased expression of a number of different genes - Wnt pathway, Notch pathway, apoptosis | increased expression of a number of different genes - pluripotency markers, Wnt pathway, apoptosis |
Nuclear Organization | larger nuclei, irregularly shaped | larger nuclei, irregularly shaped, multinucleate cells |
Tissue/Organ Development | epidermal defects, gonad defects | n/a |
Wnt Signaling Pathway | increased expression of beta-catenins, mis-localization of WRM-1 beta-catenin, mis-localization of POP-1 TCF/LEF | increased expression of beta-catenin, HMGA1 |
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 | high anterior seam cell daughter confers non-seam fate, low posterior seam cell daughter confers seam fate | increased in posterior seam daughter |
POP-1::GFP | TCF/LEF transcription factor | higher in Z1.p and Z4.a (proximal, P) | proximal cells equal to, or lower, than distal (D) cells |
GFP::HLH-2 | basic helix-loop-helix transcription factor | present in both distal tip cells (DTCs) | decreased expression - seen in only one or no DTCs |
ced-9 | anti-apoptosis factor | not described in paper | increased expression (significant), qRT-PCR |
Summary of Molecular Markers Affected in BCL7B Knockdown in KATOIII cells
Gene/Marker Name | Molecular Identity | Result |
---|---|---|
Nanog | homeodomain transcription factor - maintains pluripotency | increased - qRT-PCR |
Oct3/4 | POU domain transcription factor - expressed in ES cells | increased - qRT-PCR |
Sox2 | Sry-related transcription factor - marker for pluripotency | increased - qRT-PCR |
NEAT1 | lncRNA - core molecule of nuclear paraspeckles | increased - qRT-PCR |
beta-catenin | Wnt signaling pathway | increased - qRT-PCR |
HMGA1 | high mobility group protein - Wnt signaling pathway target | increased - qRT-PCR |
c-FLIP | apoptosis inhibitor | increased - qRT-PCR |
Bcl2 | apoptosis inhibitor | increased - qRT-PCR |
PTEN | lipid phosphatase - pro-apoptotic factor | no significant change - qRT-PCR |
Bax | pro-apoptotic factor | increased - qRT-PCR (not as great an increase as Bcl2) |
Annotations
Gene/Marker Name | GO term | Comment | Evidence Code | Annotation Extension | Comment | Annotation Extension | Comment | Annotation Extension | Comment |
---|---|---|---|---|---|---|---|---|---|
bcl-7 | nucleus | IDA | part_of | range of cell types were filled in, including: seam cells, hyp7, neurons, intestine, distal tip cell, germ cell, gonadal sheath cell | |||||
egl-27 | nucleus | IDA | part_of | intestine - but immunofluorescence experiment was actually performed with the egl-27 promoter only | |||||
pop-1 | nucleus | IDA | part_of | Z1 and Z4, hermaphrodite somatic gonad cell, somatic gonad precursor | |||||
wrm-1 | cell cortex | IDA | part_of | seam cell | exists_during | L2 stage (note that wiki documentation states that GO:BP is allowed value here) | |||
bcl-7 | cell differentiation | regulation of cell differentiation? new term: seam cell differentiation? | IMP | results_in_acquisition_of_features_of (results_in_differentiation_of?) | seam cell, hyp7? | happens_during | L1 stage (but text said 'except L1 stage'?) | part_of | asymmetric cell division |
bcl-7 | cell differentiation | IMP | acts_on_population_of | seam cell | |||||
bcl-7 | cell differentiation | regulation of cell differentiation? | IMP | results_in_acquisition_of_features_of (results_in_differentiation_of?) | distal tip cells, sister cells? | ||||
bcl-7 | stem cell differentiation | IMP | |||||||
bcl-7 | stem cell development | IMP | |||||||
bcl-7 | asymmetric cell division | IMP | |||||||
bcl-7 | asymmetric stem cell division | IMP | |||||||
bcl-7 | somatic stem cell maintenance | IMP | |||||||
bcl-7 | epidermis development | IMP | |||||||
bcl-7 | epidermis morphogenesis | IMP | |||||||
bcl-7 | epithelial cell development | IMP | |||||||
bcl-7 | external genitalia morphogenesis | IMP | |||||||
bcl-7 | gonad development | IMP | |||||||
bcl-7 | gonad morphogenesis | IMP | |||||||
bcl-7 | distal tip cell migration | placeholder - would prefer to have new term: 'distal tip cell differentiation' | IMP | ||||||
bcl-7 | germ cell migration | IMP | |||||||
bcl-7 | germline cell cycle switching, mitotic to meiotic cell cycle | IMP | |||||||
bcl-7 | regulation of gene expression | IMP | |||||||
bcl-7 | negative regulation of gene expression | IMP | |||||||
BCL7B | negative regulation of gene expression | IMP | |||||||
bcl-7 | regulation of RNA metabolic process | IMP | |||||||
bcl-7 | regulation of Wnt signaling pathway | IMP | |||||||
bcl-7 | negative regulation of Wnt signaling pathway | IMP | |||||||
bcl-7 | negative regulation of canonical Wnt signaling pathway | IMP | |||||||
BCL7B | negative regulation of canonical Wnt signaling pathway | IMP | |||||||
bcl-7 | cellular protein localization | IMP | |||||||
bcl-7 | asymmetric protein localization involved in cell fate determination | IMP | |||||||
wrm-1 | protein localization to nucleus | NAS | has_regulation_target | POP-1 | |||||
bcl-7 | regulation of protein localization to nucleus | IMP | |||||||
bcl-7 | nucleus organization | IMP | |||||||
bcl-7 | regulation of nucleus organization | IMP | |||||||
BCL7B | nucleus organization | IMP | |||||||
BCL7B | regulation of nucleus organization | IMP | |||||||
bcl-7 | positive regulation of apoptotic process | IMP | |||||||
BCL7B | positive regulation of apoptotic process | IMP | |||||||
bcl-7 | negative regulation of apoptotic process | IMP | |||||||
BCL7B | regulation of G1/S transition of mitotic cell cycle | IMP | |||||||
BCL7B | positive regulation of G1/S transition of mitotic cell cycle | IMP |