Difference between revisions of "Annotation Conf. Call, February 24, 2015"

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Revision as of 08:23, 24 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:

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, Z1.p
wrm-1 cell cortex IDA part_of seam cell exists_during L2 stage (note that wiki documentation states that GO:BP is allowed value for exists_during)
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? part_of asymmetric cell division
bcl-7 stem cell development IMP
bcl-7 stem cell differentiation IMP
bcl-7 asymmetric cell division IMP occurs_in seam cell, hermaphrodite somatic gonad cell
bcl-7 asymmetric stem cell division IMP occurs_in seam cell
bcl-7 somatic stem cell maintenance IMP
bcl-7 epidermis development IMP
bcl-7 regulation of epidermis development IMP
bcl-7 epidermis morphogenesis IMP
bcl-7 epithelial cell development IMP results_in_development_of seam cell
bcl-7 external genitalia morphogenesis IMP
bcl-7 vulval development 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 multi-organism reproductive process IMP
bcl-7 germ cell migration IMP
bcl-7 germline cell cycle switching, mitotic to meiotic cell cycle IMP part_of gonad development
bcl-7 regulation of gene expression IMP
bcl-7 negative regulation of gene expression new term? negative regulation of Wnt signaling pathway by negative regulation of gene expression IMP has_regulation_target bar-1, sys-1, wrm-1 part_of negative regulation of Wnt signaling pathway
bcl-7 negative regulation of gene expression IMP has_regulation_target ced-9
BCL7B negative regulation of gene expression IMP has_regulation_target beta-catenin, HMGA1
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
BCL7B negative regulation of Wnt signaling pathway IMP
bcl-7 negative regulation of Wnt signaling pathway With/From: wrm-1 or lsy-22 (suppressor screen) IGI
bcl-7 negative regulation of Wnt signaling pathway IEP Are cell lines used for annnotation extensions?
bcl-7 negative regulation of canonical Wnt signaling pathway With/From: negative regulation of gene expression IC
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 has_input WRM-1
wrm-1 protein localization to nucleus NAS has_regulation_target POP-1
bcl-7 regulation of protein localization to nucleus IMP has_regulation_target wrm-1, pop-1 part_of asymmetric cell division
bcl-7 nucleus organization IMP
BCL7B nucleus organization IMP
bcl-7 regulation of 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 cell cycle IMP
BCL7B regulation of G1/S transition of mitotic cell cycle IMP
BCL7B positive regulation of G1/S transition of mitotic cell cycle IMP

Possible New GO Terms

  • seam cell division
  • seam cell asymmetric division
  • seam cell differentiation
  • seam cell terminal differentiation (note that 'terminal differentiation' is a related synonym of 'cell development')
  • negative regulation of Wnt signaling pathway by negative regulation of gene expression
  • negative regulation of Wnt signaling pathway by regulation of asymmetric protein localization
  • positive regulation of apoptosis by negative regulation of gene expression
  • Wnt/beta-catenin asymmetry signaling pathway (and appropriate regulation terms)

General Questions/Issues

  • When to use development vs. differentiation vs. asymmetric cell division?
  • Is regulation of expression of genes known to be involved in a process sufficient evidence for regulation of that process? What more evidence might be needed?
  • How much understanding of mechanism of action is needed for annotating to regulation of a process vs to the process?
  • How much understanding of mechanism is needed for assessing downstream effects, e.g. nucleus organization?