Noctua model curation tracking table
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Jump to navigationJump to searchContributor(s) | Broad Category | Pathway | WBProcess | Noctua Model Title | Genes | GO Term(s), IDs | Module(s) | Noctua Model URL | Model Status | Annotation Issues | To Do | |
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Kimberly | Apoptosis | Execution phase | Apoptotic process involved in development - C. elegans NSM sister cell death | http://noctua.berkeleybop.org/editor/graph/gomodel:5745387b00001432 | Development | |||||||
Kimberly | Apoptosis | Cell corpse engulfment - ced-1/-6/-7 and ced-2-/5/-12 pathways | Localization - C. elegans apoptotic cell engulfment | ced-1, ced-2, ced-5, ced-6, ced-7, ced-10, ced-12, chc-1, dyn-1 | http://noctua.berkeleybop.org/editor/graph/gomodel:56aac7ad00000175 | Development | ||||||
Kimberly | Axon regeneration | Rac module; upstream of JNK-MAPK | C. elegans regulation of axon regeneration | http://noctua.berkeleybop.org/editor/graph/gomodel:591f58ab00000003 | Development | |||||||
Kimberly | Dosage Compensation | C. elegans X chromosome dosage compensation | http://noctua.berkeleybop.org/editor/graph/gomodel:59dc728000000147 | Development | ||||||||
EGF Signaling | ||||||||||||
FGF Signaling | ||||||||||||
Kimberly | Distal tip cell migration | Glycosylation | The directed migration of gonadal distal tip cells in Caenorhabditis elegans requires NGAT-1, a ß1,4-N-acetylgalactosaminyltransferase enzyme | http://noctua.berkeleybop.org/editor/graph/gomodel:5993df9e00000138 | Development | |||||||
Kimberly | Dauer | GPCR Signaling | Two chemoreceptors mediate developmental effects of dauer pheromone in C. elegans. | http://noctua.berkeleybop.org/editor/graph/gomodel:59dc728000000454 | Development | |||||||
Jae, Jane, Kimberly | Egg laying | GPCR Signaling | GRK-2 egg laying regulation JM | http://noctua.berkeleybop.org/editor/graph/gomodel:59dc728000000287 | Development | 1 | Finish up annotations for other genes in the paper | |||||
Kimberly | Innate immune response | GPCR Signaling | The DAF-16/FOXO transcription factor functions as a regulator of epidermal innate immunity. | http://noctua.berkeleybop.org/editor/graph/gomodel:5993df9e00000158 | Development | |||||||
Kimberly | Innate immune response | GPCR Signaling and MAPK signaling | C_elegans_defense_response_to_fungus | http://noctua.berkeleybop.org/editor/graph/gomodel:564622cc00000003 | Development | |||||||
Kimberly | Heterochronic pathway | Control of C. elegans larval developmental timing - the heterochronic pathway | http://noctua.berkeleybop.org/editor/graph/gomodel:59dc728000000246 | Development | ||||||||
Kimberly | Insulin Signaling | Signaling - C. elegans insulin receptor signaling | http://noctua.berkeleybop.org/editor/graph/gomodel:5667fdd400000696 | Development | ||||||||
Kimberly | Germ line stem cell maintenance | Notch Signaling | C. elegans germline stem cell maintenance - Notch pathway | Notch signaling pathway (GO:0007219), positive regulation of stem cell population maintenance (GO:1902459), positive regulation of stem cell proliferation (GO:2000648) | http://noctua.berkeleybop.org/editor/graph/gomodel:5745387b00001750 | Development | ||||||
Kimberly | Neuronal morphogenesis - AFD thermosensory neuron | Receptor guanylyl cyclase | Cellular Component Organization or Biogenesis - C. elegans Glial Control of Neuron Receptor Ending Shape | http://noctua.berkeleybop.org/editor/graph/gomodel:5716c41300000192 | Development | |||||||
Kimberly | Olfactory behavior | Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways. (PMID:27351255) | http://noctua.berkeleybop.org/editor/graph/gomodel:59237a3c00000026 | Development | ||||||||
Kimberly | Thermosensory behavior | Cyclic nucleotide-gated ion channels | C. elegans CNG-3 in non-motile cilium of AFD (same reference) | cng-3 | http://noctua.berkeleybop.org/editor/graph/gomodel:5900dc7400001096 | Development | 1) How should we annotate different evidence for CC vs tissue? 2) Annotation extensions that don't use the same evidence code should not appear in the GPAD output. 3) Add relations for positive and negative effect for causally upstream of or within. | |||||
Kimberly | Striated muscle mitochondrial patterning | Receptor tyrosine phosphatase | The secreted MSP domain of C. elegans VAPB homolog VPR-1 patterns the adult striated muscle mitochondrial reticulum via SMN-1 | http://noctua.berkeleybop.org/editor/graph/gomodel:5970219a00000566 | Development | |||||||
Kimberly | Germ line stem cell maintenance | TGFbeta Signaling | Linking the environment, DAF-7/TGFβ signaling and LAG-2/DSL ligand expression in the germline stem cell niche | http://noctua.berkeleybop.org/editor/graph/gomodel:59bee34700000074 | Development | |||||||
Kimberly | DA/DB motor neuron axon outgrowth | Wnt Signaling | The ENU-3 protein family members function in the Wnt pathway parallel to UNC-6/Netrin to promote motor neuron axon outgrowth in C. elegans. | http://noctua.berkeleybop.org/editor/graph/gomodel:598826eb00000296 | Development | |||||||
Chris | Q neuroblast descendant migration | Wnt Signaling | Canonical Wnt signaling in C. elegans - QL neuroblast descendant migration | canonical Wnt signaling pathway (GO:0060070), cell migration (GO:0016477), transcription from RNA polymerase II promoter (GO:0006366) | http://noctua.berkeleybop.org/editor/graph/gomodel:595a9ee700000584 | Development |
Annotations Issues
- What is the correct relation to use between an upstream MF that creates or removes a small molecule that is the input of a downstream MF?
- What is the correct way to evidence a CC when there is experimental data for expression at the tissue- or cellular level, but no subcellular localization?
- Where do the binding activities of a ligand and its receptor occur?
- How should the MFs of protein complexes and their constituent members be represented in GO-CAMs?